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Nickel in PDB 3gor: Crystal Structure of Putative Metal-Dependent Hydrolase APC36150

Protein crystallography data

The structure of Crystal Structure of Putative Metal-Dependent Hydrolase APC36150, PDB code: 3gor was solved by D.R.Cooper, K.Grelewska, Z.S.Derewenda, Integrated Center For Structureand Function Innovation (Isfi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.62 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.477, 71.470, 123.256, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 24.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Putative Metal-Dependent Hydrolase APC36150 (pdb code 3gor). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Putative Metal-Dependent Hydrolase APC36150, PDB code: 3gor:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3gor

Go back to Nickel Binding Sites List in 3gor
Nickel binding site 1 out of 4 in the Crystal Structure of Putative Metal-Dependent Hydrolase APC36150


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Putative Metal-Dependent Hydrolase APC36150 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni200

b:56.8
occ:1.00
NE2 A:HIS127 2.1 53.7 1.0
NE2 A:HIS131 2.3 45.1 1.0
NE2 A:HIS47 2.3 50.9 1.0
CD2 A:HIS127 3.0 30.8 1.0
CE1 A:HIS127 3.1 54.2 1.0
CE1 A:HIS131 3.2 46.2 1.0
CE1 A:HIS47 3.2 36.6 1.0
CD2 A:HIS131 3.3 32.0 1.0
CD2 A:HIS47 3.3 33.6 1.0
CG A:HIS127 4.2 39.5 1.0
ND1 A:HIS127 4.2 43.2 1.0
ND1 A:HIS131 4.3 48.8 1.0
ND1 A:HIS47 4.3 46.5 1.0
CG A:HIS131 4.4 56.6 1.0
CG A:HIS47 4.5 46.5 1.0

Nickel binding site 2 out of 4 in 3gor

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Nickel binding site 2 out of 4 in the Crystal Structure of Putative Metal-Dependent Hydrolase APC36150


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Putative Metal-Dependent Hydrolase APC36150 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni200

b:37.9
occ:1.00
NE2 B:HIS47 2.1 45.4 1.0
NE2 B:HIS127 2.2 44.8 1.0
NE2 B:HIS131 2.2 48.4 1.0
CE1 B:HIS47 3.0 31.6 1.0
CE1 B:HIS127 3.1 47.6 1.0
CD2 B:HIS47 3.1 32.9 1.0
CE1 B:HIS131 3.2 41.5 1.0
CD2 B:HIS127 3.2 34.3 1.0
CD2 B:HIS131 3.2 28.7 1.0
ND1 B:HIS47 4.1 45.5 1.0
CG B:HIS47 4.2 46.5 1.0
ND1 B:HIS127 4.2 42.2 1.0
CG B:HIS127 4.3 41.0 1.0
ND1 B:HIS131 4.3 37.9 1.0
CG B:HIS131 4.4 56.4 1.0

Nickel binding site 3 out of 4 in 3gor

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Nickel binding site 3 out of 4 in the Crystal Structure of Putative Metal-Dependent Hydrolase APC36150


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Putative Metal-Dependent Hydrolase APC36150 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni200

b:50.7
occ:1.00
NE2 C:HIS47 2.2 49.9 1.0
NE2 C:HIS131 2.3 43.0 1.0
NE2 C:HIS127 2.4 45.1 1.0
CE1 C:HIS131 3.1 41.7 1.0
CE1 C:HIS47 3.1 43.1 1.0
CD2 C:HIS47 3.2 26.4 1.0
CD2 C:HIS131 3.4 38.4 1.0
CE1 C:HIS127 3.4 48.5 1.0
CD2 C:HIS127 3.4 39.5 1.0
ND1 C:HIS47 4.2 39.3 1.0
CG C:HIS47 4.3 43.4 1.0
ND1 C:HIS131 4.3 49.1 1.0
CG C:HIS131 4.4 49.7 1.0
ND1 C:HIS127 4.5 44.3 1.0
CG C:HIS127 4.6 49.2 1.0

Nickel binding site 4 out of 4 in 3gor

Go back to Nickel Binding Sites List in 3gor
Nickel binding site 4 out of 4 in the Crystal Structure of Putative Metal-Dependent Hydrolase APC36150


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Putative Metal-Dependent Hydrolase APC36150 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni200

b:39.0
occ:1.00
NE2 D:HIS47 2.2 46.5 1.0
NE2 D:HIS131 2.2 36.3 1.0
NE2 D:HIS127 2.3 55.7 1.0
CE1 D:HIS47 3.1 37.2 1.0
CE1 D:HIS131 3.1 39.2 1.0
CD2 D:HIS47 3.2 20.0 1.0
CE1 D:HIS127 3.2 43.6 1.0
CD2 D:HIS131 3.2 23.4 1.0
CD2 D:HIS127 3.3 35.0 1.0
ND1 D:HIS47 4.2 31.7 1.0
ND1 D:HIS131 4.2 39.6 1.0
CG D:HIS47 4.3 39.3 1.0
ND1 D:HIS127 4.3 37.5 1.0
CG D:HIS131 4.3 43.3 1.0
CG D:HIS127 4.4 39.5 1.0

Reference:

D.R.Cooper, K.Grelewska, C.Y.Kim, A.Joachimiak, Z.S.Derewenda. The Structure of Dinb From Geobacillus Stearothermophilus: A Representative of A Unique Four-Helix-Bundle Superfamily. Acta Crystallogr.,Sect.F V. 66 219 2010.
ISSN: ESSN 1744-3091
PubMed: 20208147
DOI: 10.1107/S1744309109053913
Page generated: Fri Sep 25 08:22:55 2020
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