Magnesium in PDB 4lps: Crystal Structure of Hypb From Helicobacter Pylori in Complex with Nickel

The structure of Crystal Structure of Hypb From Helicobacter Pylori in Complex with Nickel, PDB code: 4lps was solved by H.Lebrette, A.M.Sydor, R.Ariyakumaran, D.B.Zamble, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.15 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.820, 50.160, 53.680, 102.16, 99.05, 90.65
R / Rfree (%)	17 / 19.6

The structure of Crystal Structure of Hypb From Helicobacter Pylori in Complex with Nickel also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

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

Magnesium binding site 1 out of 2 in the Crystal Structure of Hypb From Helicobacter Pylori in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hypb From Helicobacter Pylori in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:19.6 occ:1.00 O2 A:PO4303 2.2 18.6 1.0 O2B A:GDP302 2.2 8.1 1.0 O A:HOH535 2.3 20.8 1.0 OG1 A:THR60 2.3 18.0 1.0 OE1 A:GLU135 2.4 18.1 1.0 OD2 A:ASP86 2.6 19.5 1.0 CG A:ASP86 2.9 18.3 1.0 OD1 A:ASP86 3.0 23.2 1.0 PB A:GDP302 3.3 14.3 1.0 O1B A:GDP302 3.4 15.0 1.0 CB A:THR60 3.5 11.9 1.0 NZ B:LYS168 3.5 28.8 1.0 CD A:GLU135 3.5 15.9 1.0 P A:PO4303 3.6 20.6 1.0 O B:HOH483 3.9 12.9 1.0 OE2 A:GLU135 4.0 16.0 1.0 CB A:ASP86 4.0 16.8 1.0 N A:THR60 4.0 9.5 1.0 O3B A:GDP302 4.1 15.2 1.0 O1 A:PO4303 4.2 27.6 1.0 O4 A:PO4303 4.2 26.6 1.0 CA A:THR60 4.3 10.2 1.0 O2A A:GDP302 4.4 17.9 1.0 O3A A:GDP302 4.6 18.9 1.0 O3 A:PO4303 4.6 19.0 1.0 CG2 A:THR60 4.6 13.2 1.0 OE2 A:GLU78 4.8 21.6 1.0 CB A:LYS59 4.8 8.5 1.0 NZ A:LYS59 4.8 15.4 1.0 CG A:GLU135 4.8 14.0 1.0 CE A:LYS59 4.8 15.1 1.0 PA A:GDP302 4.9 17.3 1.0 CE B:LYS168 5.0 25.2 1.0 NH2 A:ARG89 5.0 21.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hypb From Helicobacter Pylori in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Hypb From Helicobacter Pylori in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:21.7 occ:0.61 O4 B:PO4303 2.2 33.1 1.0 OG1 B:THR60 2.4 22.8 1.0 O1B B:GDP302 2.5 14.1 1.0 OD2 B:ASP86 2.5 54.7 1.0 OE1 B:GLU135 2.6 21.0 1.0 O B:HOH407 2.7 41.4 1.0 CG B:ASP86 3.2 54.2 1.0 OD1 B:ASP86 3.4 56.1 1.0 O3B B:GDP302 3.5 18.5 1.0 PB B:GDP302 3.5 16.8 1.0 P B:PO4303 3.5 30.0 1.0 CB B:THR60 3.6 20.0 1.0 OE2 B:GLU78 3.7 52.7 1.0 CD B:GLU135 3.8 17.4 1.0 NZ A:LYS168 3.8 40.3 1.0 O2 B:PO4303 4.0 27.1 1.0 O3 B:PO4303 4.0 36.6 1.0 O B:HOH516 4.0 16.1 1.0 OE2 B:GLU135 4.2 23.0 1.0 N B:THR60 4.2 14.2 1.0 O2B B:GDP302 4.3 17.4 1.0 CB B:ASP86 4.3 50.9 1.0 CA B:THR60 4.5 16.8 1.0 O2A B:GDP302 4.6 23.5 1.0 CG2 B:THR60 4.6 16.3 1.0 O1 B:PO4303 4.7 25.1 1.0 O3A B:GDP302 4.8 22.8 1.0 CD B:GLU78 4.9 46.5 1.0 NZ B:LYS59 4.9 18.4 1.0 CE B:LYS59 4.9 18.8 1.0 CE A:LYS168 4.9 37.0 1.0 CB B:LYS59 5.0 15.7 1.0 CG B:GLU135 5.0 11.5 1.0

A.M.Sydor, H.Lebrette, R.Ariyakumaran, C.Cavazza, D.B.Zamble. Relationship Between Ni(II) and Zn(II) Coordination and Nucleotide Binding By the Helicobacter Pylori [Nife]-Hydrogenase and Urease Maturation Factor Hypb. J.Biol.Chem. V. 289 3828 2014.
ISSN: ISSN 0021-9258
PubMed: 24338018
DOI: 10.1074/JBC.M113.502781