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Copper in PDB 6d52: Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution

Enzymatic activity of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution

All present enzymatic activity of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution:
1.15.1.1;

Protein crystallography data

The structure of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution, PDB code: 6d52 was solved by P.W.Newhouse Ix, K.T.Forest, K.A.Satyshur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.530, 68.571, 122.172, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.4

Other elements in 6d52:

The structure of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution (pdb code 6d52). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution, PDB code: 6d52:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6d52

Go back to Copper Binding Sites List in 6d52
Copper binding site 1 out of 4 in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:19.3
occ:1.00
 ND1 B:HIS49 2.0 14.3 1.0
NE2 B:HIS51 2.0 13.0 1.0
NE2 B:HIS130 2.0 17.3 1.0
HB2 B:HIS49 2.8 20.4 1.0
HE2 B:HIS74 2.9 24.6 1.0
CE1 B:HIS49 2.9 16.7 1.0
CE1 B:HIS51 2.9 17.0 1.0
HB3 B:MET128 3.0 20.8 1.0
CD2 B:HIS130 3.0 15.4 1.0
CG B:HIS49 3.0 16.0 1.0
CD2 B:HIS51 3.0 14.6 1.0
HE1 B:HIS49 3.1 20.0 1.0
CE1 B:HIS130 3.1 20.1 1.0
HD2 B:HIS130 3.1 18.5 1.0
HE1 B:HIS51 3.1 20.4 1.0
NE2 B:HIS74 3.2 20.4 1.0
HD2 B:HIS51 3.2 17.5 1.0
HG2 B:MET128 3.3 20.5 1.0
HE1 B:HIS130 3.3 24.2 1.0
CB B:HIS49 3.4 17.0 1.0
CD2 B:HIS74 3.6 18.8 1.0
HD2 B:HIS74 3.6 22.5 1.0
CB B:MET128 3.8 17.3 1.0
CG B:MET128 3.9 17.1 1.0
O B:HOH419 3.9 23.4 1.0
H B:HIS49 4.0 14.8 1.0
CE1 B:HIS74 4.0 20.8 1.0
NE2 B:HIS49 4.0 16.3 1.0
HB2 B:MET128 4.1 20.8 1.0
ND1 B:HIS51 4.1 17.6 1.0
CD2 B:HIS49 4.1 16.3 1.0
HB3 B:HIS49 4.1 20.4 1.0
CG B:HIS130 4.1 17.0 1.0
CG B:HIS51 4.1 17.7 1.0
ND1 B:HIS130 4.2 18.7 1.0
HG3 B:MET128 4.2 20.5 1.0
N B:HIS49 4.3 12.4 1.0
CA B:HIS49 4.3 14.1 1.0
O B:HOH388 4.3 21.5 1.0
HE1 B:HIS74 4.3 25.0 1.0
CG B:HIS74 4.5 20.8 1.0
O B:HIS49 4.6 16.9 1.0
C B:HIS49 4.7 14.5 1.0
ND1 B:HIS74 4.7 18.7 1.0
O B:MET128 4.7 15.3 1.0
HE2 B:HIS49 4.8 19.5 1.0
HD1 B:HIS51 4.8 21.1 1.0
HE3 B:MET128 4.9 20.8 1.0
HD1 B:HIS130 5.0 22.4 1.0
HD2 B:HIS49 5.0 19.6 1.0
CA B:MET128 5.0 14.0 1.0

Copper binding site 2 out of 4 in 6d52

Go back to Copper Binding Sites List in 6d52
Copper binding site 2 out of 4 in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu202

b:17.5
occ:1.00
 ND1 D:HIS49 2.0 14.2 1.0
NE2 D:HIS130 2.0 13.8 1.0
NE2 D:HIS51 2.0 14.7 1.0
HB2 D:HIS49 2.8 18.4 1.0
HE2 D:HIS74 2.8 21.6 1.0
CE1 D:HIS49 3.0 13.9 1.0
CD2 D:HIS130 3.0 14.1 1.0
HB3 D:MET128 3.0 16.4 1.0
CE1 D:HIS51 3.0 15.7 1.0
CG D:HIS49 3.0 12.9 1.0
CE1 D:HIS130 3.1 14.9 1.0
CD2 D:HIS51 3.1 13.0 1.0
HD2 D:HIS130 3.1 16.9 1.0
HE1 D:HIS49 3.1 16.7 1.0
NE2 D:HIS74 3.2 18.0 1.0
HE1 D:HIS51 3.2 18.9 1.0
HD2 D:HIS51 3.2 15.7 1.0
HE1 D:HIS130 3.3 17.9 1.0
HG2 D:MET128 3.3 18.2 1.0
CB D:HIS49 3.4 15.3 1.0
HD2 D:HIS74 3.5 22.2 1.0
CD2 D:HIS74 3.5 18.5 1.0
CB D:MET128 3.8 13.6 1.0
O D:HOH434 3.8 19.9 1.0
CG D:MET128 3.9 15.1 1.0
H D:HIS49 4.0 14.9 1.0
CE1 D:HIS74 4.1 18.2 1.0
NE2 D:HIS49 4.1 13.9 1.0
HB2 D:MET128 4.1 16.4 1.0
HB3 D:HIS49 4.1 18.4 1.0
ND1 D:HIS51 4.1 16.4 1.0
CG D:HIS130 4.1 14.6 1.0
CD2 D:HIS49 4.1 12.6 1.0
ND1 D:HIS130 4.1 15.2 1.0
CG D:HIS51 4.2 17.9 1.0
HG3 D:MET128 4.2 18.2 1.0
O D:HOH414 4.3 21.4 1.0
N D:HIS49 4.3 12.4 1.0
CA D:HIS49 4.3 13.4 1.0
HE1 D:HIS74 4.4 21.9 1.0
CG D:HIS74 4.5 15.9 1.0
O D:HIS49 4.6 14.6 1.0
C D:HIS49 4.7 14.3 1.0
ND1 D:HIS74 4.8 15.5 1.0
O D:MET128 4.8 14.6 1.0
HE2 D:HIS49 4.9 16.6 1.0
HD1 D:HIS51 4.9 19.7 1.0
HG2 D:ARG149 4.9 18.2 1.0
HD1 D:HIS130 4.9 18.3 1.0
HE3 D:MET128 4.9 21.6 1.0
HD2 D:HIS49 5.0 15.1 1.0

Copper binding site 3 out of 4 in 6d52

Go back to Copper Binding Sites List in 6d52
Copper binding site 3 out of 4 in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu202

b:20.8
occ:1.00
 NE2 C:HIS51 2.0 17.3 1.0
ND1 C:HIS49 2.0 16.2 1.0
NE2 C:HIS130 2.0 19.6 1.0
HE2 C:HIS74 2.8 26.3 1.0
HB2 C:HIS49 2.9 22.2 1.0
CD2 C:HIS130 2.9 19.6 1.0
CE1 C:HIS49 2.9 20.0 1.0
HB3 C:MET128 2.9 23.5 1.0
CD2 C:HIS51 3.0 18.2 1.0
CE1 C:HIS51 3.0 21.5 1.0
HD2 C:HIS130 3.0 23.6 1.0
HE1 C:HIS49 3.1 24.0 1.0
CG C:HIS49 3.1 16.4 1.0
CE1 C:HIS130 3.1 21.9 1.0
NE2 C:HIS74 3.2 21.9 1.0
HD2 C:HIS51 3.2 21.9 1.0
HE1 C:HIS51 3.2 25.8 1.0
HG2 C:MET128 3.3 26.3 1.0
HE1 C:HIS130 3.3 26.4 1.0
CB C:HIS49 3.5 18.5 1.0
HD2 C:HIS74 3.5 27.1 1.0
CD2 C:HIS74 3.5 22.6 1.0
CB C:MET128 3.7 19.6 1.0
O C:HOH379 3.9 24.0 1.0
CG C:MET128 3.9 21.9 1.0
H C:HIS49 4.0 19.7 1.0
HB2 C:MET128 4.0 23.5 1.0
CE1 C:HIS74 4.0 18.4 1.0
NE2 C:HIS49 4.1 17.7 1.0
CG C:HIS130 4.1 21.2 1.0
ND1 C:HIS51 4.1 19.8 1.0
CG C:HIS51 4.1 21.9 1.0
ND1 C:HIS130 4.1 20.1 1.0
CD2 C:HIS49 4.2 17.7 1.0
HG3 C:MET128 4.2 26.3 1.0
HB3 C:HIS49 4.2 22.2 1.0
O C:HOH356 4.3 25.8 1.0
N C:HIS49 4.3 16.4 1.0
CA C:HIS49 4.4 13.7 1.0
HE1 C:HIS74 4.4 22.1 1.0
CG C:HIS74 4.5 19.0 1.0
O C:HIS49 4.6 17.3 1.0
C C:HIS49 4.7 16.1 1.0
ND1 C:HIS74 4.7 22.2 1.0
O C:MET128 4.8 21.0 1.0
HE2 C:HIS49 4.8 21.3 1.0
HD1 C:HIS51 4.9 23.8 1.0
HE3 C:MET128 4.9 27.0 1.0
HD1 C:HIS130 4.9 24.1 1.0
HG2 C:ARG149 4.9 27.8 1.0
CA C:MET128 5.0 21.4 1.0

Copper binding site 4 out of 4 in 6d52

Go back to Copper Binding Sites List in 6d52
Copper binding site 4 out of 4 in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:17.3
occ:1.00
 ND1 A:HIS49 2.0 12.7 1.0
NE2 A:HIS130 2.0 13.5 1.0
NE2 A:HIS51 2.0 14.6 1.0
HB2 A:HIS49 2.7 18.4 1.0
HE2 A:HIS74 2.9 22.4 1.0
CD2 A:HIS130 2.9 14.2 1.0
CE1 A:HIS51 3.0 16.2 1.0
CE1 A:HIS49 3.0 14.1 1.0
CG A:HIS49 3.0 12.8 1.0
HB3 A:MET128 3.0 16.6 1.0
CE1 A:HIS130 3.0 16.9 1.0
CD2 A:HIS51 3.0 14.0 1.0
HD2 A:HIS130 3.1 17.1 1.0
HE1 A:HIS51 3.1 19.4 1.0
HE1 A:HIS49 3.2 16.9 1.0
NE2 A:HIS74 3.2 18.6 1.0
HE1 A:HIS130 3.2 20.2 1.0
HD2 A:HIS51 3.3 16.8 1.0
HG2 A:MET128 3.3 18.2 1.0
CB A:HIS49 3.3 15.4 1.0
HD2 A:HIS74 3.6 20.6 1.0
CD2 A:HIS74 3.6 17.2 1.0
O A:HOH398 3.7 17.5 1.0
CB A:MET128 3.8 13.8 1.0
CG A:MET128 3.9 15.1 1.0
CE1 A:HIS74 4.0 17.0 1.0
H A:HIS49 4.0 14.9 1.0
HB3 A:HIS49 4.0 18.4 1.0
ND1 A:HIS51 4.1 14.3 1.0
NE2 A:HIS49 4.1 15.1 1.0
CG A:HIS130 4.1 14.2 1.0
ND1 A:HIS130 4.1 15.6 1.0
HB2 A:MET128 4.1 16.6 1.0
CD2 A:HIS49 4.1 14.4 1.0
CG A:HIS51 4.2 14.9 1.0
O A:HOH389 4.2 19.9 1.0
HG3 A:MET128 4.2 18.2 1.0
N A:HIS49 4.3 12.4 1.0
CA A:HIS49 4.3 12.6 1.0
HE1 A:HIS74 4.3 20.4 1.0
CG A:HIS74 4.5 14.7 1.0
O A:HIS49 4.6 14.3 1.0
C A:HIS49 4.7 12.2 1.0
ND1 A:HIS74 4.7 16.9 1.0
O A:MET128 4.8 14.3 1.0
HD1 A:HIS51 4.9 17.2 1.0
HE2 A:HIS49 4.9 18.1 1.0
HD1 A:HIS130 4.9 18.8 1.0
HD2 A:HIS49 5.0 17.3 1.0
HG2 A:ARG149 5.0 17.9 1.0

Reference:

P.W.Newhouse Ix, K.A.Satyshur, K.T.Forest, J.M.Slauch. Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution To Be Published.
Page generated: Sun Dec 13 11:22:10 2020

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