Zinc in PDB 3h2p: Human SOD1 D124V Variant

All present enzymatic activity of Human SOD1 D124V Variant:
1.15.1.1;

The structure of Human SOD1 D124V Variant, PDB code: 3h2p was solved by S.V.Seetharaman, D.D.Winkler, A.B.Taylor, X.Cao, L.J.Whitson, P.A.Doucette, J.S.Valentine, M.C.Carroll, V.C.Culotta, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.92 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.919, 57.972, 105.021, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 20.2

The binding sites of Zinc atom in the Human SOD1 D124V Variant (pdb code 3h2p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human SOD1 D124V Variant, PDB code: 3h2p:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human SOD1 D124V Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SOD1 D124V Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn154 b:19.8 occ:0.61 NE2 A:HIS48 2.1 17.8 1.0 NE2 A:HIS120 2.1 19.5 1.0 O8 A:MLI156 2.3 39.2 0.8 ND1 A:HIS46 2.4 27.3 1.0 NE2 A:HIS63 2.5 38.3 0.0 CE1 A:HIS48 2.8 17.6 1.0 CD2 A:HIS63 2.9 37.1 0.0 CE1 A:HIS120 3.0 21.2 1.0 C3 A:MLI156 3.1 40.6 0.8 CD2 A:HIS120 3.1 19.9 1.0 CD2 A:HIS48 3.3 14.7 1.0 CG A:HIS46 3.3 22.8 1.0 O9 A:MLI156 3.3 39.4 0.8 CE1 A:HIS46 3.4 28.0 1.0 CB A:HIS46 3.4 18.1 1.0 CE1 A:HIS63 3.7 38.2 0.0 ND1 A:HIS48 4.0 16.1 1.0 ND1 A:HIS120 4.1 22.7 1.0 CG A:HIS63 4.1 35.0 1.0 CG A:HIS120 4.2 19.6 1.0 CG A:HIS48 4.3 13.2 1.0 C1 A:MLI156 4.4 41.4 0.8 CD2 A:HIS46 4.4 27.5 1.0 ND1 A:HIS63 4.5 37.5 1.0 NE2 A:HIS46 4.5 27.6 1.0 C2 A:MLI156 4.5 42.3 0.8 O7 A:MLI156 4.6 40.2 0.8 CA A:HIS46 4.8 14.6 1.0 CB A:VAL118 4.9 13.8 1.0 CG1 A:VAL118 4.9 16.9 1.0

Zinc binding site 2 out of 3 in the Human SOD1 D124V Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SOD1 D124V Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn155 b:49.8 occ:0.31 ND1 A:HIS63 1.8 37.5 1.0 ND1 A:HIS80 2.4 43.4 1.0 CE1 A:HIS63 2.7 38.2 0.0 CG A:HIS63 2.9 35.0 1.0 CG A:HIS80 3.2 42.4 1.0 CE1 A:HIS80 3.3 45.0 1.0 CB A:HIS80 3.4 37.8 1.0 CB A:HIS63 3.4 28.8 1.0 NE2 A:HIS63 3.8 38.3 0.0 CD2 A:HIS63 3.9 37.1 0.0 CB A:ASP83 4.3 27.1 1.0 CD2 A:HIS80 4.3 44.9 1.0 NE2 A:HIS80 4.4 46.4 1.0 CA A:HIS80 4.7 35.1 1.0 CG A:ASP83 4.8 32.0 1.0 N A:HIS80 4.8 38.5 1.0 CA A:HIS63 4.9 22.3 1.0

Zinc binding site 3 out of 3 in the Human SOD1 D124V Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SOD1 D124V Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn154 b:19.1 occ:1.00 O6 B:MLI155 1.9 25.4 0.9 NE2 B:HIS48 2.1 15.8 1.0 NE2 B:HIS120 2.1 19.4 1.0 ND1 B:HIS46 2.2 19.0 1.0 CE1 B:HIS48 3.0 15.5 1.0 C2 B:MLI155 3.0 28.3 0.9 CE1 B:HIS120 3.0 21.2 1.0 CD2 B:HIS120 3.1 17.4 1.0 CG B:HIS46 3.1 16.4 1.0 CE1 B:HIS46 3.2 20.6 1.0 CD2 B:HIS48 3.2 14.7 1.0 O7 B:MLI155 3.3 29.8 0.9 CB B:HIS46 3.4 15.8 1.0 O B:HOH229 3.9 27.1 1.0 ND1 B:HIS120 4.1 18.3 1.0 ND1 B:HIS48 4.1 15.3 1.0 CG B:HIS120 4.2 16.3 1.0 NE2 B:HIS46 4.3 21.4 1.0 CD2 B:HIS46 4.3 19.6 1.0 CG B:HIS48 4.3 13.4 1.0 ND1 B:HIS63 4.3 30.5 1.0 C1 B:MLI155 4.3 32.5 0.9 CG B:HIS63 4.5 29.2 1.0 C3 B:MLI155 4.6 39.6 0.9 CE1 B:HIS63 4.7 30.8 1.0 O9 B:MLI155 4.7 40.7 0.9 CB B:HIS63 4.8 26.2 1.0 CA B:HIS46 4.8 14.6 1.0 CG1 B:VAL118 4.9 16.5 1.0 CD2 B:HIS63 5.0 31.3 1.0

S.V.Seetharaman, D.D.Winkler, A.B.Taylor, X.Cao, L.J.Whitson, P.A.Doucette, J.S.Valentine, M.C.Carroll, V.C.Culotta, P.J.Hart. Structures of Pathogenic SOD1 Mutants H80R and D124V: Disrupted Zinc-Binding and Compromised Post-Translational Modification By the Copper Chaperone Ccs To Be Published.