Zinc in PDB 8ccx: 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;

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

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

Copper

(Cu)

2 atoms

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 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 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 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 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

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.