Nickel in PDB 4uhq: Crystal Structure of the Pyocin AP41 Dnase

The structure of Crystal Structure of the Pyocin AP41 Dnase, PDB code: 4uhq was solved by A.Joshi, S.Chen, J.A.Wojdyla, R.Kaminska, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.979 / 1.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.575, 100.575, 71.532, 90.00, 90.00, 90.00
R / Rfree (%)	17.38 / 19.13

The binding sites of Nickel atom in the Crystal Structure of the Pyocin AP41 Dnase (pdb code 4uhq). 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 the Pyocin AP41 Dnase, PDB code: 4uhq:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the Pyocin AP41 Dnase


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 the Pyocin AP41 Dnase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1778 b:18.2 occ:1.00 HO7 A:CIT1776 1.3 24.0 1.0 NE2 A:HIS763 2.1 16.4 1.0 O6 A:CIT1776 2.1 18.6 1.0 ND1 A:HIS738 2.1 17.7 1.0 NE2 A:HIS767 2.1 18.2 1.0 O A:HOH2057 2.2 17.5 1.0 O7 A:CIT1776 2.2 20.0 1.0 CE1 A:HIS738 2.9 18.1 1.0 C6 A:CIT1776 2.9 20.1 1.0 CE1 A:HIS767 3.0 21.2 1.0 CD2 A:HIS763 3.0 16.2 1.0 CE1 A:HIS763 3.1 21.4 1.0 C3 A:CIT1776 3.1 19.6 1.0 CD2 A:HIS767 3.2 19.7 1.0 CG A:HIS738 3.2 16.9 1.0 CB A:HIS738 3.8 17.2 1.0 H41 A:CIT1776 3.9 24.8 1.0 O2 A:CIT1776 4.0 19.7 1.0 N A:HIS739 4.0 16.3 1.0 CA A:HIS738 4.0 16.4 1.0 C4 A:CIT1776 4.1 20.6 1.0 NE2 A:HIS738 4.1 17.7 1.0 O5 A:CIT1776 4.1 20.5 1.0 ND1 A:HIS767 4.2 23.0 1.0 O A:HIS739 4.2 17.8 1.0 ND1 A:HIS763 4.2 20.5 1.0 CG A:HIS763 4.2 17.7 1.0 CD2 A:HIS738 4.3 17.2 1.0 CG A:HIS767 4.3 18.7 1.0 C2 A:CIT1776 4.3 18.6 1.0 O3 A:CIT1776 4.3 26.5 1.0 C1 A:CIT1776 4.4 21.3 1.0 C A:HIS738 4.5 17.2 1.0 C5 A:CIT1776 4.7 27.9 1.0 H21 A:CIT1776 4.8 22.3 1.0 C A:HIS739 4.9 16.8 1.0 CA A:HIS739 4.9 17.3 1.0 H42 A:CIT1776 5.0 24.8 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of the Pyocin AP41 Dnase


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 the Pyocin AP41 Dnase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1777 b:21.4 occ:1.00 HO7 B:CIT1776 1.2 29.3 1.0 NE2 B:HIS763 2.0 21.8 1.0 O6 B:CIT1776 2.1 21.2 1.0 O B:HOH2034 2.1 18.5 1.0 ND1 B:HIS738 2.1 22.8 1.0 NE2 B:HIS767 2.1 26.6 1.0 O7 B:CIT1776 2.2 24.4 1.0 C6 B:CIT1776 2.9 20.7 1.0 CE1 B:HIS738 3.0 21.5 1.0 CE1 B:HIS767 3.0 30.2 1.0 CD2 B:HIS763 3.0 22.6 1.0 CE1 B:HIS763 3.1 23.5 1.0 C3 B:CIT1776 3.1 19.6 1.0 CD2 B:HIS767 3.2 28.6 1.0 CG B:HIS738 3.3 20.2 1.0 CB B:HIS738 3.7 19.8 1.0 H41 B:CIT1776 3.9 31.3 1.0 O2 B:CIT1776 4.0 22.4 1.0 N B:HIS739 4.0 17.6 1.0 CA B:HIS738 4.0 18.9 1.0 C4 B:CIT1776 4.1 26.1 1.0 O5 B:CIT1776 4.1 24.2 1.0 NE2 B:HIS738 4.2 23.5 1.0 ND1 B:HIS763 4.2 26.3 1.0 O B:HIS739 4.2 20.1 1.0 ND1 B:HIS767 4.2 32.3 1.0 CG B:HIS763 4.2 24.0 1.0 C2 B:CIT1776 4.3 21.0 1.0 CD2 B:HIS738 4.3 20.2 1.0 CG B:HIS767 4.3 28.1 1.0 O3 B:CIT1776 4.3 30.0 1.0 C1 B:CIT1776 4.4 27.4 1.0 C B:HIS738 4.5 19.8 1.0 C5 B:CIT1776 4.7 30.6 1.0 H21 B:CIT1776 4.8 25.2 1.0 C B:HIS739 4.9 19.1 1.0 CA B:HIS739 4.9 18.1 1.0 H42 B:CIT1776 5.0 31.3 1.0

A.Joshi, R.Grinter, I.Josts, S.Chen, J.A.Wojdyla, E.D.Lowe, R.Kaminska, C.Sharp, L.Mccaughey, A.W.Roszak, R.J.Cogdell, O.Byron, D.Walker, C.Kleanthous. Structures of the Ultra-High Affinity Protein-Protein Complexes of Pyocins S2 and AP41 and Their Cognate Immunity Proteins From Pseudomonas Aeruginosa J.Mol.Biol. V. 427 2852 2015.
ISSN: ISSN 0022-2836
PubMed: 26215615
DOI: 10.1016/J.JMB.2015.07.014