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Zinc in PDB 3qqd: Human SOD1 H80R Variant, P212121 Crystal Form

Enzymatic activity of Human SOD1 H80R Variant, P212121 Crystal Form

All present enzymatic activity of Human SOD1 H80R Variant, P212121 Crystal Form:
1.15.1.1;

Protein crystallography data

The structure of Human SOD1 H80R Variant, P212121 Crystal Form, PDB code: 3qqd was solved by S.V.Seetharaman, D.D.Winkler, A.B.Taylor, X.Cao, L.J.Whitson, P.A.Doucette, J.S.Valentine, V.Schirf, B.Demeler, 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) 39.02 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.245, 58.427, 104.825, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SOD1 H80R Variant, P212121 Crystal Form (pdb code 3qqd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human SOD1 H80R Variant, P212121 Crystal Form, PDB code: 3qqd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3qqd

Go back to Zinc Binding Sites List in 3qqd
Zinc binding site 1 out of 2 in the Human SOD1 H80R Variant, P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SOD1 H80R Variant, P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn154

b:28.4
occ:0.36
NE2 A:HIS120 2.1 23.6 1.0
NE2 A:HIS48 2.3 17.6 1.0
ND1 A:HIS46 2.3 29.7 1.0
NE2 A:HIS63 2.4 36.4 1.0
O1 A:SO4155 2.8 47.2 0.7
CE1 A:HIS48 2.9 19.8 1.0
CE1 A:HIS120 2.9 26.5 1.0
CD2 A:HIS63 3.0 35.1 1.0
CD2 A:HIS120 3.1 23.8 1.0
CG A:HIS46 3.1 24.3 1.0
CE1 A:HIS63 3.2 37.3 1.0
CB A:HIS46 3.2 19.9 1.0
CE1 A:HIS46 3.3 29.1 1.0
CD2 A:HIS48 3.4 16.1 1.0
CG A:HIS63 4.0 30.9 1.0
ND1 A:HIS120 4.0 23.5 1.0
ND1 A:HIS63 4.0 35.7 1.0
S A:SO4155 4.0 45.3 0.7
ND1 A:HIS48 4.1 16.6 1.0
CG A:HIS120 4.1 22.5 1.0
CD2 A:HIS46 4.3 26.1 1.0
CG A:HIS48 4.4 14.8 1.0
NE2 A:HIS46 4.4 26.1 1.0
O2 A:SO4155 4.4 45.4 0.7
O4 A:SO4155 4.5 43.8 0.7
CA A:HIS46 4.7 14.8 1.0
CB A:VAL118 4.9 11.9 1.0
CG1 A:VAL118 4.9 16.5 1.0

Zinc binding site 2 out of 2 in 3qqd

Go back to Zinc Binding Sites List in 3qqd
Zinc binding site 2 out of 2 in the Human SOD1 H80R Variant, P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SOD1 H80R Variant, P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn154

b:21.8
occ:0.53
NE2 B:HIS120 2.1 21.6 1.0
NE2 B:HIS48 2.1 18.4 1.0
ND1 B:HIS46 2.1 23.5 1.0
O1 B:SO4155 2.2 38.9 0.7
CE1 B:HIS48 2.9 18.9 1.0
CE1 B:HIS120 3.0 22.4 1.0
CG B:HIS46 3.0 20.1 1.0
CD2 B:HIS120 3.1 19.6 1.0
S B:SO4155 3.1 44.1 0.7
CE1 B:HIS46 3.2 24.1 1.0
CB B:HIS46 3.2 17.6 1.0
CD2 B:HIS48 3.3 15.6 1.0
O3 B:SO4155 3.3 45.7 0.7
O2 B:SO4155 3.6 42.1 0.7
ND1 B:HIS63 4.0 35.1 1.0
ND1 B:HIS48 4.1 15.7 1.0
ND1 B:HIS120 4.1 20.1 1.0
CG B:HIS120 4.1 19.0 1.0
CD2 B:HIS46 4.2 21.5 1.0
NE2 B:HIS46 4.3 22.9 1.0
CG B:HIS48 4.3 13.5 1.0
O4 B:SO4155 4.4 43.3 0.7
CE1 B:HIS63 4.6 36.6 1.0
CA B:HIS46 4.7 14.2 1.0
CG B:HIS63 4.7 32.8 1.0
CG1 B:VAL118 4.9 15.7 1.0
CB B:VAL118 5.0 13.2 1.0

Reference:

S.V.Seetharaman, D.D.Winkler, A.B.Taylor, X.Cao, L.J.Whitson, P.A.Doucette, J.S.Valentine, V.Schirf, B.Demeler, M.C.Carroll, V.C.Culotta, P.J.Hart. Disrupted Zinc-Binding Sites in Structures of Pathogenic SOD1 Variants D124V and H80R. Biochemistry V. 49 5714 2010.
ISSN: ISSN 0006-2960
PubMed: 20515040
DOI: 10.1021/BI100314N
Page generated: Wed Dec 16 04:45:52 2020

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