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Copper in PDB 7fb9: Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)

Enzymatic activity of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)

All present enzymatic activity of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1):
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1), PDB code: 7fb9 was solved by Y.Baek, N.-C.Ha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.52 / 2.70
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 112.43, 112.43, 209.28, 90, 90, 120
R / Rfree (%) 23 / 24.7

Other elements in 7fb9:

The structure of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) also contains other interesting chemical elements:

Zinc (Zn) 14 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) (pdb code 7fb9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1), PDB code: 7fb9:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7fb9

Go back to Copper Binding Sites List in 7fb9
Copper binding site 1 out of 6 in the Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:77.5
occ:1.00
 NE2 A:HIS63 2.2 43.1 1.0
ND1 A:HIS46 2.2 38.3 1.0
NE2 A:HIS120 2.3 39.9 1.0
NE2 A:HIS48 2.7 35.7 1.0
CE1 A:HIS120 2.9 38.3 1.0
CD2 A:HIS63 3.0 42.5 1.0
CE1 A:HIS63 3.1 39.6 1.0
CE1 A:HIS46 3.1 42.2 1.0
CG A:HIS46 3.2 35.6 1.0
CD2 A:HIS120 3.2 36.4 1.0
CB A:HIS46 3.5 37.8 1.0
CE1 A:HIS48 3.5 40.4 1.0
CD2 A:HIS48 3.7 38.6 1.0
ND1 A:HIS120 3.9 34.1 1.0
CG A:HIS63 4.0 39.5 1.0
ND1 A:HIS63 4.1 40.1 1.0
CG A:HIS120 4.1 34.0 1.0
NE2 A:HIS46 4.2 46.4 1.0
CD2 A:HIS46 4.3 41.6 1.0
ND1 A:HIS48 4.6 42.1 1.0
CA A:HIS46 4.7 37.2 1.0
CG A:HIS48 4.8 39.8 1.0
N A:HIS46 4.9 40.5 1.0
CB A:ALA140 4.9 41.8 1.0
O A:THR137 4.9 40.2 1.0

Copper binding site 2 out of 6 in 7fb9

Go back to Copper Binding Sites List in 7fb9
Copper binding site 2 out of 6 in the Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu202

b:68.7
occ:1.00
 ND1 D:HIS46 2.3 37.2 1.0
NE2 D:HIS120 2.4 36.5 1.0
CB D:HIS46 2.5 40.2 1.0
CG D:HIS46 2.7 37.1 1.0
NE2 D:HIS48 2.7 38.9 1.0
NE2 D:HIS63 2.9 37.2 1.0
CD2 D:HIS120 3.3 35.1 1.0
CE1 D:HIS120 3.3 40.9 1.0
CD2 D:HIS48 3.4 37.2 1.0
CE1 D:HIS63 3.5 35.6 1.0
CD2 D:HIS63 3.5 36.2 1.0
CA D:HIS46 3.5 43.6 1.0
CE1 D:HIS46 3.6 35.6 1.0
N D:HIS46 3.8 40.8 1.0
CE1 D:HIS48 3.8 44.9 1.0
C D:HIS46 3.9 39.3 1.0
O D:HIS46 3.9 36.8 1.0
CD2 D:HIS46 4.0 37.1 1.0
ND1 D:HIS63 4.2 35.2 1.0
CG D:HIS63 4.3 35.8 1.0
O D:VAL118 4.3 35.5 1.0
ND1 D:HIS120 4.4 42.9 1.0
CG D:HIS120 4.4 35.8 1.0
NE2 D:HIS46 4.4 35.7 1.0
CB D:VAL118 4.5 35.6 1.0
CG D:HIS48 4.6 39.9 1.0
N D:VAL47 4.7 38.6 1.0
ND1 D:HIS48 4.8 44.4 1.0
C D:PHE45 4.9 38.8 1.0
CG1 D:VAL118 4.9 35.4 1.0

Copper binding site 3 out of 6 in 7fb9

Go back to Copper Binding Sites List in 7fb9
Copper binding site 3 out of 6 in the Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu202

b:60.2
occ:1.00
 NE2 H:HIS120 2.2 36.0 1.0
NE2 H:HIS48 2.2 38.5 1.0
ND1 H:HIS46 2.7 36.5 1.0
CD2 H:HIS120 2.9 37.4 1.0
NE2 H:HIS63 3.0 41.8 1.0
CB H:HIS46 3.0 39.0 1.0
CD2 H:HIS48 3.1 34.7 1.0
CG H:HIS46 3.2 39.8 1.0
CE1 H:HIS48 3.3 37.9 1.0
CE1 H:HIS120 3.3 37.5 1.0
CD2 H:HIS63 3.4 38.6 1.0
CE1 H:HIS46 3.8 39.6 1.0
CG1 H:VAL118 4.0 36.2 1.0
CB H:VAL118 4.0 38.1 1.0
CE1 H:HIS63 4.0 41.2 1.0
O H:VAL118 4.1 39.2 1.0
CA H:HIS46 4.1 37.1 1.0
CG H:HIS120 4.2 38.3 1.0
O H:HIS46 4.3 35.6 1.0
CG H:HIS48 4.3 37.1 1.0
ND1 H:HIS120 4.3 38.4 1.0
ND1 H:HIS48 4.3 38.9 1.0
N H:HIS46 4.4 34.4 1.0
CD2 H:HIS46 4.4 41.5 1.0
C H:HIS46 4.5 34.0 1.0
CG H:HIS63 4.5 38.3 1.0
NE2 H:HIS46 4.7 43.1 1.0
C H:VAL118 4.7 37.3 1.0
ND1 H:HIS63 4.8 41.9 1.0
CA H:VAL118 4.9 36.2 1.0

Copper binding site 4 out of 6 in 7fb9

Go back to Copper Binding Sites List in 7fb9
Copper binding site 4 out of 6 in the Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu202

b:91.2
occ:1.00
 NE2 I:HIS120 2.2 48.1 1.0
NE2 I:HIS63 2.2 45.2 1.0
ND1 I:HIS46 2.6 40.5 1.0
CD2 I:HIS63 2.7 42.9 1.0
NE2 I:HIS48 2.8 37.0 1.0
CE1 I:HIS63 3.0 40.8 1.0
CE1 I:HIS120 3.0 51.6 1.0
CB I:HIS46 3.1 42.8 1.0
CD2 I:HIS120 3.1 43.4 1.0
CG I:HIS46 3.1 39.0 1.0
CE1 I:HIS48 3.6 35.9 1.0
CD2 I:HIS48 3.6 38.4 1.0
CG I:HIS63 3.6 40.0 1.0
CE1 I:HIS46 3.7 42.5 1.0
ND1 I:HIS63 3.7 44.1 1.0
ND1 I:HIS120 4.0 44.1 1.0
CG I:HIS120 4.1 41.7 1.0
CA I:HIS46 4.2 37.6 1.0
CD2 I:HIS46 4.4 40.3 1.0
N I:HIS46 4.4 34.9 1.0
C I:HIS46 4.5 37.2 1.0
ND1 I:HIS48 4.6 36.7 1.0
NE2 I:HIS46 4.6 42.9 1.0
CG I:HIS48 4.6 37.2 1.0
O I:HIS46 4.7 37.0 1.0
CG1 I:VAL118 4.8 40.6 1.0
CB I:HIS63 4.9 38.2 1.0
CB I:VAL118 4.9 37.8 1.0
O I:VAL118 4.9 39.6 1.0

Copper binding site 5 out of 6 in 7fb9

Go back to Copper Binding Sites List in 7fb9
Copper binding site 5 out of 6 in the Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu202

b:66.0
occ:1.00
 NE2 J:HIS120 2.1 37.0 1.0
NE2 J:HIS48 2.2 32.0 1.0
NE2 J:HIS63 2.7 42.7 1.0
CE1 J:HIS120 3.0 37.1 1.0
CB J:HIS46 3.0 34.9 1.0
CD2 J:HIS48 3.1 35.8 1.0
CE1 J:HIS48 3.1 29.1 1.0
CD2 J:HIS63 3.2 35.6 1.0
ND1 J:HIS46 3.2 38.1 1.0
CD2 J:HIS120 3.3 36.5 1.0
CG J:HIS46 3.5 33.7 1.0
CB J:VAL118 3.9 34.2 1.0
CE1 J:HIS63 3.9 37.0 1.0
CG1 J:VAL118 3.9 32.1 1.0
CA J:HIS46 4.1 38.8 1.0
O J:VAL118 4.1 33.9 1.0
ND1 J:HIS120 4.2 39.6 1.0
ND1 J:HIS48 4.2 32.1 1.0
CG J:HIS48 4.2 35.0 1.0
O J:HIS46 4.3 36.8 1.0
CG J:HIS120 4.3 39.5 1.0
C J:HIS46 4.3 37.5 1.0
CG J:HIS63 4.4 31.2 1.0
N J:HIS46 4.4 34.0 1.0
CE1 J:HIS46 4.5 39.3 1.0
ND1 J:HIS63 4.7 32.9 1.0
C J:VAL118 4.7 35.0 1.0
CA J:VAL118 4.8 35.1 1.0
CG2 J:VAL118 4.8 36.0 1.0
CD2 J:HIS46 4.8 39.2 1.0

Copper binding site 6 out of 6 in 7fb9

Go back to Copper Binding Sites List in 7fb9
Copper binding site 6 out of 6 in the Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu202

b:55.8
occ:1.00
 NE2 K:HIS120 2.4 38.8 1.0
NE2 K:HIS48 2.4 37.5 1.0
ND1 K:HIS46 2.7 43.6 1.0
NE2 K:HIS63 2.8 41.3 1.0
CD2 K:HIS120 2.9 34.2 1.0
CB K:HIS46 2.9 38.1 1.0
CG K:HIS46 3.1 38.0 1.0
CD2 K:HIS63 3.1 43.0 1.0
CD2 K:HIS48 3.1 35.1 1.0
CE1 K:HIS48 3.5 36.7 1.0
CE1 K:HIS120 3.6 36.3 1.0
CE1 K:HIS63 3.8 39.2 1.0
CE1 K:HIS46 3.8 41.6 1.0
CA K:HIS46 3.9 40.0 1.0
CB K:VAL118 4.1 34.6 1.0
O K:HIS46 4.1 38.2 1.0
N K:HIS46 4.2 37.9 1.0
CG K:HIS63 4.2 40.6 1.0
CG1 K:VAL118 4.2 33.2 1.0
C K:HIS46 4.2 40.8 1.0
CG K:HIS120 4.2 38.0 1.0
CD2 K:HIS46 4.3 40.5 1.0
CG K:HIS48 4.3 31.8 1.0
O K:VAL118 4.5 39.2 1.0
ND1 K:HIS48 4.5 35.9 1.0
ND1 K:HIS63 4.5 41.8 1.0
ND1 K:HIS120 4.5 35.5 1.0
NE2 K:HIS46 4.6 43.5 1.0
CG2 K:VAL118 5.0 35.8 1.0

Reference:

Y.Baek, T.G.Woo, J.Ahn, D.Lee, Y.Kwon, B.J.Park, N.C.Ha. Structural Analysis of the Overoxidized Cu/Zn-Superoxide Dismutase in Ros-Induced Als Filament Formation. Commun Biol V. 5 1085 2022.
ISSN: ESSN 2399-3642
PubMed: 36224351
DOI: 10.1038/S42003-022-04017-0
Page generated: Wed Jul 31 08:32:35 2024

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