Nickel in PDB 4ls3: The Crystal Structure of Helicobacter Pylori Ceue(HP1561)/Ni-His Compl

The structure of The Crystal Structure of Helicobacter Pylori Ceue(HP1561)/Ni-His Compl, PDB code: 4ls3 was solved by M.Salamina, M.M.Shaik, L.Cendron, G.Zanotti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.32 / 1.70
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.420, 60.650, 77.130, 90.00, 91.02, 90.00
R / Rfree (%)	16.8 / 20.4

The binding sites of Nickel atom in the The Crystal Structure of Helicobacter Pylori Ceue(HP1561)/Ni-His Compl (pdb code 4ls3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of Helicobacter Pylori Ceue(HP1561)/Ni-His Compl, PDB code: 4ls3:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The Crystal Structure of Helicobacter Pylori Ceue(HP1561)/Ni-His Compl


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Helicobacter Pylori Ceue(HP1561)/Ni-His Compl within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni603 b:13.8 occ:1.00 O A:HIS602 2.1 14.7 0.9 ND1 A:HIS601 2.1 14.3 1.0 N A:HIS601 2.1 10.6 1.0 NE2 A:HIS103 2.1 13.2 1.0 OXT A:HIS601 2.1 13.5 1.0 N A:HIS602 2.2 10.2 0.9 C A:HIS602 2.8 16.8 0.9 C A:HIS601 2.8 15.9 1.0 CA A:HIS601 2.8 12.7 1.0 CA A:HIS602 2.9 12.5 0.9 CE1 A:HIS601 3.0 14.1 1.0 CD2 A:HIS103 3.1 16.6 1.0 CG A:HIS601 3.1 15.2 1.0 CE1 A:HIS103 3.2 12.6 1.0 CB A:HIS601 3.4 11.3 1.0 OXT A:HIS602 4.0 17.5 0.9 O A:HIS601 4.0 13.9 1.0 NE2 A:HIS601 4.2 14.0 1.0 NH1 A:ARG230 4.2 14.9 1.0 CD2 A:HIS601 4.2 14.9 1.0 CG A:HIS103 4.2 14.0 1.0 ND1 A:HIS103 4.2 14.2 1.0 CB A:HIS602 4.3 14.5 0.9 O A:GLY58 4.5 11.9 1.0 O A:HOH945 4.6 22.8 1.0 NH2 A:ARG230 4.7 15.0 1.0 O A:HOH707 4.7 17.3 1.0 CZ A:ARG230 4.7 13.2 1.0 CZ2 A:TRP249 4.8 11.7 1.0 O A:HOH1166 4.8 18.6 1.0 CE2 A:PHE123 4.8 13.3 1.0 CD2 A:PHE123 4.9 14.1 1.0 O A:HOH713 5.0 17.2 1.0

Nickel binding site 2 out of 2 in the The Crystal Structure of Helicobacter Pylori Ceue(HP1561)/Ni-His Compl


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Helicobacter Pylori Ceue(HP1561)/Ni-His Compl within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni603 b:14.1 occ:1.00 O B:HIS602 2.0 12.8 0.9 NE2 B:HIS103 2.1 14.4 1.0 ND1 B:HIS601 2.1 12.0 1.0 N B:HIS601 2.1 11.4 1.0 OXT B:HIS601 2.2 14.2 1.0 N B:HIS602 2.2 10.8 0.9 C B:HIS602 2.8 15.4 0.9 C B:HIS601 2.8 14.6 1.0 CA B:HIS601 2.9 11.6 1.0 CA B:HIS602 2.9 13.2 0.9 CD2 B:HIS103 3.0 17.9 1.0 CE1 B:HIS601 3.0 13.7 1.0 CE1 B:HIS103 3.1 13.1 1.0 CG B:HIS601 3.1 13.3 1.0 CB B:HIS601 3.5 12.1 1.0 OXT B:HIS602 4.0 19.8 0.9 O B:HIS601 4.0 11.8 1.0 NE2 B:HIS601 4.2 15.7 1.0 CG B:HIS103 4.2 15.6 1.0 ND1 B:HIS103 4.2 15.5 1.0 NH1 B:ARG230 4.2 14.2 1.0 CD2 B:HIS601 4.2 14.7 1.0 CB B:HIS602 4.3 16.2 0.9 O B:GLY58 4.5 12.2 1.0 O B:HOH883 4.6 21.1 1.0 O B:HOH723 4.6 17.9 1.0 NH2 B:ARG230 4.6 14.1 1.0 CZ B:ARG230 4.7 13.3 1.0 O B:HOH713 4.8 16.0 1.0 CZ2 B:TRP249 4.8 11.6 1.0 CE2 B:PHE123 4.9 12.5 1.0 CD2 B:PHE123 4.9 13.9 1.0 O B:HOH710 5.0 16.8 1.0

M.M.Shaik, L.Cendron, M.Salamina, M.Ruzzene, G.Zanotti. Helicobacter Pylori Periplasmic Receptor Ceue (HP1561) Modulates Its Nickel Affinity Via Organic Metallophores. Mol.Microbiol. V. 91 724 2014.
ISSN: ISSN 0950-382X
PubMed: 24330328
DOI: 10.1111/MMI.12487