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Nickel in PDB 2qe9: Crystal Structure of A Putative Metal-Dependent Hydrolase (Yiza, BSU10800) From Bacillus Subtilis at 1.90 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Metal-Dependent Hydrolase (Yiza, BSU10800) From Bacillus Subtilis at 1.90 A Resolution, PDB code: 2qe9 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.184, 53.184, 251.364, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Putative Metal-Dependent Hydrolase (Yiza, BSU10800) From Bacillus Subtilis at 1.90 A Resolution (pdb code 2qe9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of A Putative Metal-Dependent Hydrolase (Yiza, BSU10800) From Bacillus Subtilis at 1.90 A Resolution, PDB code: 2qe9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2qe9

Go back to Nickel Binding Sites List in 2qe9
Nickel binding site 1 out of 2 in the Crystal Structure of A Putative Metal-Dependent Hydrolase (Yiza, BSU10800) From Bacillus Subtilis at 1.90 A Resolution


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 A Putative Metal-Dependent Hydrolase (Yiza, BSU10800) From Bacillus Subtilis at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni200

b:29.0
occ:1.00
O1 A:CIT201 2.1 31.0 1.0
NE2 A:HIS44 2.1 32.4 1.0
O5 A:CIT201 2.2 35.9 1.0
NE2 A:HIS128 2.2 38.4 1.0
O7 A:CIT201 2.2 35.7 1.0
NE2 A:HIS124 2.2 37.0 1.0
C6 A:CIT201 2.9 41.1 1.0
C3 A:CIT201 2.9 44.8 1.0
CD2 A:HIS44 3.0 35.5 1.0
CD2 A:HIS124 3.1 40.3 1.0
C1 A:CIT201 3.1 45.3 1.0
CE1 A:HIS44 3.1 32.2 1.0
CD2 A:HIS128 3.1 40.4 1.0
CE1 A:HIS124 3.2 37.5 1.0
CE1 A:HIS128 3.2 41.0 1.0
C2 A:CIT201 3.6 46.2 1.0
O A:HOH300 4.0 48.1 1.0
O6 A:CIT201 4.1 49.2 1.0
O4 A:CIT201 4.1 58.4 1.0
CG A:HIS124 4.2 34.5 1.0
ND1 A:HIS124 4.2 35.8 1.0
CG A:HIS44 4.2 35.6 1.0
ND1 A:HIS44 4.2 34.1 1.0
O2 A:CIT201 4.2 50.8 1.0
ND1 A:HIS128 4.3 34.6 1.0
CG A:HIS128 4.3 33.4 1.0
C4 A:CIT201 4.3 55.9 1.0
C5 A:CIT201 4.7 59.5 1.0
O A:HOH274 4.9 49.3 1.0

Nickel binding site 2 out of 2 in 2qe9

Go back to Nickel Binding Sites List in 2qe9
Nickel binding site 2 out of 2 in the Crystal Structure of A Putative Metal-Dependent Hydrolase (Yiza, BSU10800) From Bacillus Subtilis at 1.90 A Resolution


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 A Putative Metal-Dependent Hydrolase (Yiza, BSU10800) From Bacillus Subtilis at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni200

b:25.5
occ:1.00
NE2 B:HIS44 2.1 33.3 1.0
O1 B:CIT201 2.1 25.8 1.0
NE2 B:HIS128 2.1 35.4 1.0
NE2 B:HIS124 2.1 35.6 1.0
O7 B:CIT201 2.1 28.9 1.0
O5 B:CIT201 2.2 25.3 1.0
C6 B:CIT201 2.9 39.4 1.0
C3 B:CIT201 3.0 38.1 1.0
CD2 B:HIS44 3.0 39.9 1.0
CD2 B:HIS124 3.1 36.4 1.0
CE1 B:HIS128 3.1 36.6 1.0
CE1 B:HIS124 3.1 38.6 1.0
C1 B:CIT201 3.1 38.8 1.0
CD2 B:HIS128 3.1 36.3 1.0
CE1 B:HIS44 3.1 39.9 1.0
C2 B:CIT201 3.5 38.7 1.0
O6 B:CIT201 4.1 39.6 1.0
ND1 B:HIS124 4.2 35.4 1.0
O4 B:CIT201 4.2 41.9 1.0
CG B:HIS124 4.2 36.1 1.0
ND1 B:HIS128 4.2 32.2 1.0
CG B:HIS44 4.2 36.1 1.0
O2 B:CIT201 4.2 37.1 1.0
ND1 B:HIS44 4.2 33.2 1.0
CG B:HIS128 4.2 31.3 1.0
C4 B:CIT201 4.3 42.4 1.0
C5 B:CIT201 4.7 50.2 1.0
CG2 B:VAL48 5.0 37.3 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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