Atomistry » Nickel » PDB 2pr0-2w3u » 2rd9
Atomistry »
  Nickel »
    PDB 2pr0-2w3u »
      2rd9 »

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

Go back to Nickel Binding Sites List in 2rd9
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

Go back to Nickel Binding Sites List in 2rd9
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

Go back to Nickel Binding Sites List in 2rd9
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

Go back to Nickel Binding Sites List in 2rd9
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.
Page generated: Mon Aug 18 18:21:44 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy