Copper in PDB 6vbt: The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution

Enzymatic activity of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution

All present enzymatic activity of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution:
1.15.1.1;

Protein crystallography data

The structure of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution, PDB code: 6vbt was solved by K.A.Satyshur, K.T.Forest, P.W.Newhouse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.57 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.052, 57.428, 120.548, 90, 90, 90
R / Rfree (%) 17.5 / 21.2

Other elements in 6vbt:

The structure of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution (pdb code 6vbt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution, PDB code: 6vbt:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6vbt

Go back to Copper Binding Sites List in 6vbt
Copper binding site 1 out of 2 in the The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:57.7
occ:1.00
 NE2 A:HIS130 2.0 23.6 1.0
NE2 A:HIS51 2.2 17.4 1.0
ND1 A:HIS49 2.2 12.1 1.0
HB2 A:HIS49 2.5 12.7 1.0
HE2 A:HIS74 2.7 19.3 1.0
CD2 A:HIS130 2.8 22.1 1.0
HD2 A:HIS130 3.0 26.5 1.0
HB3 A:MET128 3.0 21.7 1.0
CG A:HIS49 3.0 9.0 1.0
CE1 A:HIS130 3.1 19.0 1.0
NE2 A:HIS74 3.1 16.1 1.0
CD2 A:HIS51 3.1 13.2 1.0
CE1 A:HIS51 3.1 17.8 1.0
CB A:HIS49 3.2 10.6 1.0
CE1 A:HIS49 3.3 13.0 1.0
HD2 A:HIS51 3.3 15.9 1.0
HE1 A:HIS130 3.3 22.8 1.0
HE1 A:HIS51 3.3 21.4 1.0
HD2 A:HIS74 3.3 19.4 1.0
CD2 A:HIS74 3.4 16.2 1.0
HE1 A:HIS49 3.5 15.6 1.0
HG2 A:MET128 3.6 21.8 1.0
HB3 A:HIS49 3.9 12.7 1.0
CB A:MET128 3.9 18.1 1.0
CE1 A:HIS74 4.0 13.1 1.0
H A:HIS49 4.0 9.6 1.0
CG A:HIS130 4.0 20.3 1.0
ND1 A:HIS130 4.1 19.2 1.0
CG A:MET128 4.2 18.2 1.0
HB2 A:MET128 4.2 21.7 1.0
CA A:HIS49 4.2 11.1 1.0
CD2 A:HIS49 4.2 9.6 1.0
ND1 A:HIS51 4.2 13.8 1.0
N A:HIS49 4.3 8.0 1.0
CG A:HIS51 4.3 12.6 1.0
NE2 A:HIS49 4.3 11.9 1.0
O A:HOH406 4.3 26.8 1.0
O A:HOH437 4.4 22.4 1.0
HE1 A:HIS74 4.4 15.8 1.0
HG3 A:MET128 4.4 21.8 1.0
CG A:HIS74 4.5 14.9 1.0
O A:HIS49 4.5 13.1 1.0
O A:MET128 4.6 9.2 1.0
C A:HIS49 4.6 13.0 1.0
ND1 A:HIS74 4.7 14.6 1.0
HD1 A:HIS130 4.9 23.1 1.0
C A:MET128 4.9 13.6 1.0
CA A:MET128 5.0 11.3 1.0

Copper binding site 2 out of 2 in 6vbt

Go back to Copper Binding Sites List in 6vbt
Copper binding site 2 out of 2 in the The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The P212121 Crystal Structure of Sodci Superoxide Dismutase with 2 Molecules in the Asymmetric Unit at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:61.7
occ:1.00
 NE2 B:HIS130 2.0 31.8 1.0
NE2 B:HIS51 2.2 11.2 1.0
ND1 B:HIS49 2.3 10.1 1.0
HE2 B:HIS74 2.6 19.8 1.0
HB2 B:HIS49 2.7 12.0 1.0
CD2 B:HIS130 2.9 22.6 1.0
HB3 B:MET128 3.0 17.7 1.0
CE1 B:HIS130 3.0 25.4 1.0
NE2 B:HIS74 3.1 16.5 1.0
HD2 B:HIS130 3.1 27.1 1.0
CE1 B:HIS51 3.1 12.8 1.0
CG B:HIS49 3.2 10.9 1.0
HE1 B:HIS51 3.2 15.4 1.0
HE1 B:HIS130 3.2 30.4 1.0
CE1 B:HIS49 3.3 13.2 1.0
CD2 B:HIS51 3.3 12.9 1.0
HG2 B:MET128 3.3 19.2 1.0
HD2 B:HIS74 3.4 19.6 1.0
CB B:HIS49 3.4 10.0 1.0
CD2 B:HIS74 3.4 16.4 1.0
HE1 B:HIS49 3.5 15.9 1.0
HD2 B:HIS51 3.5 15.4 1.0
CB B:MET128 3.8 14.7 1.0
CG B:MET128 3.9 16.0 1.0
CE1 B:HIS74 4.0 13.6 1.0
HB3 B:HIS49 4.0 12.0 1.0
CG B:HIS130 4.1 19.3 1.0
ND1 B:HIS130 4.1 20.4 1.0
O B:HOH415 4.1 25.6 1.0
HB2 B:MET128 4.1 17.7 1.0
H B:HIS49 4.1 10.4 1.0
HG3 B:MET128 4.2 19.2 1.0
O B:HOH425 4.2 22.6 1.0
ND1 B:HIS51 4.3 13.1 1.0
CD2 B:HIS49 4.3 10.9 1.0
NE2 B:HIS49 4.4 13.1 1.0
HE1 B:HIS74 4.4 16.3 1.0
CG B:HIS51 4.4 11.7 1.0
N B:HIS49 4.4 8.7 1.0
CA B:HIS49 4.4 9.1 1.0
CG B:HIS74 4.5 13.5 1.0
HG2 B:ARG149 4.6 38.1 1.0
O B:MET128 4.7 9.4 1.0
O B:HIS49 4.8 9.8 1.0
ND1 B:HIS74 4.8 12.3 1.0
HD1 B:HIS130 4.9 24.5 1.0
C B:HIS49 4.9 8.1 1.0
HE3 B:MET128 4.9 21.3 1.0
C B:MET128 5.0 11.9 1.0
CA B:MET128 5.0 9.9 1.0

Reference:

P.W.Newhouse, K.A.Satyshur, J.M.Slauch, K.T.Forest. Structure and Muropeptide Binding of the Virulence Factor Superoxide Dismutase C1 From Salmonella Typhimurium To Be Published.
Page generated: Sun Jan 24 15:05:59 2021

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