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Zinc in PDB 6vbs: The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.

Enzymatic activity of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.

All present enzymatic activity of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.:
1.15.1.1;

Protein crystallography data

The structure of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit., PDB code: 6vbs 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) 35.88 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 152.838, 69.474, 95.288, 90, 116.89, 90
R / Rfree (%) 17.9 / 21.9

Other elements in 6vbs:

The structure of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit. also contains other interesting chemical elements:

Copper (Cu) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit. (pdb code 6vbs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit., PDB code: 6vbs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6vbs

Go back to Zinc Binding Sites List in 6vbs
Zinc binding site 1 out of 6 in the The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:11.2
occ:1.00
OD1 A:ASP95 1.9 10.6 1.0
ND1 A:HIS83 2.0 15.6 1.0
ND1 A:HIS92 2.0 13.7 1.0
ND1 A:HIS74 2.0 15.1 1.0
CG A:ASP95 2.7 17.4 1.0
HB2 A:HIS92 2.9 20.3 1.0
CE1 A:HIS83 2.9 21.0 1.0
CE1 A:HIS92 2.9 20.0 1.0
OD2 A:ASP95 3.0 11.2 1.0
CE1 A:HIS74 3.0 18.4 1.0
HE1 A:HIS83 3.0 25.2 1.0
CG A:HIS83 3.1 18.7 1.0
CG A:HIS92 3.1 16.9 1.0
HE1 A:HIS92 3.1 24.0 1.0
CG A:HIS74 3.1 16.4 1.0
HE1 A:HIS74 3.1 22.0 1.0
HA A:HIS83 3.1 23.2 1.0
HB2 A:HIS83 3.2 27.3 1.0
HB3 A:HIS74 3.2 20.6 1.0
CB A:HIS92 3.4 16.9 1.0
HB2 A:HIS74 3.5 20.6 1.0
CB A:HIS74 3.5 17.2 1.0
CB A:HIS83 3.5 22.8 1.0
CA A:HIS83 3.8 19.4 1.0
HB3 A:HIS92 3.8 20.3 1.0
HD22 A:LEU143 3.9 32.3 1.0
NE2 A:HIS83 4.0 17.3 1.0
NE2 A:HIS92 4.1 18.8 1.0
NE2 A:HIS74 4.1 20.5 1.0
CD2 A:HIS83 4.1 18.8 1.0
CD2 A:HIS92 4.2 17.5 1.0
CB A:ASP95 4.2 17.6 1.0
CD2 A:HIS74 4.2 20.6 1.0
HA A:ASP95 4.3 19.8 1.0
H A:HIS92 4.4 17.2 1.0
HB3 A:HIS83 4.4 27.3 1.0
HB3 A:ASP95 4.6 21.1 1.0
H A:LEU84 4.6 18.2 1.0
HD2 A:HIS49 4.6 22.6 1.0
HA A:LEU143 4.7 28.2 1.0
HD23 A:LEU143 4.7 32.3 1.0
CA A:ASP95 4.7 16.5 1.0
CD2 A:LEU143 4.7 26.9 1.0
HB2 A:ASP95 4.8 21.1 1.0
CA A:HIS92 4.8 18.9 1.0
CD2 A:HIS49 4.8 18.8 1.0
HB3 A:HIS49 4.8 19.8 1.0
N A:HIS83 4.8 18.1 1.0
HE2 A:HIS83 4.8 20.8 1.0
HE2 A:HIS92 4.8 22.6 1.0
O A:LYS82 4.8 14.3 1.0
C A:HIS83 4.8 19.7 1.0
HE2 A:HIS74 4.9 24.5 1.0
H A:GLY85 4.9 17.4 1.0
N A:ASP95 4.9 13.6 1.0
H A:ASP95 4.9 16.3 1.0
N A:HIS92 4.9 14.4 1.0
CA A:HIS74 5.0 16.6 1.0

Zinc binding site 2 out of 6 in 6vbs

Go back to Zinc Binding Sites List in 6vbs
Zinc binding site 2 out of 6 in the The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:10.4
occ:1.00
OD1 B:ASP95 1.9 9.9 1.0
ND1 B:HIS74 2.0 12.2 1.0
ND1 B:HIS83 2.0 13.2 1.0
ND1 B:HIS92 2.0 16.6 1.0
CG B:ASP95 2.8 15.4 1.0
HB2 B:HIS92 2.9 18.8 1.0
CE1 B:HIS74 2.9 17.1 1.0
CE1 B:HIS83 2.9 17.9 1.0
CE1 B:HIS92 3.0 22.4 1.0
OD2 B:ASP95 3.0 10.9 1.0
HE1 B:HIS74 3.1 20.5 1.0
HE1 B:HIS83 3.1 21.5 1.0
CG B:HIS83 3.1 17.8 1.0
CG B:HIS74 3.1 16.9 1.0
HE1 B:HIS92 3.1 26.8 1.0
CG B:HIS92 3.1 18.0 1.0
HB2 B:HIS83 3.1 22.8 1.0
HA B:HIS83 3.2 18.5 1.0
HB3 B:HIS74 3.3 21.3 1.0
HB2 B:HIS74 3.4 21.3 1.0
CB B:HIS92 3.4 15.7 1.0
CB B:HIS83 3.5 19.0 1.0
CB B:HIS74 3.5 17.8 1.0
HB3 B:HIS92 3.8 18.8 1.0
CA B:HIS83 3.8 15.4 1.0
HD23 B:LEU143 3.9 25.6 1.0
NE2 B:HIS74 4.1 16.9 1.0
NE2 B:HIS83 4.1 13.9 1.0
NE2 B:HIS92 4.1 16.5 1.0
CD2 B:HIS83 4.2 15.4 1.0
CD2 B:HIS74 4.2 18.8 1.0
CB B:ASP95 4.2 15.4 1.0
CD2 B:HIS92 4.2 18.5 1.0
HA B:ASP95 4.3 16.9 1.0
HB3 B:HIS83 4.4 22.8 1.0
H B:HIS92 4.4 16.9 1.0
HD2 B:HIS49 4.6 21.5 1.0
H B:LEU84 4.6 18.5 1.0
HB3 B:ASP95 4.6 18.5 1.0
CA B:ASP95 4.7 14.1 1.0
HA B:LEU143 4.7 22.6 1.0
CD2 B:HIS49 4.7 17.9 1.0
HD21 B:LEU143 4.7 25.6 1.0
CD2 B:LEU143 4.7 21.3 1.0
HB2 B:ASP95 4.8 18.5 1.0
CA B:HIS92 4.8 16.0 1.0
N B:HIS83 4.8 11.9 1.0
HB3 B:HIS49 4.8 22.2 1.0
HE2 B:HIS74 4.8 20.2 1.0
HE2 B:HIS83 4.8 16.6 1.0
C B:HIS83 4.8 18.1 1.0
H B:GLY85 4.9 15.8 1.0
HE2 B:HIS92 4.9 19.8 1.0
N B:ASP95 4.9 12.5 1.0
O B:LYS82 4.9 12.6 1.0
H B:ASP95 4.9 14.9 1.0
N B:HIS92 5.0 14.1 1.0

Zinc binding site 3 out of 6 in 6vbs

Go back to Zinc Binding Sites List in 6vbs
Zinc binding site 3 out of 6 in the The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:10.7
occ:1.00
OD1 C:ASP95 1.9 9.5 1.0
ND1 C:HIS83 2.0 16.5 1.0
ND1 C:HIS74 2.0 12.6 1.0
ND1 C:HIS92 2.1 17.7 1.0
CG C:ASP95 2.7 18.7 1.0
HB2 C:HIS92 2.8 17.5 1.0
CE1 C:HIS83 2.9 16.8 1.0
OD2 C:ASP95 2.9 8.6 1.0
CE1 C:HIS74 2.9 19.7 1.0
CE1 C:HIS92 3.0 19.1 1.0
HE1 C:HIS83 3.0 20.1 1.0
HE1 C:HIS74 3.1 23.6 1.0
CG C:HIS83 3.1 19.5 1.0
CG C:HIS92 3.1 17.4 1.0
HA C:HIS83 3.1 22.6 1.0
CG C:HIS74 3.1 18.6 1.0
HE1 C:HIS92 3.2 22.9 1.0
HB2 C:HIS83 3.2 23.5 1.0
HB3 C:HIS74 3.3 19.6 1.0
CB C:HIS92 3.4 14.6 1.0
HB2 C:HIS74 3.5 19.6 1.0
CB C:HIS83 3.5 19.6 1.0
CB C:HIS74 3.5 16.4 1.0
HB3 C:HIS92 3.8 17.5 1.0
CA C:HIS83 3.8 18.9 1.0
HD21 C:LEU143 3.8 30.5 1.0
NE2 C:HIS83 4.0 15.8 1.0
NE2 C:HIS74 4.1 15.7 1.0
CD2 C:HIS83 4.1 17.0 1.0
NE2 C:HIS92 4.1 15.4 1.0
CB C:ASP95 4.2 17.2 1.0
CD2 C:HIS74 4.2 19.2 1.0
CD2 C:HIS92 4.2 17.9 1.0
HA C:ASP95 4.3 18.1 1.0
H C:HIS92 4.4 18.5 1.0
HB3 C:HIS83 4.4 23.5 1.0
HD22 C:LEU143 4.5 30.5 1.0
HD2 C:HIS49 4.6 24.4 1.0
HB3 C:ASP95 4.6 20.6 1.0
CD2 C:LEU143 4.6 25.4 1.0
H C:LEU84 4.6 19.5 1.0
HA C:LEU143 4.6 30.7 1.0
CA C:ASP95 4.7 15.1 1.0
N C:HIS83 4.7 19.0 1.0
HB2 C:ASP95 4.7 20.6 1.0
CA C:HIS92 4.8 18.7 1.0
CD2 C:HIS49 4.8 20.4 1.0
HB3 C:HIS49 4.8 20.9 1.0
HE2 C:HIS83 4.8 19.0 1.0
C C:HIS83 4.8 20.1 1.0
HE2 C:HIS74 4.8 18.9 1.0
O C:LYS82 4.8 13.1 1.0
H C:GLY85 4.9 19.6 1.0
N C:ASP95 4.9 12.2 1.0
HE2 C:HIS92 4.9 18.5 1.0
H C:ASP95 4.9 14.7 1.0
HB3 C:LEU143 5.0 21.9 1.0
N C:HIS92 5.0 15.5 1.0

Zinc binding site 4 out of 6 in 6vbs

Go back to Zinc Binding Sites List in 6vbs
Zinc binding site 4 out of 6 in the The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:11.6
occ:1.00
OD1 D:ASP95 1.9 7.3 1.0
ND1 D:HIS74 2.0 12.7 1.0
ND1 D:HIS83 2.0 16.3 1.0
ND1 D:HIS92 2.1 14.7 1.0
CG D:ASP95 2.7 17.1 1.0
CE1 D:HIS74 2.9 21.4 1.0
HB2 D:HIS92 2.9 18.8 1.0
CE1 D:HIS83 2.9 18.2 1.0
OD2 D:ASP95 2.9 13.4 1.0
CE1 D:HIS92 3.0 17.3 1.0
HE1 D:HIS74 3.0 25.6 1.0
HE1 D:HIS83 3.0 21.9 1.0
CG D:HIS83 3.1 18.2 1.0
CG D:HIS74 3.1 13.0 1.0
CG D:HIS92 3.1 15.8 1.0
HE1 D:HIS92 3.1 20.7 1.0
HB2 D:HIS83 3.2 28.5 1.0
HA D:HIS83 3.2 25.1 1.0
HB3 D:HIS74 3.2 20.5 1.0
CB D:HIS92 3.5 15.7 1.0
CB D:HIS83 3.5 23.8 1.0
CB D:HIS74 3.5 17.1 1.0
HB2 D:HIS74 3.5 20.5 1.0
HD21 D:LEU143 3.8 25.2 1.0
HB3 D:HIS92 3.8 18.8 1.0
CA D:HIS83 3.8 21.0 1.0
NE2 D:HIS74 4.0 17.2 1.0
NE2 D:HIS83 4.1 15.9 1.0
NE2 D:HIS92 4.1 15.6 1.0
CD2 D:HIS83 4.2 16.5 1.0
CD2 D:HIS74 4.2 19.0 1.0
CB D:ASP95 4.2 19.5 1.0
CD2 D:HIS92 4.2 17.2 1.0
HA D:ASP95 4.3 17.7 1.0
HB3 D:HIS83 4.4 28.5 1.0
H D:HIS92 4.4 14.6 1.0
HA D:LEU143 4.5 27.1 1.0
HB3 D:ASP95 4.6 23.3 1.0
HD2 D:HIS49 4.6 24.8 1.0
H D:LEU84 4.6 17.5 1.0
CD2 D:LEU143 4.6 21.1 1.0
HD22 D:LEU143 4.7 25.2 1.0
CA D:ASP95 4.7 14.7 1.0
HB2 D:ASP95 4.8 23.3 1.0
O D:LYS82 4.8 13.9 1.0
CD2 D:HIS49 4.8 20.7 1.0
HB3 D:HIS49 4.8 19.4 1.0
N D:HIS83 4.8 17.3 1.0
CA D:HIS92 4.8 16.2 1.0
HE2 D:HIS74 4.8 20.6 1.0
HE2 D:HIS83 4.8 19.0 1.0
C D:HIS83 4.9 20.9 1.0
HE2 D:HIS92 4.9 18.7 1.0
N D:ASP95 4.9 10.1 1.0
H D:GLY85 4.9 20.6 1.0
H D:ASP95 5.0 12.1 1.0
N D:HIS92 5.0 12.2 1.0

Zinc binding site 5 out of 6 in 6vbs

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Zinc binding site 5 out of 6 in the The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:20.8
occ:1.00
ND1 E:HIS83 1.9 22.0 1.0
OD1 E:ASP95 1.9 17.9 1.0
ND1 E:HIS74 2.0 24.1 1.0
ND1 E:HIS92 2.1 24.2 1.0
CG E:ASP95 2.7 38.0 1.0
CE1 E:HIS83 2.7 30.7 1.0
HB2 E:HIS92 2.8 34.4 1.0
HE1 E:HIS83 2.8 36.9 1.0
OD2 E:ASP95 2.9 26.7 1.0
CE1 E:HIS74 2.9 33.3 1.0
CG E:HIS83 3.0 30.9 1.0
HE1 E:HIS74 3.0 39.9 1.0
CE1 E:HIS92 3.0 37.4 1.0
CG E:HIS92 3.0 25.1 1.0
CG E:HIS74 3.1 28.7 1.0
HA E:HIS83 3.2 36.0 1.0
HE1 E:HIS92 3.2 44.8 1.0
HB2 E:HIS83 3.3 36.9 1.0
CB E:HIS92 3.4 28.7 1.0
HB3 E:HIS74 3.4 27.9 1.0
HB2 E:HIS74 3.4 27.9 1.0
CB E:HIS83 3.5 30.8 1.0
CB E:HIS74 3.5 23.3 1.0
HB3 E:HIS92 3.7 34.4 1.0
HD22 E:LEU143 3.8 37.5 1.0
CA E:HIS83 3.8 30.0 1.0
NE2 E:HIS83 3.9 23.0 1.0
CD2 E:HIS83 4.0 31.7 1.0
NE2 E:HIS74 4.1 25.6 1.0
CB E:ASP95 4.1 28.7 1.0
HA E:ASP95 4.1 30.0 1.0
NE2 E:HIS92 4.1 23.9 1.0
CD2 E:HIS92 4.2 32.9 1.0
CD2 E:HIS74 4.2 27.9 1.0
HA E:LEU143 4.4 42.2 1.0
HB3 E:HIS83 4.5 36.9 1.0
H E:HIS92 4.5 29.2 1.0
HB2 E:ASP95 4.5 34.4 1.0
CA E:ASP95 4.6 25.0 1.0
HD23 E:LEU143 4.6 37.5 1.0
CD2 E:LEU143 4.6 31.3 1.0
HD2 E:HIS49 4.6 24.6 1.0
HE2 E:HIS83 4.6 27.6 1.0
H E:LEU84 4.7 27.9 1.0
HB3 E:ASP95 4.7 34.4 1.0
CA E:HIS92 4.7 34.2 1.0
CD2 E:HIS49 4.8 20.5 1.0
H E:GLY85 4.8 34.7 1.0
N E:ASP95 4.8 18.5 1.0
H E:ASP95 4.8 22.2 1.0
N E:HIS83 4.8 29.6 1.0
HB3 E:HIS49 4.8 28.3 1.0
C E:HIS83 4.8 28.0 1.0
HE2 E:HIS74 4.8 30.7 1.0
O E:LYS82 4.8 23.2 1.0
HB3 E:LEU143 4.9 35.9 1.0
HE2 E:HIS92 4.9 28.7 1.0
HD2 E:HIS83 4.9 38.0 1.0
N E:HIS92 5.0 24.3 1.0

Zinc binding site 6 out of 6 in 6vbs

Go back to Zinc Binding Sites List in 6vbs
Zinc binding site 6 out of 6 in the The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The C2 Crystal Form of Sodci Superoxide Dismutase at 1.7 A Resolution with 6 Molecules in the Asymmetric Unit. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:13.6
occ:1.00
OD1 F:ASP95 1.9 12.9 1.0
ND1 F:HIS74 2.0 16.8 1.0
ND1 F:HIS83 2.0 17.0 1.0
ND1 F:HIS92 2.1 17.3 1.0
OD2 F:ASP95 2.6 14.5 1.0
CG F:ASP95 2.6 17.1 1.0
HB2 F:HIS92 2.8 24.5 1.0
CE1 F:HIS74 2.9 23.3 1.0
CE1 F:HIS83 2.9 18.7 1.0
CE1 F:HIS92 3.0 28.0 1.0
HE1 F:HIS83 3.1 22.5 1.0
HE1 F:HIS74 3.1 28.0 1.0
CG F:HIS92 3.1 19.8 1.0
CG F:HIS74 3.1 20.1 1.0
CG F:HIS83 3.1 19.0 1.0
HA F:HIS83 3.1 25.5 1.0
HE1 F:HIS92 3.2 33.6 1.0
HB2 F:HIS83 3.2 24.4 1.0
HB3 F:HIS74 3.2 20.3 1.0
CB F:HIS92 3.4 20.4 1.0
HB2 F:HIS74 3.4 20.3 1.0
CB F:HIS74 3.5 16.9 1.0
CB F:HIS83 3.5 20.4 1.0
CA F:HIS83 3.8 21.3 1.0
HB3 F:HIS92 3.8 24.5 1.0
HD23 F:LEU143 3.8 35.9 1.0
CB F:ASP95 4.1 16.6 1.0
NE2 F:HIS74 4.1 21.6 1.0
NE2 F:HIS83 4.1 18.1 1.0
NE2 F:HIS92 4.1 17.5 1.0
CD2 F:HIS74 4.2 25.5 1.0
CD2 F:HIS92 4.2 24.1 1.0
CD2 F:HIS83 4.2 19.8 1.0
H F:HIS92 4.3 23.9 1.0
HA F:ASP95 4.3 20.4 1.0
HB3 F:HIS83 4.5 24.4 1.0
HB3 F:ASP95 4.5 19.9 1.0
HD2 F:HIS49 4.5 22.9 1.0
HB2 F:ASP95 4.6 19.9 1.0
H F:LEU84 4.6 23.2 1.0
HA F:LEU143 4.6 23.8 1.0
CD2 F:LEU143 4.6 29.9 1.0
CA F:ASP95 4.6 17.0 1.0
HD21 F:LEU143 4.7 35.9 1.0
CA F:HIS92 4.7 22.4 1.0
CD2 F:HIS49 4.7 19.1 1.0
H F:GLY85 4.7 15.7 1.0
N F:HIS83 4.7 20.9 1.0
O F:LYS82 4.8 18.2 1.0
C F:HIS83 4.8 22.2 1.0
HB3 F:HIS49 4.8 23.1 1.0
HE2 F:HIS74 4.8 25.9 1.0
HE2 F:HIS83 4.9 21.6 1.0
N F:HIS92 4.9 20.0 1.0
N F:ASP95 4.9 14.1 1.0
HE2 F:HIS92 4.9 20.9 1.0
H F:ASP95 4.9 16.9 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: Tue Oct 29 08:58:30 2024

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