Atomistry » Copper » PDB 1rju-1tl4 » 1srd
Atomistry »
  Copper »
    PDB 1rju-1tl4 »
      1srd »

Copper in PDB 1srd: Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution

Enzymatic activity of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution

All present enzymatic activity of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution:
1.15.1.1;

Protein crystallography data

The structure of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution, PDB code: 1srd was solved by Y.Kitagawa, Y.Katsube, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.270, 45.970, 85.680, 90.00, 99.38, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1srd:

The structure of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution (pdb code 1srd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution, PDB code: 1srd:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1srd

Go back to Copper Binding Sites List in 1srd
Copper binding site 1 out of 4 in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu155

b:13.0
occ:1.00
 ND1 A:HIS46 2.0 9.3 1.0
NE2 A:HIS48 2.1 10.0 1.0
NE2 A:HIS120 2.1 9.8 1.0
NE2 A:HIS63 2.1 9.0 1.0
CE1 A:HIS120 2.3 9.8 1.0
CE1 A:HIS48 2.8 9.6 1.0
CD2 A:HIS63 2.8 8.4 1.0
CG A:HIS46 3.0 8.9 1.0
CE1 A:HIS46 3.0 8.9 1.0
CE1 A:HIS63 3.2 8.7 1.0
CD2 A:HIS48 3.2 9.4 1.0
CD2 A:HIS120 3.3 9.5 1.0
CB A:HIS46 3.3 8.6 1.0
ND1 A:HIS120 3.4 9.7 1.0
NE2 A:HIS46 4.0 9.0 1.0
ND1 A:HIS48 4.0 9.3 1.0
CG A:HIS120 4.0 9.4 1.0
CG A:HIS63 4.0 8.2 1.0
CD2 A:HIS46 4.1 8.9 1.0
CG A:HIS48 4.2 9.3 1.0
ND1 A:HIS63 4.2 8.4 1.0
CA A:HIS46 4.6 8.4 1.0
N A:HIS46 4.7 8.4 1.0
CG2 A:THR137 4.8 10.1 1.0

Copper binding site 2 out of 4 in 1srd

Go back to Copper Binding Sites List in 1srd
Copper binding site 2 out of 4 in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu155

b:13.1
occ:1.00
 NE2 B:HIS63 2.0 9.0 1.0
NE2 B:HIS120 2.1 9.8 1.0
ND1 B:HIS46 2.1 9.3 1.0
NE2 B:HIS48 2.1 10.0 1.0
CE1 B:HIS120 2.1 9.8 1.0
CD2 B:HIS63 2.7 8.4 1.0
CE1 B:HIS48 2.9 9.6 1.0
CG B:HIS46 3.0 8.9 1.0
CE1 B:HIS46 3.1 9.1 1.0
CE1 B:HIS63 3.2 8.7 1.0
CD2 B:HIS48 3.3 9.4 1.0
ND1 B:HIS120 3.3 9.8 1.0
CB B:HIS46 3.3 8.6 1.0
CD2 B:HIS120 3.3 9.5 1.0
CG B:HIS120 3.9 9.4 1.0
CG B:HIS63 3.9 8.2 1.0
ND1 B:HIS48 4.1 9.4 1.0
CD2 B:HIS46 4.1 8.9 1.0
NE2 B:HIS46 4.1 9.0 1.0
ND1 B:HIS63 4.2 8.4 1.0
CG B:HIS48 4.3 9.3 1.0
CA B:HIS46 4.5 8.4 1.0
CG2 B:THR137 4.5 10.1 1.0
N B:HIS46 4.7 8.4 1.0
O B:VAL118 4.8 7.7 1.0
O B:HOH178 4.8 19.0 1.0
CG1 B:VAL118 4.9 7.5 1.0
CB B:VAL118 5.0 7.3 1.0

Copper binding site 3 out of 4 in 1srd

Go back to Copper Binding Sites List in 1srd
Copper binding site 3 out of 4 in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu155

b:13.5
occ:1.00
 NE2 C:HIS63 2.0 9.1 1.0
NE2 C:HIS120 2.1 9.8 1.0
NE2 C:HIS48 2.2 10.0 1.0
ND1 C:HIS46 2.3 9.2 1.0
CE1 C:HIS120 2.3 9.8 1.0
CD2 C:HIS63 2.9 8.4 1.0
CE1 C:HIS48 2.9 9.6 1.0
CG C:HIS46 3.1 8.8 1.0
CE1 C:HIS63 3.1 8.7 1.0
CD2 C:HIS120 3.2 9.6 1.0
CE1 C:HIS46 3.2 9.0 1.0
CB C:HIS46 3.3 8.6 1.0
CD2 C:HIS48 3.4 9.4 1.0
ND1 C:HIS120 3.4 9.7 1.0
CG C:HIS120 3.9 9.4 1.0
CG C:HIS63 4.0 8.2 1.0
ND1 C:HIS48 4.1 9.4 1.0
CD2 C:HIS46 4.2 8.9 1.0
ND1 C:HIS63 4.2 8.4 1.0
CG2 C:THR137 4.2 10.2 1.0
NE2 C:HIS46 4.2 8.9 1.0
CG C:HIS48 4.3 9.3 1.0
CA C:HIS46 4.8 8.4 1.0
O C:HOH175 4.8 19.0 1.0
O C:THR137 4.9 9.5 1.0

Copper binding site 4 out of 4 in 1srd

Go back to Copper Binding Sites List in 1srd
Copper binding site 4 out of 4 in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu155

b:13.4
occ:1.00
 NE2 D:HIS120 2.0 9.8 1.0
NE2 D:HIS48 2.0 9.9 1.0
ND1 D:HIS46 2.0 9.3 1.0
NE2 D:HIS63 2.1 9.1 1.0
CE1 D:HIS120 2.5 9.9 1.0
CE1 D:HIS48 2.8 9.6 1.0
CG D:HIS46 2.8 8.8 1.0
CD2 D:HIS63 2.9 8.4 1.0
CD2 D:HIS120 3.0 9.6 1.0
CB D:HIS46 3.1 8.6 1.0
CE1 D:HIS63 3.1 8.7 1.0
CD2 D:HIS48 3.1 9.4 1.0
CE1 D:HIS46 3.1 9.0 1.0
ND1 D:HIS120 3.6 9.7 1.0
ND1 D:HIS48 3.9 9.4 1.0
CG D:HIS120 4.0 9.4 1.0
CD2 D:HIS46 4.0 8.9 1.0
CG D:HIS63 4.0 8.2 1.0
NE2 D:HIS46 4.1 9.0 1.0
ND1 D:HIS63 4.1 8.3 1.0
CG D:HIS48 4.1 9.3 1.0
CA D:HIS46 4.4 8.3 1.0
N D:HIS46 4.5 8.5 1.0
CB D:VAL118 5.0 7.3 1.0

Reference:

Y.Kitagawa, N.Tanaka, Y.Hata, M.Kusunoki, G.P.Lee, Y.Katsube, K.Asada, S.Aibara, Y.Morita. Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 A Resolution. J.Biochem.(Tokyo) V. 109 477 1991.
ISSN: ISSN 0021-924X
PubMed: 1880134
Page generated: Tue Jul 30 22:47:36 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy