Nickel in PDB 5zt9: Sirb From Bacillus Subtilis with NI2+

All present enzymatic activity of Sirb From Bacillus Subtilis with NI2+:
4.99.1.4;

The structure of Sirb From Bacillus Subtilis with NI2+, PDB code: 5zt9 was solved by T.Fujishiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.43 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.730, 53.700, 78.020, 90.00, 107.66, 90.00
R / Rfree (%)	21.2 / 24.5

The binding sites of Nickel atom in the Sirb From Bacillus Subtilis with NI2+ (pdb code 5zt9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Sirb From Bacillus Subtilis with NI2+, PDB code: 5zt9:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Sirb From Bacillus Subtilis with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Sirb From Bacillus Subtilis with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:83.3 occ:1.00 O A:HOH424 1.9 81.5 1.0 OE2 A:GLU83 2.5 82.6 1.0 O A:HOH403 2.6 43.7 1.0 NE2 A:HIS79 2.8 71.4 1.0 O A:HOH428 2.9 46.7 1.0 CD A:GLU83 3.2 80.2 1.0 OE1 A:GLU83 3.3 81.4 1.0 CD2 A:HIS79 3.5 70.9 1.0 CE1 A:HIS79 3.9 69.0 1.0 CG A:GLU83 4.7 74.1 1.0 CG A:HIS79 4.8 65.8 1.0 ND1 A:HIS79 4.9 65.8 1.0

Nickel binding site 2 out of 4 in the Sirb From Bacillus Subtilis with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Sirb From Bacillus Subtilis with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:51.0 occ:1.00 NE2 A:HIS115 2.1 74.3 1.0 NE2 A:HIS229 2.3 45.3 1.0 O A:HOH425 2.4 39.1 1.0 O A:HOH430 2.5 30.7 1.0 O A:HOH436 2.5 43.5 1.0 CE1 A:HIS115 3.0 74.0 1.0 CE1 A:HIS229 3.2 46.2 1.0 CD2 A:HIS115 3.3 70.6 1.0 CD2 A:HIS229 3.4 42.0 1.0 ND1 A:HIS115 4.1 71.8 1.0 CG A:HIS115 4.3 67.4 1.0 ND1 A:HIS229 4.3 44.4 1.0 CG A:HIS229 4.5 41.5 1.0

Nickel binding site 3 out of 4 in the Sirb From Bacillus Subtilis with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Sirb From Bacillus Subtilis with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:80.1 occ:1.00 OE1 B:GLU83 2.1 0.3 1.0 NE2 B:HIS79 2.4 79.6 1.0 O B:HOH413 2.5 65.9 1.0 O B:HOH418 2.5 33.3 1.0 CD2 B:HIS79 3.2 78.5 1.0 CD B:GLU83 3.2 0.4 1.0 CE1 B:HIS79 3.5 77.6 1.0 OE2 B:GLU83 3.6 0.4 1.0 CG B:HIS79 4.4 73.7 1.0 CG B:GLU83 4.5 0.8 1.0 ND1 B:HIS79 4.5 74.2 1.0

Nickel binding site 4 out of 4 in the Sirb From Bacillus Subtilis with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Sirb From Bacillus Subtilis with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:94.7 occ:1.00 NE2 B:HIS229 3.1 46.7 1.0 NE2 B:HIS115 3.4 58.3 1.0 CE1 B:HIS115 3.5 58.4 1.0 CE1 B:HIS229 3.9 46.4 1.0 CD2 B:HIS229 4.0 45.8 1.0 CD2 B:HIS115 4.1 57.4 1.0 ND1 B:HIS115 4.3 57.9 1.0 O A:GLY121 4.6 63.0 1.0 O B:HOH414 4.6 41.4 1.0 O A:ILE120 4.6 49.1 1.0 CG B:HIS115 4.6 56.9 1.0 O B:HOH411 4.9 49.9 1.0

T.Fujishiro, T.Fujishiro. N/A N/A.