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Zinc in PDB 1p1v: Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A

Enzymatic activity of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A

All present enzymatic activity of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A, PDB code: 1p1v was solved by J.S.Elam, K.Malek, J.A.Rodriguez, P.A.Doucette, A.B.Taylor, L.J.Hayward, D.E.Cabelli, J.S.Valentine, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 70.449, 101.140, 143.080, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A (pdb code 1p1v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A, PDB code: 1p1v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1p1v

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Zinc binding site 1 out of 6 in the Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:11.0
occ:1.00
 O1 A:SO4801 2.0 13.2 1.0
ND1 A:HIS46 2.0 10.8 1.0
NE2 A:HIS48 2.0 10.4 1.0
NE2 A:HIS120 2.0 11.9 1.0
CE1 A:HIS48 2.9 11.0 1.0
CE1 A:HIS46 2.9 11.4 1.0
CE1 A:HIS120 2.9 11.7 1.0
CD2 A:HIS120 3.0 11.1 1.0
CG A:HIS46 3.1 11.6 1.0
CD2 A:HIS48 3.2 10.9 1.0
S A:SO4801 3.2 13.4 1.0
CB A:HIS46 3.5 11.0 1.0
O2 A:SO4801 3.5 12.6 1.0
NE2 A:HIS63 3.6 12.1 1.0
CD2 A:HIS63 3.9 13.7 1.0
ND1 A:HIS120 4.0 11.6 1.0
NE2 A:HIS46 4.1 11.7 1.0
O4 A:SO4801 4.1 17.6 1.0
ND1 A:HIS48 4.1 10.6 1.0
O3 A:SO4801 4.1 19.0 1.0
CG A:HIS120 4.1 11.9 1.0
CD2 A:HIS46 4.2 12.5 1.0
CG A:HIS48 4.3 10.4 1.0
O A:HOH823 4.4 19.6 1.0
CG1 A:VAL118 4.5 12.1 1.0
CE1 A:HIS63 4.6 12.6 1.0
NE A:ARG143 4.7 10.6 1.0
CB A:VAL118 4.7 9.4 1.0
CA A:HIS46 4.9 10.1 1.0

Zinc binding site 2 out of 6 in 1p1v

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Zinc binding site 2 out of 6 in the Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:11.6
occ:1.00
 OD1 A:ASP83 2.0 12.0 1.0
ND1 A:HIS63 2.0 11.1 1.0
ND1 A:HIS80 2.0 13.3 1.0
ND1 A:HIS71 2.0 12.0 1.0
CG A:ASP83 2.7 10.9 1.0
OD2 A:ASP83 2.7 12.0 1.0
CE1 A:HIS71 2.9 11.9 1.0
CE1 A:HIS80 2.9 14.3 1.0
CE1 A:HIS63 2.9 12.6 1.0
CG A:HIS80 3.0 12.9 1.0
CG A:HIS63 3.1 12.4 1.0
CG A:HIS71 3.2 12.0 1.0
CB A:HIS63 3.5 11.8 1.0
CB A:HIS80 3.5 12.0 1.0
CB A:HIS71 3.6 12.7 1.0
CA A:HIS71 3.8 14.3 1.0
NE2 A:HIS80 4.0 14.8 1.0
NE2 A:HIS63 4.1 12.1 1.0
CD2 A:HIS80 4.1 13.2 1.0
NE2 A:HIS71 4.1 12.9 1.0
O A:LYS136 4.1 29.6 1.0
CB A:ASP83 4.1 11.5 1.0
CD2 A:HIS63 4.2 13.7 1.0
CD2 A:HIS71 4.2 13.7 1.0
O A:HOH904 4.4 32.2 1.0
N A:GLY72 4.7 13.2 1.0
N A:HIS80 4.7 11.3 1.0
CA A:ASP83 4.7 10.2 1.0
CA A:HIS80 4.7 11.0 1.0
C A:HIS71 4.8 13.1 1.0
N A:HIS71 4.8 13.5 1.0
N A:ASP83 4.9 10.1 1.0

Zinc binding site 3 out of 6 in 1p1v

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Zinc binding site 3 out of 6 in the Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:25.1
occ:1.00
 O2 B:SO4802 1.9 30.0 1.0
NE2 B:HIS120 1.9 21.0 1.0
NE2 B:HIS48 2.0 23.4 1.0
ND1 B:HIS46 2.0 22.4 1.0
CE1 B:HIS120 2.7 19.7 1.0
CE1 B:HIS48 2.8 27.1 1.0
CE1 B:HIS46 2.9 25.6 1.0
CD2 B:HIS120 3.0 20.3 1.0
S B:SO4802 3.1 32.2 1.0
CG B:HIS46 3.1 23.1 1.0
CD2 B:HIS48 3.2 22.9 1.0
O3 B:SO4802 3.3 30.6 1.0
NE2 B:HIS63 3.4 29.3 1.0
CB B:HIS46 3.5 22.6 1.0
CD2 B:HIS63 3.8 29.8 1.0
ND1 B:HIS120 3.9 20.9 1.0
ND1 B:HIS48 4.0 27.5 1.0
O4 B:SO4802 4.0 43.6 1.0
CG B:HIS120 4.1 20.2 1.0
O1 B:SO4802 4.1 50.5 1.0
NE2 B:HIS46 4.1 24.0 1.0
CD2 B:HIS46 4.2 23.0 1.0
CG B:HIS48 4.2 23.3 1.0
CE1 B:HIS63 4.5 31.8 1.0
O B:HOH881 4.6 33.6 1.0
CG1 B:VAL118 4.6 19.2 1.0
CB B:VAL118 4.7 18.0 1.0
NE B:ARG143 4.7 25.8 1.0
CA B:HIS46 4.9 21.6 1.0
CG B:ARG143 4.9 25.7 1.0
CG B:HIS63 5.0 29.9 1.0

Zinc binding site 4 out of 6 in 1p1v

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Zinc binding site 4 out of 6 in the Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn204

b:34.0
occ:1.00
 OD1 B:ASP83 1.8 31.8 1.0
ND1 B:HIS80 2.0 37.3 1.0
ND1 B:HIS63 2.0 34.4 1.0
ND1 B:HIS71 2.1 34.3 1.0
CG B:ASP83 2.6 30.1 1.0
OD2 B:ASP83 2.6 33.5 1.0
CE1 B:HIS80 2.9 37.6 1.0
CE1 B:HIS71 2.9 33.1 1.0
CE1 B:HIS63 2.9 31.8 1.0
CG B:HIS80 3.0 36.2 1.0
CG B:HIS63 3.1 29.9 1.0
CG B:HIS71 3.2 37.4 1.0
CB B:HIS80 3.4 37.2 1.0
CB B:HIS63 3.5 29.0 1.0
CB B:HIS71 3.7 39.9 1.0
CA B:HIS71 3.9 42.0 1.0
NE2 B:HIS80 4.0 39.0 1.0
CB B:ASP83 4.0 28.1 1.0
CD2 B:HIS80 4.1 36.6 1.0
NE2 B:HIS71 4.1 33.0 1.0
NE2 B:HIS63 4.1 29.3 1.0
CD2 B:HIS63 4.2 29.8 1.0
CD2 B:HIS71 4.3 37.4 1.0
N B:HIS80 4.5 37.5 1.0
N B:GLY72 4.5 43.3 1.0
CA B:HIS80 4.6 37.4 1.0
CA B:ASP83 4.7 27.0 1.0
C B:HIS71 4.8 41.3 1.0
CB B:THR137 4.8 72.5 1.0
N B:HIS71 4.9 40.9 1.0
N B:ASP83 4.9 32.0 1.0
O B:GLY72 4.9 40.0 1.0

Zinc binding site 5 out of 6 in 1p1v

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Zinc binding site 5 out of 6 in the Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn205

b:9.8
occ:1.00
 O1 C:SO4803 2.0 10.2 1.0
ND1 C:HIS46 2.0 9.1 1.0
NE2 C:HIS48 2.0 9.2 1.0
NE2 C:HIS120 2.0 10.1 1.0
CE1 C:HIS48 2.9 9.2 1.0
CE1 C:HIS120 2.9 10.0 1.0
CE1 C:HIS46 2.9 10.1 1.0
CD2 C:HIS120 3.1 9.6 1.0
CG C:HIS46 3.1 10.0 1.0
CD2 C:HIS48 3.2 9.4 1.0
S C:SO4803 3.2 11.7 1.0
CB C:HIS46 3.5 10.5 1.0
O3 C:SO4803 3.5 11.6 1.0
NE2 C:HIS63 3.5 10.5 1.0
CD2 C:HIS63 3.9 9.6 1.0
ND1 C:HIS120 4.1 10.4 1.0
ND1 C:HIS48 4.1 8.8 1.0
O2 C:SO4803 4.1 17.7 1.0
NE2 C:HIS46 4.1 10.3 1.0
CG C:HIS120 4.2 10.1 1.0
O4 C:SO4803 4.2 18.2 1.0
CD2 C:HIS46 4.2 9.2 1.0
CG C:HIS48 4.2 8.8 1.0
O C:HOH819 4.4 18.5 1.0
CG1 C:VAL118 4.5 11.1 1.0
CE1 C:HIS63 4.6 11.1 1.0
CB C:VAL118 4.6 9.4 1.0
NE C:ARG143 4.7 10.1 1.0
CA C:HIS46 4.9 8.9 1.0

Zinc binding site 6 out of 6 in 1p1v

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Zinc binding site 6 out of 6 in the Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Fals-Associated Human Copper-Zinc Superoxide Dismutase (Cuznsod) Mutant D125H to 1.4A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn206

b:10.3
occ:1.00
 OD1 C:ASP83 2.0 11.4 1.0
ND1 C:HIS80 2.0 10.7 1.0
ND1 C:HIS71 2.0 11.0 1.0
ND1 C:HIS63 2.0 10.2 1.0
CG C:ASP83 2.7 10.8 1.0
OD2 C:ASP83 2.8 11.5 1.0
CE1 C:HIS71 2.9 10.7 1.0
CE1 C:HIS80 2.9 11.0 1.0
CE1 C:HIS63 2.9 11.1 1.0
CG C:HIS80 3.0 11.3 1.0
CG C:HIS63 3.1 9.6 1.0
CG C:HIS71 3.2 11.1 1.0
CB C:HIS80 3.5 11.0 1.0
CB C:HIS63 3.5 11.2 1.0
CB C:HIS71 3.6 11.3 1.0
CA C:HIS71 3.9 12.5 1.0
O C:LYS136 4.0 30.5 1.0
NE2 C:HIS80 4.0 11.7 1.0
NE2 C:HIS71 4.1 11.9 1.0
CD2 C:HIS80 4.1 11.7 1.0
NE2 C:HIS63 4.1 10.5 1.0
CB C:ASP83 4.2 10.9 1.0
CD2 C:HIS63 4.2 9.6 1.0
CD2 C:HIS71 4.2 13.3 1.0
O C:HOH864 4.5 24.5 1.0
N C:GLY72 4.7 11.4 1.0
N C:HIS80 4.7 10.9 1.0
CA C:ASP83 4.7 9.7 1.0
CA C:HIS80 4.8 12.1 1.0
C C:HIS71 4.8 12.7 1.0
N C:HIS71 4.9 13.2 1.0
N C:ASP83 4.9 10.1 1.0
O C:GLY72 5.0 13.1 1.0

Reference:

J.S.Elam, K.Malek, J.A.Rodriguez, P.A.Doucette, A.B.Taylor, L.J.Hayward, D.E.Cabelli, J.S.Valentine, P.J.Hart. An Alternative Mechanism of Bicarbonate-Mediated Peroxidation By Copper-Zinc Superoxide Dismutase: Rates Enhanced Via Proposed Enzyme-Associated Peroxycarbonate Intermediate J.Biol.Chem. V. 278 21032 2003.
ISSN: ISSN 0021-9258
PubMed: 12649272
DOI: 10.1074/JBC.M300484200
Page generated: Wed Oct 16 17:40:35 2024

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