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Copper in PDB 5z0j: Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K

Enzymatic activity of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K

All present enzymatic activity of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K, PDB code: 5z0j was solved by Y.Matoba, M.Sugiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.770, 96.970, 54.630, 90.00, 90.00, 90.00
R / Rfree (%) 13.4 / 17.8

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K (pdb code 5z0j). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K, PDB code: 5z0j:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 5z0j

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Copper binding site 1 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:13.6
occ:0.33
 CU A:CU301 0.0 13.6 0.3
CU A:CU301 1.1 13.1 0.3
NE2 A:HIS38 1.7 13.0 0.7
NE2 A:HIS63 1.9 12.0 1.0
NE2 A:HIS54 2.1 14.6 0.7
O A:HOH401 2.5 14.6 0.7
NE2 A:HIS38 2.5 13.0 0.3
NE2 A:HIS54 2.5 14.3 0.3
CD2 A:HIS38 2.6 14.1 0.7
CU A:CU301 2.6 14.1 0.3
CE1 A:HIS54 2.6 14.6 0.3
CE1 A:HIS63 2.7 10.7 1.0
O1 A:PER304 2.7 15.2 0.3
CD2 A:HIS38 2.7 13.1 0.3
O2 A:PER304 2.8 14.4 0.3
CE1 A:HIS38 2.8 13.0 0.7
CE1 A:HIS54 2.9 13.9 0.7
CD2 A:HIS63 3.2 10.8 1.0
CD2 A:HIS54 3.2 14.6 0.7
CD2 A:HIS54 3.6 13.8 0.3
ND1 A:HIS54 3.7 14.2 0.3
CG A:HIS38 3.8 13.1 0.7
CE1 A:HIS38 3.8 12.7 0.3
ND1 A:HIS38 3.8 13.0 0.7
ND1 A:HIS63 3.9 10.4 1.0
CU A:CU302 3.9 11.9 0.7
CG A:HIS38 4.0 12.5 0.3
ND1 A:HIS54 4.1 13.6 0.7
CZ A:PHE212 4.2 8.9 1.0
CG A:HIS63 4.2 10.3 1.0
CG A:HIS54 4.2 13.8 0.3
NE2 A:HIS216 4.3 11.7 1.0
CG A:HIS54 4.3 13.7 0.7
CD1 A:ILE42 4.3 17.8 0.4
CZ3 A:TRP62 4.4 11.2 1.0
CE2 A:PHE212 4.4 9.8 1.0
OE2 B:DAH98 4.4 15.8 0.4
CU A:CU302 4.5 11.8 0.3
ND1 A:HIS38 4.5 12.4 0.3
CE1 A:HIS216 4.5 10.9 1.0
OZ B:DAH98 4.6 15.9 1.0
O A:GLY53 4.9 11.4 1.0
CE3 A:TRP62 4.9 11.0 1.0

Copper binding site 2 out of 8 in 5z0j

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Copper binding site 2 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:13.1
occ:0.34
 CU A:CU301 0.0 13.1 0.3
CU A:CU301 1.1 13.6 0.3
O1 A:PER304 1.6 15.2 0.3
O A:HOH401 1.7 14.6 0.7
CU A:CU301 1.7 14.1 0.3
NE2 A:HIS54 1.9 14.3 0.3
NE2 A:HIS54 2.0 14.6 0.7
O2 A:PER304 2.0 14.4 0.3
NE2 A:HIS38 2.1 13.0 0.7
NE2 A:HIS38 2.5 13.0 0.3
NE2 A:HIS63 2.6 12.0 1.0
CE1 A:HIS54 2.6 14.6 0.3
CE1 A:HIS38 2.8 13.0 0.7
CD2 A:HIS54 2.9 14.6 0.7
CD2 A:HIS54 3.0 13.8 0.3
CU A:CU302 3.1 11.9 0.7
CE1 A:HIS63 3.2 10.7 1.0
CE1 A:HIS54 3.2 13.9 0.7
CD2 A:HIS38 3.2 13.1 0.3
OE2 B:DAH98 3.3 15.8 0.4
CD2 A:HIS38 3.3 14.1 0.7
CE1 A:HIS38 3.6 12.7 0.3
ND1 A:HIS54 3.7 14.2 0.3
CD1 A:ILE42 3.8 17.8 0.4
CD2 A:HIS63 3.8 10.8 1.0
CU A:CU302 3.8 11.8 0.3
OZ B:DAH98 3.8 15.9 1.0
CG A:HIS54 4.0 13.8 0.3
NE2 A:HIS216 4.0 11.7 1.0
ND1 A:HIS38 4.0 13.0 0.7
CG A:HIS54 4.1 13.7 0.7
ND1 A:HIS54 4.2 13.6 0.7
CG A:HIS38 4.3 13.1 0.7
CE2 A:PHE212 4.3 9.8 1.0
CE1 A:HIS216 4.4 10.9 1.0
ND1 A:HIS63 4.4 10.4 1.0
CG A:HIS38 4.5 12.5 0.3
CZ A:PHE212 4.5 8.9 1.0
CE2 B:DAH98 4.5 15.8 1.0
NE2 A:HIS190 4.6 11.0 1.0
ND1 A:HIS38 4.6 12.4 0.3
CZ B:DAH98 4.7 15.5 1.0
CG A:HIS63 4.8 10.3 1.0
CG1 A:ILE42 4.8 14.7 0.6
CE1 A:PHE59 4.8 9.9 1.0
CD1 A:ILE42 4.8 16.4 0.6
NE2 A:HIS194 4.9 10.1 1.0
CD2 A:HIS216 4.9 11.2 1.0
CG1 A:ILE42 5.0 15.2 0.4

Copper binding site 3 out of 8 in 5z0j

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Copper binding site 3 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:14.1
occ:0.33
 CU A:CU301 0.0 14.1 0.3
O1 A:PER304 1.7 15.2 0.3
CU A:CU301 1.7 13.1 0.3
O A:HOH401 1.8 14.6 0.7
O2 A:PER304 1.9 14.4 0.3
OZ B:DAH98 2.1 15.9 1.0
NE2 A:HIS54 2.1 14.3 0.3
NE2 A:HIS38 2.2 13.0 0.3
OE2 B:DAH98 2.3 15.8 0.4
CE1 A:HIS38 2.4 13.0 0.7
CD1 A:ILE42 2.6 17.8 0.4
NE2 A:HIS38 2.6 13.0 0.7
CU A:CU301 2.6 13.6 0.3
NE2 A:HIS54 2.8 14.6 0.7
CE1 A:HIS38 2.8 12.7 0.3
CE1 A:HIS54 3.0 14.6 0.3
CZ B:DAH98 3.0 15.5 1.0
CE2 B:DAH98 3.2 15.8 1.0
CU A:CU302 3.2 11.9 0.7
CD2 A:HIS54 3.3 13.8 0.3
CD2 A:HIS54 3.4 14.6 0.7
CD2 A:HIS38 3.5 13.1 0.3
CD1 A:ILE42 3.6 16.4 0.6
ND1 A:HIS38 3.7 13.0 0.7
CU A:CU302 3.8 11.8 0.3
CE1 A:HIS54 3.8 13.9 0.7
CG1 A:ILE42 3.8 14.7 0.6
CD2 A:HIS38 4.0 14.1 0.7
CG1 A:ILE42 4.1 15.2 0.4
ND1 A:HIS38 4.1 12.4 0.3
OG A:SER206 4.1 10.6 1.0
ND1 A:HIS54 4.2 14.2 0.3
NE2 A:HIS194 4.3 10.1 1.0
NE2 A:HIS63 4.3 12.0 1.0
CG A:HIS54 4.3 13.8 0.3
CE1 B:DAH98 4.3 12.9 1.0
CE1 A:HIS194 4.4 9.8 1.0
CG A:HIS38 4.4 12.5 0.3
CE2 A:PHE212 4.5 9.8 1.0
CG A:HIS38 4.5 13.1 0.7
CD2 B:DAH98 4.5 15.0 1.0
O B:HOH329 4.5 35.0 1.0
CG A:HIS54 4.6 13.7 0.7
ND1 A:HIS54 4.7 13.6 0.7
NE2 A:HIS216 4.7 11.7 1.0
NE2 A:HIS190 4.8 11.0 1.0
CB A:ILE42 4.8 14.0 0.4
CE1 A:HIS63 4.9 10.7 1.0
CE1 A:HIS190 5.0 10.6 1.0

Copper binding site 4 out of 8 in 5z0j

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Copper binding site 4 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:11.8
occ:0.33
 CU A:CU302 0.0 11.8 0.3
CU A:CU302 0.9 11.9 0.7
NE2 A:HIS194 1.8 10.1 1.0
NE2 A:HIS216 2.0 11.7 1.0
NE2 A:HIS190 2.2 11.0 1.0
O2 A:PER304 2.3 14.4 0.3
O A:HOH401 2.3 14.6 0.7
O1 A:PER304 2.5 15.2 0.3
CE1 A:HIS194 2.7 9.8 1.0
CD2 A:HIS216 2.9 11.2 1.0
CD2 A:HIS194 2.9 10.1 1.0
CE1 A:HIS216 3.0 10.9 1.0
CD2 A:HIS190 3.0 10.0 1.0
CE1 A:HIS190 3.3 10.6 1.0
OE2 B:DAH98 3.5 15.8 0.4
CU A:CU301 3.8 13.1 0.3
CU A:CU301 3.8 14.1 0.3
ND1 A:HIS194 3.9 9.1 1.0
CG A:HIS194 4.0 8.6 1.0
CD2 A:HIS215 4.0 11.7 1.0
CG A:HIS216 4.0 9.9 1.0
CE2 A:PHE212 4.0 9.8 1.0
ND1 A:HIS216 4.0 9.9 1.0
CE2 B:DAH98 4.1 15.8 1.0
CG A:HIS190 4.2 9.4 1.0
NE2 A:HIS215 4.2 12.1 1.0
OZ B:DAH98 4.2 15.9 1.0
ND1 A:HIS190 4.3 10.0 1.0
CZ B:DAH98 4.4 15.5 1.0
CU A:CU301 4.5 13.6 0.3
CD2 A:PHE212 4.6 8.5 1.0
CZ A:PHE212 4.7 8.9 1.0
NE2 A:HIS63 4.8 12.0 1.0
CD2 B:DAH98 5.0 15.0 1.0

Copper binding site 5 out of 8 in 5z0j

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Copper binding site 5 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:11.9
occ:0.67
 CU A:CU302 0.0 11.9 0.7
CU A:CU302 0.9 11.8 0.3
O1 A:PER304 1.7 15.2 0.3
O A:HOH401 1.8 14.6 0.7
O2 A:PER304 1.9 14.4 0.3
NE2 A:HIS190 2.0 11.0 1.0
NE2 A:HIS216 2.2 11.7 1.0
NE2 A:HIS194 2.2 10.1 1.0
CE1 A:HIS190 2.9 10.6 1.0
OE2 B:DAH98 2.9 15.8 0.4
CE1 A:HIS216 3.0 10.9 1.0
CD2 A:HIS190 3.1 10.0 1.0
CU A:CU301 3.1 13.1 0.3
CE1 A:HIS194 3.2 9.8 1.0
CU A:CU301 3.2 14.1 0.3
CD2 A:HIS194 3.2 10.1 1.0
CD2 A:HIS216 3.4 11.2 1.0
CE2 B:DAH98 3.7 15.8 1.0
OZ B:DAH98 3.9 15.9 1.0
CU A:CU301 3.9 13.6 0.3
ND1 A:HIS190 4.0 10.0 1.0
CZ B:DAH98 4.1 15.5 1.0
CG A:HIS190 4.2 9.4 1.0
ND1 A:HIS216 4.2 9.9 1.0
NE2 A:HIS54 4.3 14.3 0.3
CE2 A:PHE212 4.3 9.8 1.0
ND1 A:HIS194 4.3 9.1 1.0
NE2 A:HIS63 4.3 12.0 1.0
CG A:HIS194 4.4 8.6 1.0
CG A:HIS216 4.4 9.9 1.0
CE1 A:PHE59 4.6 9.9 1.0
CD2 B:DAH98 4.6 15.0 1.0
NE2 A:HIS38 4.7 13.0 0.7
CD2 A:HIS54 4.7 13.8 0.3
NE2 A:HIS38 4.7 13.0 0.3
CD2 A:HIS215 4.8 11.7 1.0
NE2 A:HIS54 4.8 14.6 0.7
NE2 A:HIS215 4.9 12.1 1.0
CD2 A:HIS63 4.9 10.8 1.0
CZ A:PHE59 4.9 9.7 1.0
CZ A:PHE212 4.9 8.9 1.0
CE1 A:HIS63 4.9 10.7 1.0
CD2 A:HIS54 4.9 14.6 0.7
CE1 A:HIS38 5.0 13.0 0.7

Copper binding site 6 out of 8 in 5z0j

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Copper binding site 6 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:44.0
occ:0.50
 NE2 A:HIS277 1.8 39.7 1.0
O A:HOH592 2.4 24.0 0.5
CE1 A:HIS277 2.7 40.2 1.0
CD2 A:HIS277 2.9 41.6 1.0
ND1 A:HIS277 3.9 42.4 1.0
CG A:HIS277 4.0 43.9 1.0
CG A:PRO231 4.7 26.0 1.0
O A:HOH447 4.8 47.4 1.0

Copper binding site 7 out of 8 in 5z0j

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Copper binding site 7 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:22.1
occ:0.34
 ND1 B:HIS68 1.9 47.8 1.0
NE2 B:HIS82 1.9 19.4 0.3
OE2 B:GLU67 2.1 58.3 1.0
N B:HIS68 2.5 56.0 1.0
O B:HIS68 2.8 61.9 1.0
CD2 B:HIS82 2.8 17.7 0.3
CE1 B:HIS68 2.8 48.4 1.0
CG B:HIS68 2.9 50.1 1.0
CE1 B:HIS82 3.0 18.2 0.3
CA B:HIS68 3.2 55.2 1.0
C B:GLU67 3.2 57.3 1.0
CB B:GLU67 3.2 56.8 1.0
C B:HIS68 3.3 56.4 1.0
CD B:GLU67 3.3 59.0 1.0
ND1 B:HIS82 3.4 17.1 0.7
CB B:HIS68 3.4 53.7 1.0
CE1 B:HIS82 3.5 17.5 0.7
CA B:GLU67 3.7 56.4 1.0
NE2 B:HIS68 3.9 50.3 1.0
CG B:GLU67 4.0 59.7 1.0
CG B:HIS82 4.0 16.1 0.3
CD2 B:HIS68 4.0 51.1 1.0
ND1 B:HIS82 4.0 17.0 0.3
O B:GLU67 4.1 60.5 1.0
O A:MET43 4.1 22.2 1.0
OE1 B:GLU67 4.3 62.6 1.0
N B:GLY69 4.6 55.7 1.0
O B:HOH364 4.6 21.7 1.0
N B:GLY70 4.6 55.0 1.0
CG B:HIS82 4.7 15.5 0.7
NE2 B:HIS82 4.8 17.3 0.7
O B:HOH320 5.0 48.6 1.0

Copper binding site 8 out of 8 in 5z0j

Go back to Copper Binding Sites List in 5z0j
Copper binding site 8 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:17.3
occ:0.66
 O1 B:NO3202 1.8 26.3 0.3
NE2 B:HIS82 2.0 17.3 0.7
NE2 B:HIS97 2.1 16.2 0.7
SD B:MET84 2.1 19.6 0.7
N B:NO3202 2.4 23.3 0.3
CE B:MET84 2.7 18.5 0.3
CE B:MET84 2.9 21.0 0.7
CE1 B:HIS97 3.0 15.9 0.7
O3 B:NO3202 3.0 19.8 0.3
CE1 B:HIS82 3.0 17.5 0.7
CD2 B:HIS82 3.0 16.7 0.7
CG B:MET84 3.1 18.2 0.7
O2 B:NO3202 3.1 22.0 0.3
CD2 B:HIS97 3.2 16.5 0.7
SD B:MET84 3.2 23.5 0.3
O A:ILE42 3.2 17.8 1.0
CB B:MET84 3.4 16.0 0.3
CB B:MET84 3.4 16.0 0.7
CE1 B:HIS97 3.5 15.9 0.3
CE1 B:HIS82 3.5 18.2 0.3
ND1 B:HIS82 3.6 17.0 0.3
CG B:MET84 3.7 16.4 0.3
ND1 B:HIS97 3.7 15.8 0.3
CA A:MET43 3.8 17.2 1.0
O A:MET43 4.0 22.2 1.0
ND1 B:HIS82 4.1 17.1 0.7
ND1 B:HIS97 4.1 15.4 0.7
C A:ILE42 4.1 14.4 1.0
CG B:HIS82 4.2 15.5 0.7
C A:MET43 4.2 16.4 1.0
CG B:HIS97 4.3 15.1 0.7
N A:MET43 4.5 14.3 1.0
CG2 A:ILE42 4.6 15.2 0.6
O A:HOH490 4.6 22.6 1.0
CA B:MET84 4.7 13.9 1.0
NE2 B:HIS97 4.7 15.6 0.3
N B:MET84 4.7 12.7 1.0
CG1 B:ILE92 4.8 15.7 1.0
NE2 B:HIS82 4.8 19.4 0.3
CB A:MET43 4.9 19.5 1.0
C B:VAL83 4.9 12.6 1.0
CG B:HIS82 4.9 16.1 0.3
CD1 B:ILE92 5.0 22.9 1.0
CG A:MET43 5.0 21.4 1.0

Reference:

Y.Matoba, M.Sugiyama. Catalytic Mechanism of Tyrosinase Implied From the Quinone Formation on the TYR98 Residue of the Caddie Protein To Be Published.
Page generated: Wed Jul 31 05:29:42 2024

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