Nickel in PDB 4inp: The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound

The structure of The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound, PDB code: 4inp was solved by 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)	52.79 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.180, 76.950, 72.780, 90.00, 94.52, 90.00
R / Rfree (%)	18.9 / 26.8

The binding sites of Nickel atom in the The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound (pdb code 4inp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound, PDB code: 4inp:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound


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) with Ni(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:43.5 occ:1.00 O A:HOH605 2.1 24.1 1.0 NE2 A:HIS103 2.2 47.0 1.0 O A:HOH609 2.7 31.9 1.0 O A:HOH607 2.8 41.6 1.0 CE1 A:HIS103 3.1 46.0 1.0 O A:HOH608 3.1 17.1 1.0 CD2 A:HIS103 3.2 46.6 1.0 NH1 A:ARG230 3.9 11.9 1.0 ND1 A:HIS103 4.2 46.7 1.0 CG A:HIS103 4.3 48.2 1.0 O A:GLY58 4.3 14.7 1.0 O A:HOH528 4.4 24.6 1.0 CZ A:ARG230 4.6 13.8 1.0 O A:HOH606 4.7 30.1 1.0 NH2 A:ARG230 4.7 12.9 1.0

Nickel binding site 2 out of 6 in the The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound


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) with Ni(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:51.6 occ:1.00 O A:HOH612 2.1 34.7 1.0 OXT A:ACT407 2.3 49.8 1.0 OE1 A:GLU153 2.3 21.1 1.0 O A:ACT407 2.4 50.2 1.0 C A:ACT407 2.7 50.6 1.0 CD A:GLU153 3.3 21.8 1.0 OE2 A:GLU153 3.5 25.4 1.0 CH3 A:ACT407 4.2 50.6 1.0 O B:HOH501 4.2 21.7 1.0 O A:HOH613 4.2 28.4 1.0 CG A:GLU153 4.7 15.8 1.0 O A:HOH614 4.7 22.1 1.0 O A:HOH588 5.0 25.5 1.0

Nickel binding site 3 out of 6 in the The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:29.7 occ:1.00 O A:HOH578 2.2 18.1 1.0 O A:HOH611 2.3 21.8 1.0 OXT A:ACT405 2.4 20.7 1.0 O A:ACT406 2.4 35.7 1.0 O A:ACT405 2.5 21.2 1.0 OXT A:ACT406 2.6 36.1 1.0 C A:ACT405 2.9 20.4 1.0 C A:ACT406 2.9 36.1 1.0 OE1 A:GLU94 4.1 24.2 1.0 CH3 A:ACT405 4.3 17.9 1.0 CH3 A:ACT406 4.4 35.2 1.0 OE2 A:GLU94 4.5 20.3 1.0 CD A:GLU94 4.7 22.3 1.0

Nickel binding site 4 out of 6 in the The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:46.2 occ:1.00 O B:ACT404 2.2 27.4 1.0 NE2 B:HIS103 2.3 46.5 1.0 O B:HOH586 2.4 36.2 1.0 OXT B:ACT404 2.7 28.6 1.0 C B:ACT404 2.8 27.8 1.0 O B:HOH585 3.0 37.8 1.0 CD2 B:HIS103 3.2 45.9 1.0 CE1 B:HIS103 3.3 45.8 1.0 NH1 B:ARG230 3.7 8.7 1.0 CH3 B:ACT404 4.3 27.5 1.0 O B:GLY58 4.4 16.9 1.0 CG B:HIS103 4.4 47.8 1.0 ND1 B:HIS103 4.4 45.9 1.0 CZ B:ARG230 4.5 13.1 1.0 NH2 B:ARG230 4.5 11.8 1.0 O B:HOH510 4.8 19.8 1.0

Nickel binding site 5 out of 6 in the The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:53.3 occ:1.00 OE1 B:GLU153 2.2 22.2 1.0 OXT B:ACT406 2.4 54.3 1.0 OXT B:ACT405 2.7 50.1 1.0 O B:ACT405 2.8 51.4 1.0 O B:ACT406 2.8 54.8 1.0 C B:ACT406 2.9 55.1 1.0 O B:HOH584 2.9 31.3 1.0 C B:ACT405 3.0 50.5 1.0 CD B:GLU153 3.2 21.1 1.0 OE2 B:GLU153 3.5 23.1 1.0 CH3 B:ACT406 4.2 55.5 1.0 CH3 B:ACT405 4.4 48.8 1.0 CG B:GLU153 4.6 13.7 1.0 OD2 B:ASP156 4.8 28.0 1.0 O B:HOH545 4.9 32.6 1.0

Nickel binding site 6 out of 6 in the The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of The Crystal Structure of Helicobacter Pylori Ceue (HP1561) with Ni(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni403 b:28.4 occ:1.00 O B:HOH582 2.2 15.7 1.0 O B:HOH583 2.3 14.5 1.0 O A:ACT404 2.4 27.3 1.0 O A:HOH610 2.4 23.3 1.0 O B:ACT407 2.4 23.5 1.0 OXT B:ACT407 2.5 25.1 1.0 C B:ACT407 2.8 24.6 1.0 C A:ACT404 3.5 27.3 1.0 OE1 B:GLU94 4.0 19.3 1.0 OXT A:ACT404 4.1 25.5 1.0 OE2 B:GLU94 4.1 15.7 1.0 OD1 A:ASP154 4.3 12.7 1.0 CH3 B:ACT407 4.3 22.2 1.0 CD B:GLU94 4.5 17.4 1.0 CH3 A:ACT404 4.6 25.8 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