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Copper in PDB 4mfh: Crystal Structure of M121G Azurin

Protein crystallography data

The structure of Crystal Structure of M121G Azurin, PDB code: 4mfh was solved by S.Tian, Y.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.15 / 1.54
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 55.747, 145.781, 97.092, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.4

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of M121G Azurin (pdb code 4mfh). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Crystal Structure of M121G Azurin, PDB code: 4mfh:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 4mfh

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Copper binding site 1 out of 9 in the Crystal Structure of M121G Azurin


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 M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:11.9
occ:0.95
 ND1 A:HIS117 2.1 8.0 1.0
SG A:CYS112 2.2 7.3 1.0
ND1 A:HIS46 2.2 11.7 1.0
O A:GLY45 2.9 7.5 1.0
O A:HOH304 2.9 20.8 1.0
CG A:HIS117 3.0 8.6 1.0
CE1 A:HIS46 3.1 11.5 1.0
CE1 A:HIS117 3.1 9.2 1.0
CB A:CYS112 3.2 8.4 1.0
CG A:HIS46 3.2 9.1 1.0
CB A:HIS117 3.4 7.8 1.0
CA A:HIS46 3.4 7.7 1.0
CB A:HIS46 3.6 8.4 1.0
CB A:PHE114 3.8 6.4 1.0
C A:GLY45 3.9 9.1 1.0
N A:HIS46 4.1 7.9 1.0
CD2 A:HIS117 4.2 8.2 1.0
NE2 A:HIS117 4.2 9.0 1.0
NE2 A:HIS46 4.2 9.7 1.0
CD2 A:HIS46 4.3 10.6 1.0
O A:HOH413 4.4 29.2 1.0
C A:HIS46 4.6 7.8 1.0
CA A:CYS112 4.6 6.7 1.0
N A:ASN47 4.6 7.1 1.0
CG A:PHE114 4.7 7.2 1.0
N A:PHE114 4.7 5.9 1.0
CA A:PHE114 4.9 6.0 1.0
CA A:HIS117 4.9 8.0 1.0

Copper binding site 2 out of 9 in 4mfh

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Copper binding site 2 out of 9 in the Crystal Structure of M121G Azurin


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 M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:11.6
occ:0.60
 CU A:CU202 0.0 11.6 0.6
CU A:CU202 1.7 19.9 0.4
N A:TRS203 1.8 12.8 1.0
NE2 A:HIS83 1.9 13.4 1.0
O B:HOH348 2.5 20.7 1.0
O B:HOH364 2.5 17.9 1.0
CE1 A:HIS83 2.7 10.9 1.0
C A:TRS203 2.8 12.0 1.0
CD2 A:HIS83 3.0 10.9 1.0
C3 A:TRS203 3.0 12.4 1.0
O3 A:TRS203 3.2 12.4 1.0
C2 A:TRS203 3.3 12.3 1.0
N B:ALA1 3.5 18.7 1.0
O B:ALA1 3.8 18.1 1.0
ND1 A:HIS83 3.9 10.5 1.0
CG A:HIS83 4.0 8.8 1.0
C1 A:TRS203 4.0 13.5 1.0
O B:SER25 4.2 10.9 1.0
OG B:SER25 4.3 12.8 1.0
SG B:CYS3 4.4 15.2 1.0
O1 A:TRS203 4.5 16.0 1.0
CD1 A:LEU73 4.5 12.4 1.0
O2 A:TRS203 4.5 14.5 1.0
CA B:ALA1 4.6 17.5 1.0
C B:ALA1 4.7 17.0 1.0
C B:SER25 4.7 11.6 1.0
CA B:CYS26 4.9 9.9 1.0
O B:HOH307 4.9 14.9 1.0
N B:CYS26 5.0 10.8 1.0

Copper binding site 3 out of 9 in 4mfh

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Copper binding site 3 out of 9 in the Crystal Structure of M121G Azurin


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 M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:19.9
occ:0.40
 CU A:CU202 0.0 19.9 0.4
CU A:CU202 1.7 11.6 0.6
N B:ALA1 2.0 18.7 1.0
N A:TRS203 2.0 12.8 1.0
O B:HOH348 2.2 20.7 1.0
O3 A:TRS203 2.5 12.4 1.0
NE2 A:HIS83 2.5 13.4 1.0
O B:ALA1 2.5 18.1 1.0
C A:TRS203 3.0 12.0 1.0
CA B:ALA1 3.0 17.5 1.0
C3 A:TRS203 3.0 12.4 1.0
C B:ALA1 3.2 17.0 1.0
CD2 A:HIS83 3.2 10.9 1.0
CE1 A:HIS83 3.6 10.9 1.0
C1 A:TRS203 3.8 13.5 1.0
CB B:ALA1 3.9 20.6 1.0
O B:HOH364 4.0 17.9 1.0
C2 A:TRS203 4.2 12.3 1.0
OG B:SER25 4.2 12.8 1.0
SG B:CYS3 4.3 15.2 1.0
O B:HOH327 4.3 11.4 1.0
CG A:HIS83 4.4 8.8 1.0
O1 A:TRS203 4.4 16.0 1.0
N B:GLU2 4.5 18.9 1.0
ND1 A:HIS83 4.6 10.5 1.0

Copper binding site 4 out of 9 in 4mfh

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Copper binding site 4 out of 9 in the Crystal Structure of M121G Azurin


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 M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:11.9
occ:1.00
 ND1 B:HIS117 2.1 8.1 1.0
ND1 B:HIS46 2.1 10.3 1.0
SG B:CYS112 2.2 8.8 1.0
O B:GLY45 2.8 9.1 1.0
O B:HOH312 2.9 29.4 1.0
CE1 B:HIS46 3.0 9.5 1.0
CE1 B:HIS117 3.0 10.0 1.0
CG B:HIS117 3.1 9.4 1.0
CG B:HIS46 3.2 8.4 1.0
CB B:CYS112 3.2 7.5 1.0
CB B:HIS117 3.4 8.3 1.0
CA B:HIS46 3.4 7.3 1.0
CB B:HIS46 3.6 7.1 1.0
CB B:PHE114 3.7 6.5 1.0
C B:GLY45 3.8 8.7 1.0
N B:HIS46 4.0 6.8 1.0
NE2 B:HIS117 4.1 9.1 1.0
NE2 B:HIS46 4.2 8.2 1.0
CD2 B:HIS117 4.2 9.5 1.0
CD2 B:HIS46 4.3 8.0 1.0
C B:HIS46 4.5 7.2 1.0
N B:ASN47 4.5 6.9 1.0
CA B:CYS112 4.6 7.5 1.0
CG B:PHE114 4.6 7.1 1.0
N B:PHE114 4.7 6.3 1.0
CA B:PHE114 4.8 6.9 1.0
CA B:HIS117 4.9 7.9 1.0
O B:MET13 5.0 35.4 1.0

Copper binding site 5 out of 9 in 4mfh

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Copper binding site 5 out of 9 in the Crystal Structure of M121G Azurin


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 M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:15.9
occ:0.60
 CU B:CU202 0.0 15.9 0.6
CU B:CU202 1.5 13.4 0.4
N B:TRS203 1.8 17.9 1.0
NE2 B:HIS83 1.9 13.1 1.0
C B:TRS203 2.6 19.0 1.0
O B:HOH395 2.7 22.9 1.0
C2 B:TRS203 2.7 16.1 1.0
CE1 B:HIS83 2.7 10.5 1.0
O2 B:TRS203 3.0 18.1 1.0
CD2 B:HIS83 3.0 12.3 1.0
C1 B:TRS203 3.2 17.1 1.0
ND1 B:HIS83 3.9 10.8 1.0
C3 B:TRS203 3.9 19.8 1.0
CG B:HIS83 4.0 9.7 1.0
CD1 B:LEU73 4.1 11.6 1.0
O3 B:TRS203 4.2 25.4 1.0
O1 B:TRS203 4.5 17.9 1.0

Copper binding site 6 out of 9 in 4mfh

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Copper binding site 6 out of 9 in the Crystal Structure of M121G Azurin


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 M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:13.4
occ:0.40
 CU B:CU202 0.0 13.4 0.4
CU B:CU202 1.5 15.9 0.6
N B:TRS203 2.2 17.9 1.0
NE2 B:HIS83 2.4 13.1 1.0
O2 B:TRS203 2.6 18.1 1.0
O B:HOH395 2.7 22.9 1.0
C2 B:TRS203 3.1 16.1 1.0
C B:TRS203 3.1 19.0 1.0
CD2 B:HIS83 3.1 12.3 1.0
CE1 B:HIS83 3.4 10.5 1.0
C3 B:TRS203 3.9 19.8 1.0
C1 B:TRS203 4.2 17.1 1.0
O3 B:TRS203 4.2 25.4 1.0
CG B:HIS83 4.3 9.7 1.0
ND1 B:HIS83 4.5 10.8 1.0

Copper binding site 7 out of 9 in 4mfh

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Copper binding site 7 out of 9 in the Crystal Structure of M121G Azurin


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 M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:11.0
occ:1.00
 ND1 C:HIS117 2.0 8.6 1.0
ND1 C:HIS46 2.1 10.6 1.0
SG C:CYS112 2.2 6.8 1.0
O C:GLY45 2.8 6.6 1.0
CE1 C:HIS117 3.0 9.2 1.0
CG C:HIS117 3.0 9.3 1.0
CE1 C:HIS46 3.0 11.1 1.0
O C:HOH398 3.1 22.6 1.0
CB C:CYS112 3.2 7.1 1.0
CG C:HIS46 3.2 8.6 1.0
CB C:HIS117 3.4 8.5 1.0
CA C:HIS46 3.4 7.0 1.0
CB C:HIS46 3.6 7.4 1.0
C C:GLY45 3.8 6.4 1.0
CB C:PHE114 3.8 6.3 1.0
NE2 C:HIS117 4.1 9.2 1.0
N C:HIS46 4.1 5.8 1.0
CD2 C:HIS117 4.1 8.2 1.0
NE2 C:HIS46 4.1 9.3 1.0
CD2 C:HIS46 4.2 8.9 1.0
CA C:CYS112 4.6 6.2 1.0
N C:ASN47 4.6 6.0 1.0
C C:HIS46 4.6 6.4 1.0
O C:MET13 4.7 16.4 1.0
CG C:PHE114 4.7 6.3 1.0
N C:PHE114 4.8 5.8 1.0
CA C:PHE114 4.9 6.0 1.0
CA C:HIS117 4.9 8.7 1.0
C C:MET13 4.9 14.2 1.0
C C:CYS112 5.0 5.2 1.0

Copper binding site 8 out of 9 in 4mfh

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Copper binding site 8 out of 9 in the Crystal Structure of M121G Azurin


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 M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu202

b:11.1
occ:0.60
 CU C:CU202 0.0 11.1 0.6
CU C:CU202 1.7 19.1 0.4
N C:TRS203 1.8 12.3 1.0
NE2 C:HIS83 1.9 10.2 1.0
O A:HOH325 2.4 18.4 1.0
O A:HOH329 2.6 16.4 1.0
CE1 C:HIS83 2.7 9.7 1.0
C C:TRS203 2.8 13.0 1.0
CD2 C:HIS83 3.0 10.0 1.0
C2 C:TRS203 3.0 12.4 1.0
O2 C:TRS203 3.2 13.5 1.0
C1 C:TRS203 3.3 13.4 1.0
N A:ALA1 3.6 19.3 1.0
O A:ALA1 3.8 16.1 1.0
ND1 C:HIS83 3.9 8.6 1.0
CG C:HIS83 4.0 7.3 1.0
C3 C:TRS203 4.1 13.4 1.0
SG A:CYS3 4.3 13.0 1.0
OG A:SER25 4.3 9.7 1.0
O A:SER25 4.3 9.3 1.0
O C:HOH417 4.4 29.8 1.0
O3 C:TRS203 4.5 14.0 1.0
CD1 C:LEU73 4.5 11.6 1.0
O1 C:TRS203 4.5 14.2 1.0
C A:ALA1 4.7 15.6 1.0
CA A:ALA1 4.7 16.9 1.0
C A:SER25 4.8 8.5 1.0
O A:HOH359 5.0 18.5 1.0
CA A:CYS26 5.0 8.7 1.0

Copper binding site 9 out of 9 in 4mfh

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Copper binding site 9 out of 9 in the Crystal Structure of M121G Azurin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of M121G Azurin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu202

b:19.1
occ:0.40
 CU C:CU202 0.0 19.1 0.4
CU C:CU202 1.7 11.1 0.6
N A:ALA1 2.0 19.3 1.0
N C:TRS203 2.1 12.3 1.0
O A:HOH325 2.2 18.4 1.0
O A:ALA1 2.4 16.1 1.0
O2 C:TRS203 2.5 13.5 1.0
NE2 C:HIS83 2.6 10.2 1.0
C2 C:TRS203 3.0 12.4 1.0
CA A:ALA1 3.0 16.9 1.0
C C:TRS203 3.1 13.0 1.0
C A:ALA1 3.1 15.6 1.0
CD2 C:HIS83 3.2 10.0 1.0
CE1 C:HIS83 3.7 9.7 1.0
CB A:ALA1 3.8 20.6 1.0
C3 C:TRS203 3.9 13.4 1.0
O A:HOH329 4.1 16.4 1.0
C1 C:TRS203 4.2 13.4 1.0
SG A:CYS3 4.2 13.0 1.0
OG A:SER25 4.3 9.7 1.0
O A:HOH353 4.3 10.7 1.0
N A:GLU2 4.4 14.7 1.0
CG C:HIS83 4.4 7.3 1.0
O3 C:TRS203 4.5 14.0 1.0
ND1 C:HIS83 4.7 8.6 1.0
O A:HOH330 4.9 15.5 1.0

Reference:

N.A.Sieracki, S.Tian, R.G.Hadt, J.L.Zhang, J.S.Woertink, M.J.Nilges, F.Sun, E.I.Solomon, Y.Lu. Copper-Sulfenate Complex From Oxidation of A Cavity Mutant of Pseudomonas Aeruginosa Azurin. Proc.Natl.Acad.Sci.Usa V. 111 924 2014.
ISSN: ISSN 0027-8424
PubMed: 24390543
DOI: 10.1073/PNAS.1316483111
Page generated: Wed Jul 31 03:17:12 2024

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