Zinc in PDB 2xjl: Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands

All present enzymatic activity of Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands:
1.15.1.1;

The structure of Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands, PDB code: 2xjl was solved by K.Saraboji, L.Leinartaite, A.Nordlund, M.Oliveberg, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.760, 49.220, 80.460, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.3

The structure of Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands (pdb code 2xjl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands, PDB code: 2xjl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn155 b:9.4 occ:1.00 OD1 A:ASP83 1.9 7.9 1.0 ND1 A:HIS63 2.0 8.7 1.0 ND1 A:HIS71 2.0 8.4 1.0 ND1 A:HIS80 2.0 8.3 1.0 CG A:ASP83 2.7 8.4 1.0 CE1 A:HIS71 2.9 8.8 1.0 CE1 A:HIS80 2.9 9.9 1.0 OD2 A:ASP83 2.9 8.2 1.0 CE1 A:HIS63 3.0 10.1 1.0 CG A:HIS63 3.1 9.5 1.0 CG A:HIS80 3.1 8.9 1.0 CG A:HIS71 3.1 9.5 1.0 CB A:HIS63 3.4 10.1 1.0 CB A:HIS80 3.5 9.3 1.0 CB A:HIS71 3.6 10.2 1.0 O A:LYS136 3.8 11.9 1.0 CA A:HIS71 4.0 10.0 1.0 NE2 A:HIS80 4.0 11.1 1.0 NE2 A:HIS71 4.1 9.4 1.0 NE2 A:HIS63 4.1 10.4 1.0 CD2 A:HIS80 4.1 9.6 1.0 CB A:ASP83 4.2 9.7 1.0 CD2 A:HIS63 4.2 9.9 1.0 CD2 A:HIS71 4.2 9.4 1.0 CA A:ASP83 4.7 9.7 1.0 N A:HIS80 4.7 10.8 1.0 CA A:HIS80 4.7 10.0 1.0 N A:GLY72 4.8 9.6 1.0 C A:LYS136 4.8 11.8 1.0 O A:HOH2131 4.8 17.9 1.0 N A:ASP83 4.9 9.4 1.0 C A:HIS71 4.9 10.4 1.0 N A:HIS71 4.9 11.2 1.0 CA A:HIS63 4.9 10.3 1.0

Zinc binding site 2 out of 4 in the Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn156 b:12.5 occ:1.00 OE2 A:GLU51 2.0 12.6 1.0 O A:HOH2143 2.1 12.5 1.0 CD A:GLU51 3.0 12.4 1.0 CG A:GLU51 3.4 12.3 1.0 OD1 A:ASP52 3.9 16.1 0.5 OD1 A:ASP52 4.0 15.0 0.5 OE1 A:GLU51 4.1 14.1 1.0 OD2 A:ASP52 4.7 15.5 0.5 CG A:ASP52 4.8 16.5 0.5 CG A:ASP52 4.8 17.2 0.5 OD2 A:ASP52 4.8 16.7 0.5 CB A:GLU51 4.9 11.8 1.0

Zinc binding site 3 out of 4 in the Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn157 b:17.5 occ:1.00 OD2 A:ASP52 1.9 16.7 0.5 OE2 A:GLU50 1.9 16.5 1.0 OD2 A:ASP52 2.0 15.5 0.5 CD A:GLU50 2.7 15.5 1.0 OE1 A:GLU50 2.8 19.3 1.0 CG A:ASP52 2.9 17.2 0.5 CG A:ASP52 3.0 16.5 0.5 CB A:ASP52 3.3 17.5 0.5 CB A:ASP52 3.3 18.0 0.5 OD1 A:ASP52 4.0 16.1 0.5 N A:ASP52 4.1 15.3 0.5 N A:ASP52 4.1 15.5 0.5 OD1 A:ASP52 4.1 15.0 0.5 CG A:GLU50 4.1 13.7 1.0 CA A:ASP52 4.3 17.4 0.5 CA A:ASP52 4.3 17.8 0.5 O A:HOH2143 4.5 12.5 1.0 N A:GLU51 4.6 10.8 1.0 N A:ASN53 4.6 22.3 0.5 CA A:GLU50 4.8 10.9 1.0 O A:HOH2059 4.9 35.4 1.0 CB A:GLU50 5.0 11.1 1.0

Zinc binding site 4 out of 4 in the Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Monomeric Human Cu,Zn Superoxide Dismutase Without Cu Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn158 b:27.8 occ:0.70 NE2 A:HIS110 2.0 20.6 1.0 O A:HOH2144 2.2 43.9 1.0 CE1 A:HIS110 2.9 21.8 1.0 CD2 A:HIS110 3.0 19.2 1.0 ND1 A:HIS110 4.0 21.6 1.0 CG A:HIS110 4.1 17.9 1.0 CB A:PRO66 4.7 14.5 1.0 O A:PRO66 4.7 17.9 1.0 O A:HOH2112 4.8 67.1 1.0 CB A:ASP109 4.9 16.4 1.0

L.Leinartaite, K.Saraboji, A.Nordlund, D.T.Logan, M.Oliveberg. Folding Catalysis By Transient Coordination of ZN2+ to the Cu Ligands of the Als-Associated Enzyme Cu/Zn Superoxide Dismutase 1. J.Am.Chem.Soc. V. 132 13495 2010.
ISSN: ISSN 0002-7863
PubMed: 20822138
DOI: 10.1021/JA1057136