Zinc 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:

Copper (Cu) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6vbt

Go back to Zinc Binding Sites List in 6vbt
Zinc 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 Zinc with other atoms in the Zn 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:Zn202

b:10.2
occ:1.00
OD1 A:ASP95 1.9 12.2 1.0
ND1 A:HIS92 2.1 12.9 1.0
ND1 A:HIS74 2.1 14.6 1.0
ND1 A:HIS83 2.1 9.2 1.0
CG A:ASP95 2.8 10.1 1.0
HB2 A:HIS92 2.8 14.5 1.0
OD2 A:ASP95 2.9 8.4 1.0
CE1 A:HIS83 3.0 9.9 1.0
CE1 A:HIS74 3.0 13.1 1.0
CE1 A:HIS92 3.0 12.6 1.0
CG A:HIS92 3.1 12.5 1.0
HE1 A:HIS83 3.1 11.8 1.0
CG A:HIS74 3.1 14.9 1.0
HA A:HIS83 3.1 15.2 1.0
CG A:HIS83 3.1 8.7 1.0
HE1 A:HIS74 3.2 15.8 1.0
HE1 A:HIS92 3.2 15.2 1.0
HB3 A:HIS74 3.2 17.7 1.0
HB2 A:HIS83 3.2 14.3 1.0
CB A:HIS92 3.4 12.1 1.0
HB2 A:HIS74 3.4 17.7 1.0
CB A:HIS74 3.5 14.7 1.0
CB A:HIS83 3.5 11.9 1.0
HB3 A:HIS92 3.7 14.5 1.0
HD22 A:LEU143 3.8 23.9 1.0
CA A:HIS83 3.8 12.7 1.0
NE2 A:HIS83 4.1 11.0 1.0
NE2 A:HIS74 4.1 16.1 1.0
NE2 A:HIS92 4.1 13.6 1.0
CB A:ASP95 4.2 8.6 1.0
CD2 A:HIS92 4.2 16.3 1.0
CD2 A:HIS74 4.2 16.2 1.0
CD2 A:HIS83 4.2 8.6 1.0
HA A:ASP95 4.3 12.3 1.0
H A:HIS92 4.4 15.3 1.0
HB3 A:HIS83 4.5 14.3 1.0
HB3 A:ASP95 4.6 10.3 1.0
H A:LEU84 4.6 13.3 1.0
HD2 A:HIS49 4.6 11.6 1.0
CA A:ASP95 4.7 10.3 1.0
HA A:LEU143 4.7 18.3 1.0
CD2 A:LEU143 4.7 19.9 1.0
CA A:HIS92 4.7 10.7 1.0
HB2 A:ASP95 4.7 10.3 1.0
HB3 A:HIS49 4.8 12.7 1.0
HD23 A:LEU143 4.8 23.9 1.0
O A:LYS82 4.8 14.6 1.0
CD2 A:HIS49 4.8 9.6 1.0
N A:HIS83 4.8 13.9 1.0
H A:GLY85 4.8 10.2 1.0
C A:HIS83 4.9 12.1 1.0
HE2 A:HIS83 4.9 13.2 1.0
N A:ASP95 4.9 8.6 1.0
HE2 A:HIS74 4.9 19.3 1.0
HE2 A:HIS92 4.9 16.3 1.0
H A:ASP95 4.9 10.3 1.0
N A:HIS92 4.9 12.8 1.0
HB3 A:LEU143 5.0 19.1 1.0
CA A:HIS74 5.0 14.4 1.0

Zinc binding site 2 out of 2 in 6vbt

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

b:10.4
occ:1.00
OD1 B:ASP95 2.0 12.1 1.0
ND1 B:HIS83 2.1 12.8 1.0
ND1 B:HIS74 2.1 12.3 1.0
ND1 B:HIS92 2.1 10.5 1.0
CG B:ASP95 2.7 12.7 1.0
HB2 B:HIS92 2.9 14.2 1.0
OD2 B:ASP95 2.9 12.5 1.0
CE1 B:HIS83 3.0 14.3 1.0
CE1 B:HIS74 3.0 13.6 1.0
HE1 B:HIS83 3.1 17.2 1.0
CE1 B:HIS92 3.1 17.7 1.0
CG B:HIS74 3.1 13.5 1.0
CG B:HIS92 3.1 11.3 1.0
CG B:HIS83 3.1 14.0 1.0
HA B:HIS83 3.2 15.4 1.0
HE1 B:HIS74 3.2 16.3 1.0
HB2 B:HIS83 3.2 13.6 1.0
HB3 B:HIS74 3.2 16.0 1.0
HE1 B:HIS92 3.2 21.3 1.0
HB2 B:HIS74 3.4 16.0 1.0
CB B:HIS92 3.5 11.8 1.0
CB B:HIS74 3.5 13.3 1.0
CB B:HIS83 3.5 11.4 1.0
CA B:HIS83 3.9 12.8 1.0
HD22 B:LEU143 3.9 22.2 1.0
HB3 B:HIS92 3.9 14.2 1.0
NE2 B:HIS83 4.1 15.4 1.0
CB B:ASP95 4.2 10.8 1.0
NE2 B:HIS74 4.2 16.5 1.0
NE2 B:HIS92 4.2 13.7 1.0
CD2 B:HIS83 4.2 16.0 1.0
HA B:ASP95 4.2 12.5 1.0
CD2 B:HIS74 4.2 16.4 1.0
CD2 B:HIS92 4.3 14.1 1.0
H B:HIS92 4.3 15.0 1.0
HB3 B:HIS83 4.5 13.6 1.0
HD2 B:HIS49 4.5 13.1 1.0
HB3 B:ASP95 4.5 13.0 1.0
CA B:ASP95 4.6 10.4 1.0
H B:LEU84 4.6 18.6 1.0
CD2 B:HIS49 4.7 10.9 1.0
CD2 B:LEU143 4.7 18.5 1.0
HA B:LEU143 4.7 20.6 1.0
HD23 B:LEU143 4.7 22.2 1.0
CA B:HIS92 4.7 14.3 1.0
HB2 B:ASP95 4.7 13.0 1.0
O B:LYS82 4.8 17.7 1.0
HB3 B:HIS49 4.8 12.0 1.0
N B:HIS83 4.8 15.5 1.0
H B:GLY85 4.8 15.2 1.0
N B:ASP95 4.9 9.5 1.0
N B:HIS92 4.9 12.5 1.0
C B:HIS83 4.9 12.6 1.0
HE2 B:HIS83 4.9 18.5 1.0
H B:ASP95 4.9 11.4 1.0
HE2 B:HIS74 4.9 19.8 1.0
HE2 B:HIS92 5.0 16.5 1.0
HB3 B:LEU143 5.0 17.4 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: Mon Jan 25 16:36:12 2021

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