Nickel in PDB 4rnz: Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal

The structure of Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal, PDB code: 4rnz was solved by D.R.An, H.S.Kim, J.Kim, H.N.Im, H.J.Yoon, J.Y.Yoon, J.Y.Jang, D.Hesek, M.Lee, S.Mobashery, S.-J.Kim, B.I.Lee, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.98
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.469, 91.469, 186.963, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.9

The structure of Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Nickel atom in the Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal (pdb code 4rnz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal, PDB code: 4rnz:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:41.3 occ:1.00 NE2 A:HIS408 2.0 52.7 1.0 NE2 A:HIS406 2.1 43.4 1.0 NE2 A:HIS390 2.2 36.1 1.0 O1 A:PO4504 2.2 55.9 1.0 CE1 A:HIS408 2.9 53.1 1.0 CD2 A:HIS408 3.0 49.7 1.0 CE1 A:HIS390 3.0 32.7 1.0 CD2 A:HIS406 3.1 41.6 1.0 CE1 A:HIS406 3.1 42.2 1.0 P A:PO4504 3.3 66.8 1.0 CD2 A:HIS390 3.3 34.4 1.0 O3 A:PO4504 3.4 65.5 1.0 O4 A:PO4504 3.8 73.3 1.0 O A:HOH697 4.0 43.3 1.0 CD2 A:LEU400 4.0 38.2 1.0 ND1 A:HIS408 4.1 54.4 1.0 CG A:HIS408 4.1 52.8 1.0 ND1 A:HIS390 4.2 32.0 1.0 ND1 A:HIS406 4.2 41.1 1.0 CG A:HIS406 4.2 41.1 1.0 CG A:HIS390 4.3 33.9 1.0 CD1 A:LEU400 4.4 36.9 1.0 O2 A:PO4504 4.5 67.7 1.0 CG A:LEU400 4.7 34.7 1.0 O A:HOH698 4.8 50.9 1.0

Nickel binding site 2 out of 2 in the Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Helicobacter Pylori CSD3 From the Hexagonal Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni503 b:27.1 occ:0.50 NE2 A:HIS409 1.9 48.4 1.0 NE2 A:HIS407 2.2 47.2 1.0 O4 A:PO4505 2.4 58.8 1.0 CE1 A:HIS409 2.6 53.3 1.0 CD2 A:HIS407 3.1 47.4 1.0 O3 A:PO4505 3.1 62.1 1.0 CE1 A:HIS407 3.1 46.7 1.0 CD2 A:HIS409 3.2 51.3 1.0 P A:PO4505 3.3 63.8 1.0 ND1 A:HIS409 3.8 53.7 1.0 CG A:HIS409 4.1 54.1 1.0 O1 A:PO4505 4.1 60.8 1.0 ND1 A:HIS407 4.2 46.5 1.0 CG A:HIS407 4.2 46.5 1.0 O2 A:PO4505 4.6 70.3 1.0

D.R.An, H.S.Kim, J.Kim, H.N.Im, H.J.Yoon, J.Y.Yoon, J.Y.Jang, D.Hesek, M.Lee, S.Mobashery, S.-J.Kim, B.I.Lee, S.W.Suh. Structure of CSD3 From Helicobacter Pylori, A Cell Shape-Determining Metallopeptidase. Acta Crystallogr.,Sect.D V. 71 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004715000152