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Copper in PDB 3ax0: Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr

Enzymatic activity of Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr

All present enzymatic activity of Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr, PDB code: 3ax0 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 / 1.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.240, 98.200, 55.210, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.5

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr (pdb code 3ax0). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr, PDB code: 3ax0:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3ax0

Go back to Copper Binding Sites List in 3ax0
Copper binding site 1 out of 6 in the Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr


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 Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:16.8
occ:0.82
 NE2 A:HIS194 2.0 9.7 1.0
NE2 A:HIS190 2.0 9.7 1.0
O A:HOH571 2.0 18.7 1.0
NE2 A:HIS216 2.1 11.7 1.0
CE1 A:HIS216 2.9 12.8 1.0
CE1 A:HIS194 2.9 10.4 1.0
CD2 A:HIS190 3.0 9.5 1.0
CE1 A:HIS190 3.0 10.8 1.0
CD2 A:HIS194 3.0 10.0 1.0
CD2 A:HIS216 3.1 11.7 1.0
O A:HOH510 4.0 19.4 0.6
CU B:CU501 4.0 35.5 0.6
CE2 A:PHE212 4.0 11.2 1.0
ND1 A:HIS216 4.1 10.4 1.0
ND1 A:HIS194 4.1 10.0 1.0
CD2 A:HIS215 4.1 12.4 1.0
CG A:HIS190 4.1 8.9 1.0
ND1 A:HIS190 4.1 9.3 1.0
CG A:HIS194 4.2 10.4 1.0
CG A:HIS216 4.2 9.7 1.0
NE2 A:HIS215 4.3 13.4 1.0
CE2 B:PHE98 4.6 13.9 1.0
CZ B:PHE98 4.6 14.1 1.0
CD2 A:PHE212 4.6 8.6 1.0
CZ A:PHE212 4.7 9.0 1.0
NE2 A:HIS63 4.8 10.1 1.0

Copper binding site 2 out of 6 in 3ax0

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Copper binding site 2 out of 6 in the Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr


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 Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:79.5
occ:0.50
 CG A:PRO231 4.2 22.6 1.0
CD A:PRO231 4.8 19.8 1.0

Copper binding site 3 out of 6 in 3ax0

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Copper binding site 3 out of 6 in the Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr


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 Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:28.8
occ:0.62
 NE2 B:HIS82 2.0 20.1 0.6
O B:HIS68 2.1 70.3 1.0
OE1 B:GLU67 2.1 57.5 1.0
ND1 B:HIS68 2.1 64.3 1.0
N B:HIS68 2.3 70.2 1.0
C B:HIS68 2.4 72.0 1.0
CA B:HIS68 2.5 70.9 1.0
CG B:HIS68 2.8 66.0 1.0
CB B:HIS68 2.9 68.8 1.0
CD2 B:HIS82 3.0 20.2 0.6
CE1 B:HIS82 3.0 17.7 0.6
CE1 B:HIS68 3.3 63.2 1.0
CD B:GLU67 3.3 56.9 1.0
C B:GLU67 3.4 68.7 1.0
N B:GLY69 3.5 73.5 1.0
ND1 B:HIS82 3.6 19.0 0.4
CE1 B:HIS82 3.8 18.6 0.4
OE2 B:GLU67 4.0 46.4 1.0
CD2 B:HIS68 4.0 63.8 1.0
CB B:GLU67 4.1 62.6 1.0
ND1 B:HIS82 4.1 17.3 0.6
CG B:HIS82 4.1 18.0 0.6
O A:MET43 4.2 23.9 1.0
O B:GLU67 4.2 58.6 1.0
NE2 B:HIS68 4.2 63.8 1.0
CA B:GLU67 4.3 68.1 1.0
CG B:GLU67 4.3 58.5 1.0
CA B:GLY69 4.4 73.3 1.0
N B:GLY70 4.6 67.5 1.0
C B:GLY69 4.7 71.1 1.0
O B:HOH620 4.7 22.9 1.0
CG B:HIS82 4.9 15.9 0.4

Copper binding site 4 out of 6 in 3ax0

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Copper binding site 4 out of 6 in the Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr


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 Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:30.0
occ:0.35
 SD B:MET84 1.7 31.5 0.5
O1 B:NO3504 2.0 27.3 0.6
NE2 B:HIS82 2.0 16.3 0.4
N B:NO3504 2.1 19.7 0.6
NE2 B:HIS97 2.3 14.5 0.3
CG B:MET84 2.5 19.4 0.5
O3 B:NO3504 2.5 18.6 0.6
O2 B:NO3504 2.6 17.6 0.6
CE B:MET84 2.7 28.2 0.5
CE1 B:HIS82 2.9 18.6 0.4
CD2 B:HIS82 3.1 17.1 0.4
CE1 B:HIS97 3.2 14.8 0.3
CD2 B:HIS97 3.4 15.0 0.3
CE B:MET84 3.4 29.1 0.5
CE1 B:HIS97 3.4 14.9 0.7
SD B:MET84 3.4 32.6 0.5
CB B:MET84 3.5 18.3 0.5
CB B:MET84 3.5 18.3 0.5
O A:ILE42 3.5 19.0 1.0
ND1 B:HIS82 3.7 17.3 0.6
CG B:MET84 3.7 22.8 0.5
ND1 B:HIS97 3.7 13.5 0.7
CE1 B:HIS82 3.7 17.7 0.6
CA A:MET43 3.9 17.5 1.0
ND1 B:HIS82 4.0 19.0 0.4
O A:HOH513 4.1 17.7 0.6
CG B:HIS82 4.2 15.9 0.4
O A:MET43 4.2 23.9 1.0
ND1 B:HIS97 4.4 13.3 0.3
C A:ILE42 4.4 16.8 1.0
C A:MET43 4.4 16.6 1.0
CG B:HIS97 4.5 13.9 0.3
N A:MET43 4.6 13.6 1.0
NE2 B:HIS97 4.6 15.0 0.7
CD1 B:ILE92 4.6 17.9 1.0
CA B:MET84 4.7 16.2 1.0
N B:MET84 4.8 14.5 1.0
CG1 B:ILE92 4.8 11.6 1.0
CB A:MET43 4.8 18.9 1.0
CG A:MET43 4.9 18.8 1.0
C B:VAL83 4.9 14.3 1.0
CG2 A:ILE42 4.9 22.9 1.0
CG B:HIS82 5.0 18.0 0.6

Copper binding site 5 out of 6 in 3ax0

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Copper binding site 5 out of 6 in the Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr


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 Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:15.7
occ:0.34
 NE2 B:HIS97 1.5 15.0 0.7
NE2 A:HIS54 1.7 9.3 0.5
CE1 B:HIS97 2.4 14.9 0.7
O B:HOH509 2.5 26.7 0.5
CE1 B:HIS97 2.5 14.8 0.3
CD2 B:HIS97 2.6 11.2 0.7
ND1 B:HIS97 2.6 13.3 0.3
CE1 A:HIS54 2.7 8.5 0.5
CD2 A:HIS54 2.8 10.3 0.5
O A:HOH513 3.2 17.7 0.6
CD1 A:ILE42 3.4 29.9 1.0
ND1 B:HIS97 3.5 13.5 0.7
CG B:HIS97 3.6 13.8 0.7
O A:ILE42 3.8 19.0 1.0
NE2 B:HIS97 3.8 14.5 0.3
ND1 A:HIS54 3.8 8.6 0.5
CG A:HIS54 3.9 9.3 0.5
NH2 A:ARG55 4.0 21.5 1.0
CG B:HIS97 4.0 13.9 0.3
CG2 A:ILE42 4.1 22.9 1.0
CZ2 A:TRP184 4.3 13.3 1.0
NE A:ARG55 4.3 17.0 1.0
CA A:ILE42 4.3 15.4 1.0
CB A:HIS54 4.4 11.5 0.5
C A:ILE42 4.5 16.8 1.0
CG A:HIS54 4.5 13.6 0.5
CB A:ILE42 4.5 17.2 1.0
CD2 B:HIS97 4.5 15.0 0.3
CG1 A:ILE42 4.6 22.4 1.0
CZ A:ARG55 4.6 19.3 1.0
CD1 B:ILE92 4.6 17.9 1.0
CH2 A:TRP184 4.7 15.1 1.0
O B:HIS97 4.8 20.2 1.0
O A:HOH533 4.9 13.4 1.0
ND1 A:HIS54 4.9 13.3 0.5
CD2 A:HIS54 4.9 14.8 0.5
CB B:HIS97 5.0 13.3 0.3

Copper binding site 6 out of 6 in 3ax0

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Copper binding site 6 out of 6 in the Crystal Structure of Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr


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 Streptomyces Tyrosinase in A Complex with Caddie Y98F Mutant Soaked in A Cu(II)-Containing Solution For 80 Hr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:35.5
occ:0.60
 NE2 A:HIS38 1.8 15.7 1.0
NE2 A:HIS54 2.1 13.6 0.5
O A:HOH571 2.2 18.7 1.0
NE2 A:HIS63 2.3 10.1 1.0
CE1 A:HIS38 2.3 12.9 1.0
CE1 A:HIS63 3.0 9.6 1.0
CD2 A:HIS54 3.0 14.8 0.5
O A:HOH510 3.0 19.4 0.6
CD2 A:HIS38 3.1 13.2 1.0
CE1 A:HIS54 3.3 11.5 0.5
CD2 A:HIS63 3.5 10.1 1.0
ND1 A:HIS38 3.6 14.5 1.0
CG A:HIS38 4.0 12.1 1.0
CU A:CU502 4.0 16.8 0.8
CG A:HIS54 4.2 13.6 0.5
NE2 A:HIS216 4.2 11.7 1.0
CZ A:PHE212 4.2 9.0 1.0
ND1 A:HIS63 4.2 10.7 1.0
CD1 A:ILE42 4.2 29.9 1.0
CE2 A:PHE212 4.3 11.2 1.0
ND1 A:HIS54 4.3 13.3 0.5
CE1 A:HIS216 4.4 12.8 1.0
CG1 A:ILE42 4.5 22.4 1.0
CG A:HIS63 4.5 8.9 1.0
CE1 A:PHE59 5.0 9.2 1.0

Reference:

Y.Matoba, N.Bando, K.Oda, M.Noda, F.Higashikawa, T.Kumagai, M.Sugiyama. A Molecular Mechanism For Copper Transportation to Tyrosinase That Is Assisted By A Metallochaperone, Caddie Protein J.Biol.Chem. V. 286 30219 2011.
ISSN: ISSN 0021-9258
PubMed: 21730070
DOI: 10.1074/JBC.M111.256818
Page generated: Wed Jul 31 00:42:19 2024

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