Atomistry » Zinc » PDB 8bwu-8ccx » 8ccx
Atomistry »
  Zinc »
    PDB 8bwu-8ccx »
      8ccx »

Zinc 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:

Copper (Cu) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Human SOD1 in Complex with S-XL6 Cross-Linker, PDB code: 8ccx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8ccx

Go back to Zinc Binding Sites List in 8ccx
Zinc binding site 1 out of 4 in the Human SOD1 in Complex with S-XL6 Cross-Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn202

b:17.4
occ:0.30
CU A:CU201 1.1 21.4 0.3
NE2 A:HIS120 1.9 16.7 1.0
O4 A:SO4204 2.0 21.8 0.5
NE2 A:HIS48 2.2 15.1 1.0
ND1 A:HIS46 2.5 19.0 1.0
CE1 A:HIS120 2.6 18.1 1.0
HE1 A:HIS48 2.7 14.0 1.0
CE1 A:HIS48 2.8 14.0 1.0
HE1 A:HIS120 2.8 17.3 1.0
CD2 A:HIS120 3.0 16.3 1.0
O A:HOH380 3.0 22.0 0.5
NE2 A:HIS63 3.2 22.7 1.0
HB2 A:HIS46 3.2 15.7 1.0
S A:SO4204 3.3 24.2 0.5
HD2 A:HIS120 3.3 16.5 1.0
CE1 A:HIS46 3.3 18.7 1.0
CD2 A:HIS48 3.4 13.9 1.0
HE1 A:HIS46 3.4 18.8 1.0
O2 A:SO4204 3.5 23.4 0.5
CG A:HIS46 3.5 17.7 1.0
HD2 A:HIS63 3.6 20.5 1.0
CD2 A:HIS63 3.7 21.0 1.0
ND1 A:HIS120 3.8 16.4 1.0
HD2 A:HIS48 3.8 13.7 1.0
CB A:HIS46 3.8 15.6 1.0
HB A:VAL118 3.9 12.4 1.0
CG A:HIS120 3.9 16.7 1.0
ND1 A:HIS48 4.0 12.9 1.0
HG12 A:VAL118 4.0 12.6 1.0
CE1 A:HIS63 4.1 21.1 1.0
O1 A:SO4204 4.1 27.9 0.5
O3 A:SO4204 4.2 23.5 0.5
HG11 A:VAL118 4.2 12.6 1.0
HB3 A:HIS46 4.2 15.7 1.0
CG A:HIS48 4.3 12.2 1.0
O A:HOH380 4.4 17.4 0.5
HE1 A:HIS63 4.4 20.6 1.0
CG1 A:VAL118 4.5 12.7 1.0
HG2 A:ARG143 4.5 17.1 1.0
NE2 A:HIS46 4.5 19.0 1.0
CB A:VAL118 4.6 12.4 1.0
CD2 A:HIS46 4.6 18.2 1.0
CG A:HIS63 4.8 18.1 1.0
HB3 A:ALA140 4.8 21.0 1.0
HG22 A:VAL118 4.8 12.5 1.0
HE A:ARG143 4.8 17.0 1.0
HH21 A:ARG143 4.9 16.8 1.0
ND1 A:HIS63 5.0 18.1 1.0

Zinc binding site 2 out of 4 in 8ccx

Go back to Zinc Binding Sites List in 8ccx
Zinc binding site 2 out of 4 in the Human SOD1 in Complex with S-XL6 Cross-Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn203

b:16.5
occ:1.00
ND1 A:HIS80 1.8 15.6 1.0
OD1 A:ASP83 1.9 14.7 1.0
ND1 A:HIS63 2.0 18.1 1.0
ND1 A:HIS71 2.2 17.3 1.0
CG A:ASP83 2.6 15.2 1.0
OD2 A:ASP83 2.7 14.6 1.0
CE1 A:HIS80 2.7 15.3 1.0
HE1 A:HIS80 2.9 15.5 1.0
CE1 A:HIS71 2.9 16.2 1.0
CE1 A:HIS63 3.0 21.1 1.0
HB2 A:HIS80 3.0 14.1 1.0
HE1 A:HIS71 3.0 16.9 1.0
CG A:HIS80 3.0 14.1 1.0
CG A:HIS63 3.0 18.1 1.0
HB3 A:HIS63 3.1 17.5 1.0
HE1 A:HIS63 3.1 20.6 1.0
HA A:HIS71 3.2 21.4 1.0
CG A:HIS71 3.3 18.8 1.0
HB2 A:HIS63 3.3 17.5 1.0
CB A:HIS63 3.4 17.5 1.0
CB A:HIS80 3.5 13.9 1.0
HB2 A:HIS71 3.5 20.9 1.0
CB A:HIS71 3.8 21.7 1.0
H A:HIS80 3.9 14.5 1.0
NE2 A:HIS80 3.9 15.8 1.0
CA A:HIS71 4.0 21.4 1.0
HB3 A:HIS80 4.0 14.1 1.0
O A:LYS136 4.0 26.9 1.0
CD2 A:HIS80 4.0 16.7 1.0
H A:GLY72 4.1 19.9 1.0
CB A:ASP83 4.1 14.6 1.0
NE2 A:HIS63 4.1 22.7 1.0
CD2 A:HIS63 4.1 21.0 1.0
NE2 A:HIS71 4.1 17.8 1.0
HA A:ASP83 4.3 14.1 1.0
CD2 A:HIS71 4.3 18.4 1.0
HB3 A:ASP83 4.5 14.5 1.0
HA A:THR137 4.5 26.7 1.0
N A:HIS80 4.7 14.4 1.0
HB2 A:ASP83 4.7 14.5 1.0
CA A:ASP83 4.7 13.8 1.0
N A:GLY72 4.7 19.8 1.0
HB3 A:HIS71 4.7 20.9 1.0
CA A:HIS80 4.7 14.5 1.0
CA A:HIS63 4.9 17.0 1.0
C A:HIS71 4.9 21.5 1.0
HD2 A:HIS80 4.9 15.8 1.0
N A:ASP83 4.9 14.3 1.0
N A:HIS71 5.0 21.1 1.0
C A:LYS136 5.0 29.0 1.0
O A:GLY72 5.0 18.5 1.0
HD2 A:HIS63 5.0 20.5 1.0

Zinc binding site 3 out of 4 in 8ccx

Go back to Zinc Binding Sites List in 8ccx
Zinc binding site 3 out of 4 in the Human SOD1 in Complex with S-XL6 Cross-Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SOD1 in Complex with S-XL6 Cross-Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:21.0
occ:0.25
CU F:CU201 1.1 23.3 0.5
NE2 F:HIS120 1.7 15.6 1.0
NE2 F:HIS48 2.2 13.6 1.0
CE1 F:HIS120 2.2 17.4 1.0
HE1 F:HIS120 2.3 16.6 1.0
HE1 F:HIS48 2.5 13.3 1.0
CE1 F:HIS48 2.7 13.6 1.0
O F:HOH349 2.9 15.6 0.6
CD2 F:HIS120 2.9 15.8 1.0
ND1 F:HIS46 2.9 19.9 1.0
NE2 F:HIS63 3.0 19.4 1.0
O F:HOH413 3.1 25.6 1.0
HD2 F:HIS120 3.4 15.5 1.0
ND1 F:HIS120 3.4 16.0 1.0
CD2 F:HIS48 3.5 13.3 1.0
HD2 F:HIS63 3.5 18.5 1.0
HB2 F:HIS46 3.6 15.2 1.0
CD2 F:HIS63 3.6 18.9 1.0
HE1 F:HIS46 3.7 18.7 1.0
CE1 F:HIS46 3.7 18.2 1.0
CG F:HIS120 3.7 14.5 1.0
HG12 F:VAL118 3.9 11.9 1.0
HD2 F:HIS48 3.9 13.0 1.0
CG F:HIS46 3.9 16.8 1.0
HB F:VAL118 3.9 11.6 1.0
ND1 F:HIS48 4.0 12.5 1.0
O F:HOH343 4.1 22.2 1.0
CE1 F:HIS63 4.1 19.1 1.0
HG2 F:ARG143 4.2 13.8 1.0
CB F:HIS46 4.2 15.8 1.0
HG11 F:VAL118 4.2 11.9 1.0
CG F:HIS48 4.4 11.7 1.0
HE1 F:HIS63 4.4 19.0 1.0
CG1 F:VAL118 4.4 12.0 1.0
HE F:ARG143 4.5 14.2 1.0
O F:HOH415 4.6 27.7 1.0
HB3 F:ALA140 4.6 20.7 1.0
CB F:VAL118 4.6 11.8 1.0
HG22 F:VAL118 4.6 11.5 1.0
HB3 F:HIS46 4.7 15.2 1.0
HH21 F:ARG143 4.7 14.2 1.0
NE F:ARG143 4.7 14.5 1.0
CG F:HIS63 4.9 17.0 1.0
O F:HOH390 4.9 32.4 1.0
NE2 F:HIS46 4.9 19.0 1.0
NH2 F:ARG143 5.0 14.3 1.0
HB F:THR137 5.0 23.6 1.0

Zinc binding site 4 out of 4 in 8ccx

Go back to Zinc Binding Sites List in 8ccx
Zinc binding site 4 out of 4 in the Human SOD1 in Complex with S-XL6 Cross-Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SOD1 in Complex with S-XL6 Cross-Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn203

b:14.8
occ:1.00
OD1 F:ASP83 1.9 13.6 1.0
ND1 F:HIS80 2.0 14.0 1.0
ND1 F:HIS71 2.0 15.0 1.0
ND1 F:HIS63 2.1 18.6 1.0
CG F:ASP83 2.8 14.3 1.0
CE1 F:HIS71 2.9 16.3 1.0
OD2 F:ASP83 2.9 14.1 1.0
HB2 F:HIS80 2.9 13.6 1.0
HE1 F:HIS71 2.9 15.9 1.0
CE1 F:HIS80 3.0 16.5 1.0
CG F:HIS63 3.1 17.0 1.0
CG F:HIS80 3.1 14.4 1.0
CE1 F:HIS63 3.1 19.1 1.0
HE1 F:HIS80 3.2 15.7 1.0
CG F:HIS71 3.2 17.7 1.0
HB3 F:HIS63 3.2 15.1 1.0
HA F:HIS71 3.2 17.8 1.0
HE1 F:HIS63 3.3 19.0 1.0
HB2 F:HIS63 3.3 15.1 1.0
HB2 F:HIS71 3.3 18.1 1.0
CB F:HIS63 3.4 15.2 1.0
CB F:HIS80 3.5 13.2 1.0
CB F:HIS71 3.6 18.4 1.0
CA F:HIS71 3.9 18.0 1.0
O F:LYS136 3.9 25.1 1.0
H F:HIS80 4.0 14.1 1.0
HB3 F:HIS80 4.0 13.6 1.0
NE2 F:HIS71 4.1 15.5 1.0
NE2 F:HIS80 4.1 16.1 1.0
CD2 F:HIS80 4.2 14.6 1.0
CB F:ASP83 4.2 15.8 1.0
NE2 F:HIS63 4.2 19.4 1.0
H F:GLY72 4.2 17.0 1.0
CD2 F:HIS63 4.2 18.9 1.0
CD2 F:HIS71 4.2 17.7 1.0
HA F:ASP83 4.3 14.1 1.0
HA F:THR137 4.5 22.4 1.0
HB3 F:HIS71 4.5 18.1 1.0
HB3 F:ASP83 4.6 14.9 1.0
CA F:ASP83 4.7 13.3 1.0
N F:HIS80 4.7 13.8 1.0
CA F:HIS80 4.7 13.6 1.0
HB2 F:ASP83 4.8 14.8 1.0
N F:GLY72 4.8 16.7 1.0
N F:HIS71 4.8 17.8 1.0
C F:LYS136 4.9 23.5 1.0
N F:ASP83 4.9 13.2 1.0
C F:HIS71 4.9 16.9 1.0
CA F:HIS63 4.9 13.3 1.0
HD2 F:HIS46 5.0 18.3 1.0
O F:HOH384 5.0 27.0 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: Thu Dec 28 12:54:09 2023

Last articles

Ca in 5Z06
Ca in 5YZ3
Ca in 5YZ4
Ca in 5YPS
Ca in 5YVK
Ca in 5YT7
Ca in 5YUC
Ca in 5YSH
Ca in 5YUB
Ca in 5YRV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy