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Copper in PDB 5ztd: X-Ray Crystal Structure of Pseudoazurin MET16VAL Variant

Protein crystallography data

The structure of X-Ray Crystal Structure of Pseudoazurin MET16VAL Variant, PDB code: 5ztd was solved by C.Sakai, T.Yamaguchi, T.Kohzuma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.21 / 1.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.070, 60.560, 54.530, 90.00, 106.20, 90.00
R / Rfree (%) 11.4 / 15.1

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Crystal Structure of Pseudoazurin MET16VAL Variant (pdb code 5ztd). 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 MET16VAL Variant, PDB code: 5ztd:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 5ztd

Go back to Copper Binding Sites List in 5ztd
Copper binding site 1 out of 2 in the X-Ray Crystal Structure of Pseudoazurin MET16VAL Variant


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 MET16VAL Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:4.7
occ:1.00
ND1 A:HIS40 2.0 5.2 1.0
ND1 A:HIS81 2.0 5.2 1.0
SG A:CYS78 2.2 5.6 1.0
SD A:MET86 2.5 4.9 1.0
HB2 A:HIS81 2.8 6.3 1.0
CE1 A:HIS40 2.9 5.1 1.0
CE1 A:HIS81 3.0 7.0 1.0
CG A:HIS81 3.1 5.2 1.0
HE1 A:HIS40 3.1 6.1 1.0
CG A:HIS40 3.1 4.0 1.0
HE1 A:HIS81 3.2 8.5 1.0
HB3 A:CYS78 3.2 5.1 1.0
HA A:HIS40 3.2 4.9 1.0
HB3 A:HIS40 3.2 5.3 1.0
CB A:CYS78 3.2 4.2 1.0
CE A:MET86 3.3 5.4 1.0
HE1 A:MET86 3.3 8.2 1.0
HB2 A:CYS78 3.3 5.1 1.0
HE3 A:MET86 3.3 8.2 1.0
CB A:HIS81 3.4 5.2 1.0
CB A:HIS40 3.5 4.4 1.0
HG2 A:PRO80 3.7 7.5 1.0
CG A:MET86 3.8 4.3 1.0
CA A:HIS40 3.8 4.1 1.0
HB3 A:HIS81 3.9 6.3 1.0
HG2 A:MET86 3.9 5.2 1.0
HB A:VAL16 4.0 5.5 1.0
HB3 A:MET86 4.0 4.5 1.0
H A:ASN41 4.1 5.3 1.0
NE2 A:HIS81 4.1 7.5 1.0
NE2 A:HIS40 4.1 5.3 1.0
CD2 A:HIS81 4.2 6.7 1.0
CD2 A:HIS40 4.2 4.4 1.0
HE2 A:MET86 4.2 8.2 1.0
HB2 A:MET86 4.2 4.5 1.0
H A:HIS81 4.2 5.9 1.0
CB A:MET86 4.3 3.7 1.0
O A:GLY39 4.4 6.8 1.0
HB2 A:HIS40 4.4 5.3 1.0
HD2 A:PRO80 4.6 6.5 1.0
CG A:PRO80 4.6 6.3 1.0
CA A:CYS78 4.6 4.4 1.0
HG3 A:MET86 4.6 5.2 1.0
N A:HIS81 4.6 4.9 1.0
CA A:HIS81 4.6 4.5 1.0
HG11 A:VAL16 4.6 8.4 1.0
N A:HIS40 4.6 4.5 1.0
HG13 A:VAL16 4.8 8.4 1.0
N A:ASN41 4.8 4.5 1.0
C A:GLY39 4.8 5.6 1.0
CB A:VAL16 4.9 4.6 1.0
HG3 A:PRO80 4.9 7.5 1.0
C A:HIS40 4.9 4.2 1.0
HA A:CYS78 5.0 5.3 1.0
CG1 A:VAL16 5.0 5.6 1.0

Copper binding site 2 out of 2 in 5ztd

Go back to Copper Binding Sites List in 5ztd
Copper binding site 2 out of 2 in the X-Ray Crystal Structure of Pseudoazurin MET16VAL Variant


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 MET16VAL Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:6.3
occ:1.00
ND1 B:HIS40 2.0 6.4 1.0
ND1 B:HIS81 2.0 6.6 1.0
SG B:CYS78 2.2 6.3 1.0
SD B:MET86 2.5 6.1 1.0
HB2 B:HIS81 2.8 7.8 1.0
CE1 B:HIS40 3.0 7.3 1.0
CE1 B:HIS81 3.0 8.4 1.0
CG B:HIS81 3.1 6.8 1.0
CG B:HIS40 3.1 6.1 1.0
HB3 B:CYS78 3.1 6.2 1.0
HE1 B:HIS40 3.1 8.8 1.0
CB B:CYS78 3.1 5.2 1.0
HA B:HIS40 3.2 7.2 1.0
HE1 B:HIS81 3.2 10.0 1.0
HB3 B:HIS40 3.2 7.7 1.0
HE1 B:MET86 3.2 12.4 1.0
CE B:MET86 3.3 8.3 1.0
HB2 B:CYS78 3.3 6.2 1.0
CB B:HIS81 3.4 6.5 1.0
HE2 B:MET86 3.4 12.4 1.0
CB B:HIS40 3.5 6.4 1.0
HG2 B:PRO80 3.6 8.4 1.0
CA B:HIS40 3.8 6.0 1.0
CG B:MET86 3.9 5.6 1.0
HB3 B:HIS81 3.9 7.8 1.0
HG2 B:MET86 4.0 6.7 1.0
HB B:VAL16 4.0 7.7 1.0
O B:GLY39 4.1 10.4 1.0
NE2 B:HIS40 4.1 6.5 1.0
NE2 B:HIS81 4.1 9.3 1.0
H B:ASN41 4.2 7.2 1.0
HB3 B:MET86 4.2 6.5 1.0
CD2 B:HIS81 4.2 8.4 1.0
CD2 B:HIS40 4.2 7.0 1.0
H B:HIS81 4.2 7.4 1.0
HE3 B:MET86 4.2 12.4 1.0
HB2 B:MET86 4.3 6.5 1.0
CB B:MET86 4.4 5.4 1.0
HB2 B:HIS40 4.4 7.7 1.0
HG11 B:VAL16 4.4 11.7 1.0
CG B:PRO80 4.5 7.0 1.0
CA B:CYS78 4.6 5.3 1.0
HB3 B:MET7 4.6 7.4 0.6
N B:HIS81 4.6 6.2 1.0
CA B:HIS81 4.6 6.4 1.0
N B:HIS40 4.6 6.4 1.0
HD2 B:PRO80 4.6 7.9 1.0
HG3 B:MET86 4.7 6.7 1.0
C B:GLY39 4.7 7.3 1.0
HG13 B:VAL16 4.7 11.7 1.0
N B:ASN41 4.8 6.0 1.0
HG3 B:PRO80 4.8 8.4 1.0
CB B:VAL16 4.9 6.4 1.0
CG1 B:VAL16 4.9 7.8 1.0
C B:HIS40 4.9 6.2 1.0
HB3 B:MET7 4.9 10.7 0.4
HA B:CYS78 4.9 6.3 1.0

Reference:

C.Sakai, T.Yamaguchi, T.Kohzuma. X-Ray Crystal Structure of Pseudoazurin MET16VAL Variant To Be Published.
Page generated: Mon Jul 14 05:52:22 2025

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