Atomistry » Zinc » PDB 6d1a-6dbv » 6d52
Atomistry »
  Zinc »
    PDB 6d1a-6dbv »
      6d52 »

Zinc 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:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Superoxide Dismutase Sodci of Salmonella Enterica Serovar Typhimurium at 1.6 Angstrom Resolution, PDB code: 6d52:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6d52

Go back to Zinc Binding Sites List in 6d52
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:19.8
occ:1.00
OD1 B:ASP95 1.9 17.7 1.0
ND1 B:HIS74 2.0 18.7 1.0
ND1 B:HIS92 2.0 20.1 1.0
ND1 B:HIS83 2.1 18.6 1.0
CG B:ASP95 2.7 18.9 1.0
HB2 B:HIS92 2.9 22.1 1.0
OD2 B:ASP95 2.9 18.6 1.0
CE1 B:HIS83 2.9 17.5 1.0
CE1 B:HIS74 2.9 20.8 1.0
CE1 B:HIS92 3.0 21.1 1.0
HE1 B:HIS83 3.1 21.1 1.0
HE1 B:HIS74 3.1 25.0 1.0
CG B:HIS92 3.1 18.7 1.0
CG B:HIS74 3.1 20.8 1.0
HE1 B:HIS92 3.1 25.3 1.0
CG B:HIS83 3.1 19.0 1.0
HA B:HIS83 3.2 24.9 1.0
HB3 B:HIS74 3.2 23.8 1.0
HB2 B:HIS83 3.2 24.3 1.0
HB2 B:HIS74 3.4 23.8 1.0
CB B:HIS92 3.5 18.4 1.0
CB B:HIS74 3.5 19.8 1.0
CB B:HIS83 3.6 20.2 1.0
HB3 B:HIS92 3.8 22.1 1.0
CA B:HIS83 3.9 20.7 1.0
HD22 B:LEU143 4.0 28.5 1.0
NE2 B:HIS74 4.1 20.4 1.0
NE2 B:HIS83 4.1 17.1 1.0
NE2 B:HIS92 4.1 21.3 1.0
CB B:ASP95 4.2 15.2 1.0
CD2 B:HIS92 4.2 22.8 1.0
CD2 B:HIS74 4.2 18.8 1.0
CD2 B:HIS83 4.2 17.6 1.0
HA B:ASP95 4.3 20.6 1.0
H B:HIS92 4.4 25.4 1.0
HD23 B:LEU143 4.5 28.5 1.0
HB3 B:HIS83 4.5 24.3 1.0
HB3 B:ASP95 4.5 18.2 1.0
HA B:LEU143 4.6 25.3 1.0
CD2 B:LEU143 4.7 23.7 1.0
CA B:ASP95 4.7 17.2 1.0
H B:LEU84 4.7 21.3 1.0
HB3 B:HIS49 4.7 20.4 1.0
HB2 B:ASP95 4.7 18.2 1.0
CA B:HIS92 4.8 18.6 1.0
HD2 B:HIS49 4.8 19.6 1.0
H B:GLY85 4.8 22.9 1.0
CD2 B:HIS49 4.8 16.3 1.0
HE2 B:HIS83 4.9 20.5 1.0
HE2 B:HIS74 4.9 24.6 1.0
O B:LYS82 4.9 21.2 1.0
N B:HIS83 4.9 22.4 1.0
HE2 B:HIS92 4.9 25.5 1.0
N B:ASP95 4.9 17.3 1.0
C B:HIS83 4.9 20.0 1.0
H B:ASP95 4.9 20.7 1.0
HB3 B:LEU143 4.9 25.2 1.0
N B:HIS92 4.9 21.1 1.0

Zinc binding site 2 out of 4 in 6d52

Go back to Zinc Binding Sites List in 6d52
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:16.0
occ:1.00
ND1 D:HIS74 2.0 15.5 1.0
OD1 D:ASP95 2.0 15.2 1.0
ND1 D:HIS83 2.0 14.9 1.0
ND1 D:HIS92 2.1 16.7 1.0
CG D:ASP95 2.8 15.0 1.0
HB2 D:HIS92 2.9 20.1 1.0
CE1 D:HIS74 2.9 18.2 1.0
CE1 D:HIS83 2.9 14.9 1.0
OD2 D:ASP95 2.9 15.9 1.0
HE1 D:HIS83 3.0 18.0 1.0
CE1 D:HIS92 3.0 17.2 1.0
HE1 D:HIS74 3.0 21.9 1.0
CG D:HIS74 3.1 15.9 1.0
CG D:HIS92 3.1 15.1 1.0
CG D:HIS83 3.1 12.7 1.0
HE1 D:HIS92 3.1 20.7 1.0
HA D:HIS83 3.2 17.9 1.0
HB3 D:HIS74 3.2 16.6 1.0
HB2 D:HIS83 3.2 16.7 1.0
HB2 D:HIS74 3.4 16.6 1.0
CB D:HIS92 3.5 16.8 1.0
CB D:HIS74 3.5 13.8 1.0
CB D:HIS83 3.6 13.9 1.0
HD22 D:LEU143 3.8 21.5 1.0
HB3 D:HIS92 3.9 20.1 1.0
CA D:HIS83 3.9 14.9 1.0
NE2 D:HIS74 4.0 18.0 1.0
NE2 D:HIS83 4.0 13.9 1.0
CD2 D:HIS74 4.1 18.5 1.0
NE2 D:HIS92 4.1 16.9 1.0
CD2 D:HIS83 4.2 14.7 1.0
CB D:ASP95 4.2 13.3 1.0
CD2 D:HIS92 4.2 16.1 1.0
HA D:ASP95 4.3 16.3 1.0
H D:HIS92 4.3 17.5 1.0
HD23 D:LEU143 4.4 21.5 1.0
HB3 D:HIS83 4.5 16.7 1.0
CD2 D:LEU143 4.6 17.9 1.0
HB3 D:ASP95 4.6 16.0 1.0
HA D:LEU143 4.6 19.4 1.0
H D:LEU84 4.7 15.8 1.0
CA D:ASP95 4.7 13.6 1.0
HB3 D:HIS49 4.7 18.4 1.0
HD2 D:HIS49 4.7 15.1 1.0
CA D:HIS92 4.7 14.9 1.0
CD2 D:HIS49 4.8 12.6 1.0
HB2 D:ASP95 4.8 16.0 1.0
HE2 D:HIS74 4.8 21.6 1.0
HE2 D:HIS83 4.8 16.8 1.0
O D:LYS82 4.8 15.9 1.0
H D:GLY85 4.8 17.7 1.0
N D:HIS83 4.9 15.9 1.0
N D:HIS92 4.9 14.6 1.0
N D:ASP95 4.9 14.7 1.0
H D:ASP95 4.9 17.7 1.0
C D:HIS83 4.9 16.0 1.0
HE2 D:HIS92 4.9 20.3 1.0
CA D:HIS74 5.0 15.2 1.0
CG D:HIS49 5.0 12.9 1.0
HD2 D:HIS74 5.0 22.2 1.0

Zinc binding site 3 out of 4 in 6d52

Go back to Zinc Binding Sites List in 6d52
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:18.5
occ:1.00
OD1 C:ASP95 2.0 17.0 1.0
ND1 C:HIS83 2.0 18.5 1.0
ND1 C:HIS74 2.0 22.2 1.0
ND1 C:HIS92 2.1 16.5 1.0
CG C:ASP95 2.8 16.1 1.0
HB2 C:HIS92 2.8 23.3 1.0
CE1 C:HIS83 2.9 19.4 1.0
OD2 C:ASP95 2.9 16.2 1.0
CE1 C:HIS74 3.0 18.4 1.0
HE1 C:HIS83 3.0 23.3 1.0
CG C:HIS74 3.1 19.0 1.0
CE1 C:HIS92 3.1 18.5 1.0
CG C:HIS83 3.1 22.2 1.0
HE1 C:HIS74 3.1 22.1 1.0
CG C:HIS92 3.1 17.2 1.0
HA C:HIS83 3.2 21.4 1.0
HB2 C:HIS83 3.2 22.1 1.0
HB3 C:HIS74 3.2 21.9 1.0
HE1 C:HIS92 3.3 22.3 1.0
HB2 C:HIS74 3.4 21.9 1.0
CB C:HIS92 3.4 19.4 1.0
CB C:HIS74 3.5 18.2 1.0
CB C:HIS83 3.5 18.4 1.0
HB3 C:HIS92 3.7 23.3 1.0
CA C:HIS83 3.8 17.8 1.0
HD22 C:LEU143 4.0 27.9 1.0
NE2 C:HIS83 4.1 17.4 1.0
NE2 C:HIS74 4.1 21.9 1.0
CB C:ASP95 4.2 15.2 1.0
CD2 C:HIS83 4.2 17.8 1.0
CD2 C:HIS74 4.2 22.6 1.0
NE2 C:HIS92 4.2 19.4 1.0
CD2 C:HIS92 4.3 20.1 1.0
HA C:ASP95 4.3 17.7 1.0
H C:HIS92 4.4 22.9 1.0
HB3 C:HIS83 4.5 22.1 1.0
HB3 C:ASP95 4.6 18.3 1.0
CA C:ASP95 4.7 14.8 1.0
HA C:LEU143 4.7 25.1 1.0
HB3 C:HIS49 4.7 22.2 1.0
H C:LEU84 4.7 24.3 1.0
HD23 C:LEU143 4.7 27.9 1.0
HD2 C:HIS49 4.7 21.3 1.0
CA C:HIS92 4.8 18.5 1.0
CD2 C:HIS49 4.8 17.7 1.0
HB2 C:ASP95 4.8 18.3 1.0
O C:LYS82 4.8 19.4 1.0
CD2 C:LEU143 4.8 23.2 1.0
N C:HIS83 4.8 19.1 1.0
H C:GLY85 4.8 21.2 1.0
HE2 C:HIS83 4.8 20.9 1.0
N C:ASP95 4.9 16.3 1.0
C C:HIS83 4.9 20.8 1.0
HE2 C:HIS74 4.9 26.3 1.0
H C:ASP95 4.9 19.6 1.0
CG C:HIS49 5.0 16.4 1.0
HB3 C:LEU143 5.0 23.4 1.0
N C:HIS92 5.0 19.1 1.0
CA C:HIS74 5.0 18.8 1.0
HE2 C:HIS92 5.0 23.3 1.0

Zinc binding site 4 out of 4 in 6d52

Go back to Zinc Binding Sites List in 6d52
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:15.4
occ:1.00
OD1 A:ASP95 1.9 15.4 1.0
ND1 A:HIS74 2.0 16.9 1.0
ND1 A:HIS92 2.1 15.0 1.0
ND1 A:HIS83 2.1 17.0 1.0
CG A:ASP95 2.8 15.7 1.0
HB2 A:HIS92 2.9 19.6 1.0
OD2 A:ASP95 2.9 14.8 1.0
CE1 A:HIS74 2.9 17.0 1.0
CE1 A:HIS83 3.0 15.7 1.0
CE1 A:HIS92 3.0 19.2 1.0
CG A:HIS74 3.1 14.7 1.0
HE1 A:HIS74 3.1 20.4 1.0
HE1 A:HIS83 3.1 18.8 1.0
CG A:HIS92 3.1 14.8 1.0
CG A:HIS83 3.1 17.2 1.0
HE1 A:HIS92 3.2 23.1 1.0
HA A:HIS83 3.2 20.3 1.0
HB2 A:HIS83 3.2 19.2 1.0
HB3 A:HIS74 3.2 19.8 1.0
HB2 A:HIS74 3.4 19.8 1.0
CB A:HIS92 3.4 16.3 1.0
CB A:HIS74 3.5 16.5 1.0
CB A:HIS83 3.5 16.0 1.0
HB3 A:HIS92 3.8 19.6 1.0
CA A:HIS83 3.8 16.9 1.0
HD22 A:LEU143 3.9 21.7 1.0
NE2 A:HIS74 4.1 18.6 1.0
NE2 A:HIS83 4.1 14.6 1.0
NE2 A:HIS92 4.1 17.2 1.0
CD2 A:HIS74 4.2 17.2 1.0
CB A:ASP95 4.2 15.2 1.0
CD2 A:HIS92 4.2 16.8 1.0
CD2 A:HIS83 4.2 14.2 1.0
HA A:ASP95 4.3 17.5 1.0
H A:HIS92 4.4 18.7 1.0
HB3 A:HIS83 4.5 19.2 1.0
HB3 A:ASP95 4.6 18.2 1.0
HB3 A:HIS49 4.6 18.4 1.0
H A:LEU84 4.7 20.7 1.0
CA A:ASP95 4.7 14.6 1.0
HA A:LEU143 4.7 18.4 1.0
HD2 A:HIS49 4.7 17.3 1.0
HB2 A:ASP95 4.8 18.2 1.0
O A:LYS82 4.8 17.8 1.0
N A:HIS83 4.8 16.8 1.0
CD2 A:LEU143 4.8 18.1 1.0
HD23 A:LEU143 4.8 21.7 1.0
CD2 A:HIS49 4.8 14.4 1.0
CA A:HIS92 4.8 15.5 1.0
H A:GLY85 4.8 20.7 1.0
HE2 A:HIS74 4.8 22.4 1.0
C A:HIS83 4.9 17.2 1.0
N A:ASP95 4.9 13.4 1.0
HE2 A:HIS83 4.9 17.6 1.0
H A:ASP95 4.9 16.1 1.0
HE2 A:HIS92 4.9 20.7 1.0
CG A:HIS49 5.0 12.8 1.0
CA A:HIS74 5.0 14.2 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: Wed Dec 16 11:39:03 2020

Last articles

Zn in 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy