Atomistry » Copper » PDB 6ri4-6vow » 6vbs
Atomistry »
  Copper »
    PDB 6ri4-6vow »
      6vbs »

Copper 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:

Zinc (Zn) 6 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 6 binding sites of Copper 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 Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6vbs

Go back to Copper Binding Sites List in 6vbs
Copper 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 Copper with other atoms in the Cu 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:Cu201

b:35.2
occ:1.00
NE2 A:HIS130 1.9 19.6 1.0
ND1 A:HIS49 2.1 18.0 1.0
NE2 A:HIS51 2.1 15.1 1.0
HE2 A:HIS74 2.6 24.5 1.0
HB2 A:HIS49 2.7 19.8 1.0
CD2 A:HIS130 2.9 18.3 1.0
CE1 A:HIS130 2.9 20.1 1.0
CE1 A:HIS51 3.0 19.7 1.0
CG A:HIS49 3.0 18.6 1.0
NE2 A:HIS74 3.1 20.5 1.0
HD2 A:HIS130 3.1 21.9 1.0
HB3 A:MET128 3.1 18.4 1.0
CE1 A:HIS49 3.1 17.7 1.0
HE1 A:HIS51 3.1 23.7 1.0
CD2 A:HIS51 3.1 17.9 1.0
HE1 A:HIS130 3.2 24.1 1.0
CB A:HIS49 3.3 16.5 1.0
HE1 A:HIS49 3.3 21.2 1.0
HD2 A:HIS51 3.4 21.4 1.0
HD2 A:HIS74 3.4 24.6 1.0
HG2 A:MET128 3.4 21.9 1.0
CD2 A:HIS74 3.5 20.6 1.0
CB A:MET128 3.9 15.4 1.0
HB3 A:HIS49 3.9 19.8 1.0
O A:HOH413 4.0 25.1 1.0
CE1 A:HIS74 4.0 18.4 1.0
ND1 A:HIS130 4.0 17.0 1.0
CG A:HIS130 4.0 18.9 1.0
CG A:MET128 4.0 18.2 1.0
H A:HIS49 4.1 14.5 1.0
ND1 A:HIS51 4.1 12.5 1.0
CD2 A:HIS49 4.1 18.8 1.0
NE2 A:HIS49 4.2 14.8 1.0
HB2 A:MET128 4.2 18.4 1.0
CG A:HIS51 4.2 16.3 1.0
HG3 A:MET128 4.3 21.9 1.0
O A:HOH368 4.3 19.5 1.0
CA A:HIS49 4.3 14.5 1.0
HE1 A:HIS74 4.3 22.0 1.0
N A:HIS49 4.3 12.1 1.0
CG A:HIS74 4.5 16.4 1.0
O A:HIS49 4.8 10.4 1.0
O A:MET128 4.8 9.8 1.0
ND1 A:HIS74 4.8 15.1 1.0
C A:HIS49 4.8 13.0 1.0
HD1 A:HIS130 4.8 20.4 1.0
HG2 A:ARG149 4.9 21.3 1.0
HD1 A:HIS51 4.9 15.0 1.0
HE2 A:HIS49 4.9 17.7 1.0
HD2 A:HIS49 5.0 22.6 1.0

Copper binding site 2 out of 6 in 6vbs

Go back to Copper Binding Sites List in 6vbs
Copper 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 Copper with other atoms in the Cu 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:Cu202

b:40.0
occ:1.00
NE2 B:HIS130 2.0 17.0 1.0
ND1 B:HIS49 2.0 14.6 1.0
NE2 B:HIS51 2.1 16.5 1.0
HB2 B:HIS49 2.6 22.2 1.0
HE2 B:HIS74 2.8 20.2 1.0
CE1 B:HIS51 2.9 19.4 1.0
CE1 B:HIS130 2.9 19.8 1.0
CG B:HIS49 2.9 16.2 1.0
HE1 B:HIS51 3.0 23.3 1.0
CD2 B:HIS130 3.0 17.2 1.0
CE1 B:HIS49 3.0 16.8 1.0
HE1 B:HIS130 3.1 23.7 1.0
HB3 B:MET128 3.1 19.0 1.0
NE2 B:HIS74 3.2 16.9 1.0
CB B:HIS49 3.2 18.5 1.0
HD2 B:HIS130 3.2 20.7 1.0
CD2 B:HIS51 3.2 17.8 1.0
HE1 B:HIS49 3.3 20.1 1.0
HD2 B:HIS74 3.4 22.5 1.0
CD2 B:HIS74 3.5 18.8 1.0
HG2 B:MET128 3.5 22.9 1.0
HD2 B:HIS51 3.5 21.3 1.0
O B:HOH417 3.8 19.4 1.0
HB3 B:HIS49 3.8 22.2 1.0
CB B:MET128 3.9 15.8 1.0
ND1 B:HIS130 4.0 17.5 1.0
CG B:HIS130 4.1 16.3 1.0
ND1 B:HIS51 4.1 13.6 1.0
CD2 B:HIS49 4.1 17.9 1.0
CE1 B:HIS74 4.1 17.1 1.0
NE2 B:HIS49 4.1 14.4 1.0
CG B:MET128 4.1 19.1 1.0
H B:HIS49 4.1 14.0 1.0
O B:HOH408 4.1 16.8 1.0
HB2 B:MET128 4.2 19.0 1.0
CG B:HIS51 4.3 17.4 1.0
CA B:HIS49 4.3 15.4 1.0
N B:HIS49 4.3 11.7 1.0
HG3 B:MET128 4.4 22.9 1.0
HE1 B:HIS74 4.5 20.5 1.0
CG B:HIS74 4.5 16.9 1.0
HD1 B:HIS130 4.8 21.0 1.0
O B:HIS49 4.8 11.4 1.0
C B:HIS49 4.8 13.9 1.0
O B:MET128 4.8 12.5 1.0
HD1 B:HIS51 4.8 16.3 1.0
ND1 B:HIS74 4.8 12.2 1.0
HE2 B:HIS49 4.9 17.2 1.0
HD2 B:HIS49 4.9 21.5 1.0
HG2 B:ARG149 4.9 19.3 1.0

Copper binding site 3 out of 6 in 6vbs

Go back to Copper Binding Sites List in 6vbs
Copper 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 Copper with other atoms in the Cu 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:Cu202

b:39.2
occ:1.00
ND1 C:HIS49 2.2 15.9 1.0
NE2 C:HIS51 2.3 14.6 1.0
HB2 C:HIS49 2.7 20.9 1.0
HB3 C:MET128 2.9 22.9 1.0
HE2 C:HIS74 2.9 18.9 1.0
NE2 C:HIS130 3.1 17.1 1.0
CG C:HIS49 3.1 17.5 1.0
HD2 C:HIS130 3.1 29.7 1.0
CE1 C:HIS51 3.2 18.5 1.0
CE1 C:HIS49 3.2 20.9 1.0
O C:HOH345 3.2 27.2 1.0
HE1 C:HIS51 3.3 22.2 1.0
HG2 C:MET128 3.3 30.4 1.0
NE2 C:HIS74 3.3 15.7 1.0
CB C:HIS49 3.3 17.4 1.0
CD2 C:HIS51 3.3 17.8 1.0
HE1 C:HIS49 3.4 25.1 1.0
CD2 C:HIS130 3.4 24.8 1.0
HD2 C:HIS51 3.5 21.4 1.0
HD2 C:HIS74 3.6 23.0 1.0
CD2 C:HIS74 3.7 19.2 1.0
CB C:MET128 3.7 19.1 1.0
CG C:MET128 3.9 25.3 1.0
H C:HIS49 4.0 14.8 1.0
HB3 C:HIS49 4.0 20.9 1.0
HB2 C:MET128 4.1 22.9 1.0
CE1 C:HIS74 4.2 19.7 1.0
CD2 C:HIS49 4.2 20.4 1.0
NE2 C:HIS49 4.3 16.8 1.0
HG3 C:MET128 4.3 30.4 1.0
N C:HIS49 4.3 12.3 1.0
CA C:HIS49 4.3 13.8 1.0
CE1 C:HIS130 4.3 20.9 1.0
ND1 C:HIS51 4.3 16.0 1.0
CG C:HIS51 4.4 20.1 1.0
HE1 C:HIS74 4.5 23.6 1.0
O C:HIS49 4.6 8.6 1.0
O C:MET128 4.6 8.6 1.0
CG C:HIS74 4.7 18.6 1.0
HE1 C:HIS130 4.7 25.1 1.0
C C:HIS49 4.7 16.4 1.0
CG C:HIS130 4.8 25.3 1.0
HE3 C:MET128 4.8 35.4 1.0
HG2 C:ARG149 4.9 40.7 1.0
C C:MET128 4.9 16.3 1.0
CA C:MET128 4.9 16.3 1.0
ND1 C:HIS74 5.0 12.6 1.0

Copper binding site 4 out of 6 in 6vbs

Go back to Copper Binding Sites List in 6vbs
Copper 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 Copper with other atoms in the Cu 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:Cu202

b:42.1
occ:1.00
ND1 D:HIS49 2.2 16.2 1.0
NE2 D:HIS51 2.3 18.0 1.0
NE2 D:HIS130 2.3 30.5 1.0
HB2 D:HIS49 2.9 19.4 1.0
HD2 D:HIS130 2.9 33.8 1.0
HE2 D:HIS74 3.0 20.6 1.0
CD2 D:HIS130 3.0 28.2 1.0
HB3 D:MET128 3.0 22.8 1.0
O D:HOH302 3.0 24.5 1.0
HG2 D:MET128 3.1 29.7 1.0
CE1 D:HIS51 3.1 20.4 1.0
HE1 D:HIS51 3.1 24.5 1.0
CE1 D:HIS49 3.2 19.4 1.0
CG D:HIS49 3.2 16.6 1.0
HE1 D:HIS49 3.3 23.3 1.0
CD2 D:HIS51 3.4 19.5 1.0
NE2 D:HIS74 3.4 17.2 1.0
CE1 D:HIS130 3.5 24.1 1.0
CB D:HIS49 3.5 16.2 1.0
HD2 D:HIS51 3.7 23.4 1.0
CG D:MET128 3.8 24.7 1.0
CB D:MET128 3.8 19.0 1.0
HD2 D:HIS74 3.8 22.8 1.0
HE1 D:HIS130 3.8 28.9 1.0
CD2 D:HIS74 3.9 19.0 1.0
HG3 D:MET128 4.1 29.7 1.0
H D:HIS49 4.1 11.8 1.0
HB3 D:HIS49 4.2 19.4 1.0
HB2 D:MET128 4.2 22.8 1.0
CG D:HIS130 4.2 25.2 1.0
ND1 D:HIS51 4.3 18.8 1.0
NE2 D:HIS49 4.3 15.5 1.0
CD2 D:HIS49 4.3 20.7 1.0
CE1 D:HIS74 4.4 21.4 1.0
N D:HIS49 4.4 9.8 1.0
CA D:HIS49 4.5 13.8 1.0
ND1 D:HIS130 4.5 29.6 1.0
CG D:HIS51 4.5 19.2 1.0
HG2 D:ARG149 4.6 35.6 1.0
O D:MET128 4.6 8.7 1.0
O4 D:SO4203 4.6 37.0 1.0
HE3 D:MET128 4.6 27.2 1.0
HE1 D:HIS74 4.6 25.6 1.0
O D:HIS49 4.7 10.3 1.0
O D:HOH320 4.7 31.4 1.0
C D:MET128 4.9 16.3 1.0
C D:HIS49 4.9 15.6 1.0
CA D:MET128 4.9 19.1 1.0
CG D:HIS74 4.9 13.0 1.0

Copper binding site 5 out of 6 in 6vbs

Go back to Copper Binding Sites List in 6vbs
Copper 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 Copper with other atoms in the Cu 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:Cu201

b:46.5
occ:1.00
NE2 E:HIS130 1.9 28.8 1.0
NE2 E:HIS51 2.0 18.9 1.0
ND1 E:HIS49 2.2 20.3 1.0
HB2 E:HIS49 2.7 28.3 1.0
CD2 E:HIS130 2.8 25.8 1.0
CE1 E:HIS51 2.9 26.1 1.0
HB3 E:MET128 2.9 25.5 1.0
HD2 E:HIS130 2.9 30.9 1.0
HE2 E:HIS74 2.9 30.7 1.0
HE1 E:HIS51 3.0 31.3 1.0
CE1 E:HIS130 3.0 28.3 1.0
CD2 E:HIS51 3.1 22.4 1.0
CG E:HIS49 3.1 21.1 1.0
CE1 E:HIS49 3.2 25.9 1.0
HG2 E:MET128 3.3 24.4 1.0
NE2 E:HIS74 3.3 25.6 1.0
HE1 E:HIS130 3.3 33.9 1.0
HD2 E:HIS51 3.3 26.8 1.0
HE1 E:HIS49 3.4 31.0 1.0
CB E:HIS49 3.4 23.6 1.0
HD2 E:HIS74 3.5 33.4 1.0
CD2 E:HIS74 3.6 27.9 1.0
CB E:MET128 3.7 21.2 1.0
O E:HOH403 3.9 33.5 1.0
CG E:MET128 3.9 20.3 1.0
CG E:HIS130 4.0 26.4 1.0
HB2 E:MET128 4.0 25.5 1.0
ND1 E:HIS51 4.0 19.2 1.0
H E:HIS49 4.0 19.1 1.0
ND1 E:HIS130 4.1 25.8 1.0
HB3 E:HIS49 4.1 28.3 1.0
CG E:HIS51 4.2 22.0 1.0
HG3 E:MET128 4.2 24.4 1.0
CE1 E:HIS74 4.3 33.3 1.0
NE2 E:HIS49 4.3 19.5 1.0
CD2 E:HIS49 4.3 20.5 1.0
N E:HIS49 4.3 15.9 1.0
CA E:HIS49 4.3 24.0 1.0
O E:HOH317 4.6 28.5 1.0
O E:HIS49 4.6 13.8 1.0
HE1 E:HIS74 4.6 39.9 1.0
O E:MET128 4.7 12.9 1.0
CG E:HIS74 4.7 28.7 1.0
C E:HIS49 4.7 20.0 1.0
HG2 E:ARG149 4.8 24.9 1.0
HD1 E:HIS51 4.8 23.0 1.0
HE3 E:MET128 4.8 34.1 1.0
HD1 E:HIS130 4.9 30.9 1.0
CA E:MET128 4.9 18.6 1.0
C E:MET128 5.0 17.3 1.0
ND1 E:HIS74 5.0 24.1 1.0

Copper binding site 6 out of 6 in 6vbs

Go back to Copper Binding Sites List in 6vbs
Copper 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 Copper with other atoms in the Cu 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:Cu202

b:44.2
occ:1.00
NE2 F:HIS130 1.8 26.4 1.0
ND1 F:HIS49 2.1 18.3 1.0
NE2 F:HIS51 2.1 20.7 1.0
HB2 F:HIS49 2.6 23.1 1.0
HE2 F:HIS74 2.7 25.9 1.0
CE1 F:HIS130 2.8 30.1 1.0
CD2 F:HIS130 2.9 26.0 1.0
HE1 F:HIS130 2.9 36.0 1.0
CE1 F:HIS51 2.9 31.6 1.0
CG F:HIS49 2.9 19.3 1.0
HE1 F:HIS51 3.0 37.9 1.0
CE1 F:HIS49 3.1 23.2 1.0
NE2 F:HIS74 3.1 21.6 1.0
HD2 F:HIS130 3.2 31.2 1.0
HB3 F:MET128 3.2 31.5 1.0
CB F:HIS49 3.2 19.2 1.0
CD2 F:HIS51 3.2 25.1 1.0
HE1 F:HIS49 3.3 27.8 1.0
HD2 F:HIS74 3.4 30.5 1.0
CD2 F:HIS74 3.5 25.5 1.0
HD2 F:HIS51 3.5 30.1 1.0
HG2 F:MET128 3.5 29.7 1.0
HB3 F:HIS49 3.8 23.1 1.0
ND1 F:HIS130 3.9 19.4 1.0
CG F:HIS130 4.0 19.2 1.0
CB F:MET128 4.0 26.3 1.0
CE1 F:HIS74 4.0 23.3 1.0
O F:HOH370 4.1 26.6 1.0
CD2 F:HIS49 4.1 19.1 1.0
ND1 F:HIS51 4.1 21.5 1.0
NE2 F:HIS49 4.1 15.2 1.0
O F:HOH391 4.1 27.2 1.0
CG F:MET128 4.2 24.7 1.0
H F:HIS49 4.2 17.0 1.0
CG F:HIS51 4.3 18.7 1.0
CA F:HIS49 4.3 17.8 1.0
HB2 F:MET128 4.3 31.5 1.0
HE1 F:HIS74 4.4 28.0 1.0
N F:HIS49 4.4 14.2 1.0
CG F:HIS74 4.5 20.1 1.0
HG3 F:MET128 4.5 29.7 1.0
HD1 F:HIS130 4.6 23.3 1.0
O F:HIS49 4.8 13.8 1.0
ND1 F:HIS74 4.8 16.8 1.0
C F:HIS49 4.8 15.6 1.0
HD1 F:HIS51 4.9 25.8 1.0
HG2 F:ARG149 4.9 34.3 1.0
HD2 F:HIS49 4.9 22.9 1.0
HE2 F:HIS49 4.9 18.2 1.0
O F:MET128 4.9 13.1 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 15:06:01 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy