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

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

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 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 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 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 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

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