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Copper in PDB 8ccx: Human SOD1 in Complex with S-XL6 Cross-Linker

Enzymatic activity of Human SOD1 in Complex with S-XL6 Cross-Linker

All present enzymatic activity of Human SOD1 in Complex with S-XL6 Cross-Linker:
1.15.1.1;

Protein crystallography data

The structure of Human SOD1 in Complex with S-XL6 Cross-Linker, PDB code: 8ccx was solved by S.V.Antonyuk, A.Hossain, J.N.Agar, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.36 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.81, 68.02, 50.69, 90, 105.85, 90
R / Rfree (%) 18.4 / 23.3

Other elements in 8ccx:

The structure of Human SOD1 in Complex with S-XL6 Cross-Linker also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Human SOD1 in Complex with S-XL6 Cross-Linker (pdb code 8ccx). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Human SOD1 in Complex with S-XL6 Cross-Linker, PDB code: 8ccx:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 8ccx

Go back to Copper Binding Sites List in 8ccx
Copper binding site 1 out of 2 in the Human SOD1 in Complex with S-XL6 Cross-Linker


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Human SOD1 in Complex with S-XL6 Cross-Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:21.4
occ:0.35
ZN A:ZN202 1.1 17.4 0.3
ND1 A:HIS46 1.9 19.0 1.0
NE2 A:HIS48 2.1 15.1 1.0
HB2 A:HIS46 2.2 15.7 1.0
NE2 A:HIS120 2.2 16.7 1.0
CG A:HIS46 2.7 17.7 1.0
CB A:HIS46 2.8 15.6 1.0
CD2 A:HIS120 3.0 16.3 1.0
HD2 A:HIS120 3.0 16.5 1.0
CD2 A:HIS48 3.0 13.9 1.0
O4 A:SO4204 3.1 21.8 0.5
CE1 A:HIS46 3.1 18.7 1.0
CE1 A:HIS48 3.1 14.0 1.0
HD2 A:HIS48 3.2 13.7 1.0
HB A:VAL118 3.3 12.4 1.0
CE1 A:HIS120 3.3 18.1 1.0
HE1 A:HIS48 3.4 14.0 1.0
HB3 A:HIS46 3.4 15.7 1.0
HE1 A:HIS46 3.4 18.8 1.0
NE2 A:HIS63 3.5 22.7 1.0
HE1 A:HIS120 3.7 17.3 1.0
O A:HOH380 3.7 22.0 0.5
CD2 A:HIS63 3.9 21.0 1.0
HD2 A:HIS63 3.9 20.5 1.0
CD2 A:HIS46 3.9 18.2 1.0
HG11 A:VAL118 4.0 12.6 1.0
H A:HIS46 4.0 13.9 1.0
CA A:HIS46 4.0 14.1 1.0
HG12 A:VAL118 4.1 12.6 1.0
NE2 A:HIS46 4.1 19.0 1.0
CB A:VAL118 4.1 12.4 1.0
CG A:HIS120 4.2 16.7 1.0
CG A:HIS48 4.2 12.2 1.0
ND1 A:HIS48 4.2 12.9 1.0
N A:HIS46 4.2 13.9 1.0
CE1 A:HIS63 4.3 21.1 1.0
CG1 A:VAL118 4.3 12.7 1.0
ND1 A:HIS120 4.3 16.4 1.0
S A:SO4204 4.3 24.2 0.5
O2 A:SO4204 4.5 23.4 0.5
O A:HIS46 4.5 11.8 1.0
HE1 A:HIS63 4.6 20.6 1.0
HG22 A:VAL118 4.6 12.5 1.0
C A:HIS46 4.6 12.7 1.0
O A:VAL118 4.6 12.6 1.0
HD2 A:HIS46 4.8 18.2 1.0
CG A:HIS63 4.8 18.1 1.0
HA A:HIS46 4.8 14.0 1.0
CG2 A:VAL118 4.9 12.6 1.0
ND1 A:HIS63 4.9 18.1 1.0
HG2 A:ARG143 5.0 17.1 1.0

Copper binding site 2 out of 2 in 8ccx

Go back to Copper Binding Sites List in 8ccx
Copper binding site 2 out of 2 in the Human SOD1 in Complex with S-XL6 Cross-Linker


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Human SOD1 in Complex with S-XL6 Cross-Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu201

b:23.3
occ:0.50
ZN F:ZN202 1.1 21.0 0.2
NE2 F:HIS120 2.0 15.6 1.0
ND1 F:HIS46 2.1 19.9 1.0
NE2 F:HIS48 2.1 13.6 1.0
HB2 F:HIS46 2.5 15.2 1.0
CD2 F:HIS120 2.9 15.8 1.0
CG F:HIS46 2.9 16.8 1.0
NE2 F:HIS63 2.9 19.4 1.0
CE1 F:HIS48 3.0 13.6 1.0
CE1 F:HIS120 3.0 17.4 1.0
HD2 F:HIS120 3.0 15.5 1.0
CD2 F:HIS48 3.1 13.3 1.0
CB F:HIS46 3.1 15.8 1.0
CE1 F:HIS46 3.1 18.2 1.0
HE1 F:HIS48 3.2 13.3 1.0
HE1 F:HIS120 3.3 16.6 1.0
HD2 F:HIS48 3.3 13.0 1.0
O F:HOH349 3.4 15.6 0.6
HE1 F:HIS46 3.4 18.7 1.0
HD2 F:HIS63 3.4 18.5 1.0
HB F:VAL118 3.5 11.6 1.0
CD2 F:HIS63 3.5 18.9 1.0
HB3 F:HIS46 3.6 15.2 1.0
CE1 F:HIS63 3.9 19.1 1.0
CG F:HIS120 4.0 14.5 1.0
ND1 F:HIS120 4.0 16.0 1.0
CD2 F:HIS46 4.1 18.8 1.0
ND1 F:HIS48 4.1 12.5 1.0
HG12 F:VAL118 4.1 11.9 1.0
O F:HOH413 4.1 25.6 1.0
HG11 F:VAL118 4.2 11.9 1.0
CG F:HIS48 4.2 11.7 1.0
HE1 F:HIS63 4.2 19.0 1.0
NE2 F:HIS46 4.2 19.0 1.0
H F:HIS46 4.2 13.5 1.0
CB F:VAL118 4.3 11.8 1.0
CA F:HIS46 4.3 12.5 1.0
CG1 F:VAL118 4.4 12.0 1.0
N F:HIS46 4.5 13.8 1.0
CG F:HIS63 4.6 17.0 1.0
HG22 F:VAL118 4.6 11.5 1.0
ND1 F:HIS63 4.7 18.6 1.0
O F:HIS46 4.8 10.1 1.0
O F:VAL118 4.8 11.6 1.0
C F:HIS46 4.9 11.0 1.0
HG2 F:ARG143 4.9 13.8 1.0
HD2 F:HIS46 4.9 18.3 1.0
CG2 F:VAL118 4.9 11.4 1.0
HB3 F:ALA140 5.0 20.7 1.0

Reference:

A.Hossain, R.Sarin, D.P.Donnellya, B.C.Miller, J.P.Salisbury, J.Amin, J.B.Conway, S.S.Watson, X.Xu, R.R.Brahme, N.Alam, H.Shahbazian, D.Sivasankar, S.Padmakumar, A.Sattarovad, A.C.Ponmudiyana, T.Gawde, W.Yang, S.Kannapadi, L.D.Plant, J.R.Auclair, L.Makowski, G.A.Petsko, D.Ringe, D.J.Greenblatti, M.J.Ondrechen, Y.Chen, R.Manetsch, S.S.Antonyuk, S.S.Hasnain, J.N.Agar. Protein Crosslinking As A Therapeutic Strategy For SOD1-Related Als To Be Published.
Page generated: Wed Jul 31 09:35:33 2024

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