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Nickel in PDB 2rd9: Crystal Structure of A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution, PDB code: 2rd9 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) 29.46 / 2.30
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 147.330, 147.330, 147.330, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 20.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution (pdb code 2rd9). 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 A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution, PDB code: 2rd9:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2rd9

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Nickel binding site 1 out of 4 in the Crystal Structure of A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 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 Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni300

b:22.1
occ:1.00
NE2 A:HIS142 2.1 22.8 1.0
O A:HOH421 2.1 24.0 1.0
NE2 A:HIS48 2.2 26.7 1.0
NE2 D:HIS-9 2.2 21.3 1.0
NE2 A:HIS146 2.2 25.3 1.0
N1 A:IMD301 2.2 30.3 1.0
CE1 A:HIS48 3.0 29.8 1.0
CE1 A:HIS142 3.0 24.3 1.0
CD2 A:HIS142 3.1 25.5 1.0
C5 A:IMD301 3.1 23.2 1.0
CE1 D:HIS-9 3.1 26.6 1.0
CE1 A:HIS146 3.2 27.1 1.0
CD2 A:HIS48 3.2 24.6 1.0
CD2 D:HIS-9 3.2 22.5 1.0
CD2 A:HIS146 3.2 26.8 1.0
C2 A:IMD301 3.3 25.5 1.0
ND1 A:HIS142 4.1 23.0 1.0
ND1 A:HIS48 4.2 26.4 1.0
CG A:HIS142 4.2 27.1 1.0
ND1 D:HIS-9 4.2 22.1 1.0
C4 A:IMD301 4.3 22.7 1.0
CG A:HIS48 4.3 25.9 1.0
O B:HOH371 4.3 23.1 1.0
ND1 A:HIS146 4.3 29.1 1.0
N3 A:IMD301 4.3 28.6 1.0
CG D:HIS-9 4.3 28.3 1.0
CG A:HIS146 4.4 26.9 1.0

Nickel binding site 2 out of 4 in 2rd9

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Nickel binding site 2 out of 4 in the Crystal Structure of A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 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 Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni300

b:25.9
occ:1.00
NE2 B:HIS142 2.1 25.4 1.0
NE2 B:HIS48 2.2 23.6 1.0
NE2 C:HIS-9 2.2 22.7 1.0
NE2 B:HIS146 2.2 25.9 1.0
N1 A:IMD303 2.2 28.8 1.0
O A:HOH393 2.4 33.2 1.0
CD2 B:HIS142 3.0 26.1 1.0
CE1 B:HIS48 3.1 31.0 1.0
CE1 B:HIS142 3.1 23.9 1.0
CE1 B:HIS146 3.1 27.6 1.0
C5 A:IMD303 3.1 24.4 1.0
CE1 C:HIS-9 3.2 24.6 1.0
CD2 C:HIS-9 3.2 21.0 1.0
CD2 B:HIS48 3.2 30.2 1.0
C2 A:IMD303 3.3 26.4 1.0
CD2 B:HIS146 3.3 26.9 1.0
ND1 B:HIS142 4.2 22.9 1.0
CG B:HIS142 4.2 25.0 1.0
ND1 B:HIS48 4.2 26.4 1.0
ND1 B:HIS146 4.3 26.8 1.0
ND1 C:HIS-9 4.3 19.8 1.0
CG B:HIS48 4.3 26.8 1.0
C4 A:IMD303 4.3 24.5 1.0
CG C:HIS-9 4.3 26.7 1.0
N3 A:IMD303 4.4 36.5 1.0
O A:HOH394 4.4 26.9 1.0
CG B:HIS146 4.4 27.0 1.0

Nickel binding site 3 out of 4 in 2rd9

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Nickel binding site 3 out of 4 in the Crystal Structure of A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution


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 A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni300

b:20.8
occ:1.00
NE2 C:HIS142 2.1 21.5 1.0
NE2 C:HIS48 2.1 26.7 1.0
NE2 B:HIS-9 2.2 23.9 1.0
O C:HOH384 2.3 18.7 1.0
N1 C:IMD302 2.3 26.0 1.0
NE2 C:HIS146 2.3 29.4 1.0
CD2 C:HIS142 3.0 26.7 1.0
CE1 C:HIS48 3.1 29.1 1.0
CE1 C:HIS142 3.1 22.2 1.0
CD2 C:HIS48 3.1 25.9 1.0
CD2 B:HIS-9 3.2 23.7 1.0
C5 C:IMD302 3.2 18.4 1.0
CE1 B:HIS-9 3.2 25.2 1.0
CE1 C:HIS146 3.3 26.2 1.0
C2 C:IMD302 3.3 21.7 1.0
CD2 C:HIS146 3.3 26.5 1.0
ND1 C:HIS142 4.2 23.6 1.0
ND1 C:HIS48 4.2 27.7 1.0
CG C:HIS142 4.2 27.2 1.0
CG C:HIS48 4.2 28.6 1.0
ND1 B:HIS-9 4.3 22.2 1.0
CG B:HIS-9 4.3 26.1 1.0
C4 C:IMD302 4.4 23.4 1.0
ND1 C:HIS146 4.4 27.7 1.0
N3 C:IMD302 4.4 26.4 1.0
CG C:HIS146 4.5 28.0 1.0
O D:HOH394 4.5 19.0 1.0

Nickel binding site 4 out of 4 in 2rd9

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Nickel binding site 4 out of 4 in the Crystal Structure of A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution


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 A Putative Yfit-Like Metal-Dependent Hydrolase (BH0186) From Bacillus Halodurans C-125 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni300

b:23.6
occ:1.00
NE2 D:HIS142 2.1 23.0 1.0
NE2 A:HIS-9 2.2 21.2 1.0
NE2 D:HIS48 2.2 24.7 1.0
NE2 D:HIS146 2.3 28.7 1.0
N1 C:IMD301 2.3 25.3 1.0
O C:HOH382 2.3 24.8 1.0
CE1 D:HIS48 3.0 28.2 1.0
CD2 D:HIS142 3.0 25.1 1.0
CE1 A:HIS-9 3.1 22.4 1.0
CE1 D:HIS146 3.1 26.7 1.0
CE1 D:HIS142 3.2 28.0 1.0
C5 C:IMD301 3.2 25.1 1.0
CD2 A:HIS-9 3.2 23.5 1.0
C2 C:IMD301 3.3 27.5 1.0
CD2 D:HIS48 3.3 29.2 1.0
CD2 D:HIS146 3.3 29.9 1.0
ND1 D:HIS48 4.2 26.9 1.0
CG D:HIS142 4.2 28.1 1.0
ND1 D:HIS142 4.2 23.9 1.0
ND1 A:HIS-9 4.3 23.0 1.0
CG D:HIS48 4.3 26.8 1.0
ND1 D:HIS146 4.3 25.5 1.0
C4 C:IMD301 4.4 26.5 1.0
CG A:HIS-9 4.4 26.9 1.0
N3 C:IMD301 4.4 28.0 1.0
O C:HOH383 4.4 24.3 1.0
CG D:HIS146 4.4 26.8 1.0
O C:HOH325 5.0 24.5 1.0

Reference:

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