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Copper in PDB 8hm9: X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0

Protein crystallography data

The structure of X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0, PDB code: 8hm9 was solved by Y.Aoyama, T.Yamaguchi, T.Kohzuma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.77 / 1.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.196, 60.476, 54.865, 90, 105.81, 90
R / Rfree (%) 12.8 / 16

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0 (pdb code 8hm9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0, PDB code: 8hm9:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 8hm9

Go back to Copper Binding Sites List in 8hm9
Copper binding site 1 out of 2 in the X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:12.9
occ:1.00
ND1 A:HIS40 2.0 13.2 1.0
ND1 A:HIS81 2.0 14.8 1.0
SG A:CYS78 2.2 12.3 1.0
SD A:MET86 2.5 12.2 1.0
CE1 A:HIS40 2.9 13.3 1.0
CE1 A:HIS81 3.0 15.4 1.0
CG A:HIS40 3.1 11.5 1.0
CG A:HIS81 3.1 14.8 1.0
CB A:CYS78 3.2 12.5 1.0
CB A:HIS81 3.4 14.7 1.0
CE A:MET86 3.4 13.5 1.0
CB A:HIS40 3.5 11.4 1.0
CA A:HIS40 3.8 11.2 1.0
CG A:MET86 3.9 13.5 1.0
NE2 A:HIS40 4.1 12.9 1.0
NE2 A:HIS81 4.2 15.6 1.0
CD2 A:HIS81 4.2 15.3 1.0
CD2 A:HIS40 4.2 12.4 1.0
O A:GLY39 4.3 13.3 1.0
CB A:MET86 4.3 13.5 1.0
N A:HIS81 4.5 13.2 1.0
CA A:HIS81 4.5 14.0 1.0
N A:HIS40 4.6 11.7 1.0
CA A:CYS78 4.6 11.7 1.0
CG A:PRO80 4.6 14.2 1.0
ND1 A:HIS16 4.6 21.4 1.0
C A:GLY39 4.7 11.8 1.0
N A:ASN41 4.7 10.9 1.0
C A:HIS40 4.9 11.0 1.0

Copper binding site 2 out of 2 in 8hm9

Go back to Copper Binding Sites List in 8hm9
Copper binding site 2 out of 2 in the X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:15.3
occ:1.00
ND1 B:HIS40 2.0 13.7 1.0
ND1 B:HIS81 2.1 15.4 1.0
SG B:CYS78 2.2 14.4 1.0
SD B:MET86 2.6 14.7 1.0
CE1 B:HIS40 3.0 15.7 1.0
CE1 B:HIS81 3.0 17.2 1.0
CG B:HIS40 3.1 12.9 1.0
CG B:HIS81 3.1 15.3 1.0
CB B:CYS78 3.2 12.7 1.0
CE B:MET86 3.3 17.5 1.0
CB B:HIS81 3.4 14.9 1.0
CB B:HIS40 3.4 12.6 1.0
CA B:HIS40 3.7 12.6 1.0
CG B:MET86 4.0 13.9 1.0
O B:GLY39 4.1 16.9 1.0
NE2 B:HIS81 4.1 18.8 1.0
NE2 B:HIS40 4.2 15.3 1.0
CD2 B:HIS81 4.2 17.4 1.0
CD2 B:HIS40 4.2 13.4 1.0
CG B:PRO80 4.4 15.8 1.0
CB B:MET86 4.5 12.6 1.0
N B:HIS81 4.5 14.3 1.0
N B:HIS40 4.5 13.8 1.0
CA B:HIS81 4.6 13.9 1.0
C B:GLY39 4.6 14.8 1.0
CA B:CYS78 4.6 11.5 1.0
N B:ASN41 4.8 12.3 1.0
C B:HIS40 4.8 12.8 1.0

Reference:

Y.Aoyama, T.Yamaguchi, T.Kohzuma. X-Ray Crystal Structure of Pseudoazurin MET16HIS Variant at pH 4.0 To Be Published.
Page generated: Mon Jul 14 08:59:38 2025

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