Magnesium in PDB 2oek: Crystal Structure of A Rubisco-Like Protein From Geobacillus Kaustophilus Liganded with MG2+ Ions

The structure of Crystal Structure of A Rubisco-Like Protein From Geobacillus Kaustophilus Liganded with MG2+ Ions, PDB code: 2oek was solved by A.A.Fedorov, H.J.Imker, E.V.Fedorov, S.C.Almo, J.A.Gerlt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.83 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.765, 59.545, 109.282, 90.00, 103.24, 90.00
R / Rfree (%)	18.5 / 20.8

The binding sites of Magnesium atom in the Crystal Structure of A Rubisco-Like Protein From Geobacillus Kaustophilus Liganded with MG2+ Ions (pdb code 2oek). 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 A Rubisco-Like Protein From Geobacillus Kaustophilus Liganded with MG2+ Ions, PDB code: 2oek:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Rubisco-Like Protein From Geobacillus Kaustophilus Liganded with MG2+ Ions


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 A Rubisco-Like Protein From Geobacillus Kaustophilus Liganded with MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:17.8 occ:1.00 OD1 A:ASP175 2.2 10.8 1.0 OQ2 A:KCX173 2.2 10.2 1.0 OE1 A:GLU176 2.3 11.4 1.0 O A:HOH1174 2.3 13.3 1.0 O A:HOH1173 2.3 18.8 1.0 O A:HOH1175 2.4 12.5 1.0 CD A:GLU176 3.2 11.7 1.0 CG A:ASP175 3.2 12.6 1.0 CX A:KCX173 3.2 10.1 1.0 OE2 A:GLU176 3.4 13.6 1.0 OQ1 A:KCX173 3.5 11.6 1.0 O A:HOH984 3.8 14.9 1.0 OD2 A:ASP175 3.8 14.2 1.0 N A:GLU176 3.8 9.3 1.0 CA A:ASP175 4.2 10.1 1.0 CB A:ASP175 4.3 11.9 1.0 O A:HOH1072 4.4 23.3 1.0 NZ A:KCX173 4.4 11.5 1.0 C A:ASP175 4.5 9.4 1.0 CG A:GLU176 4.5 11.6 1.0 O A:HOH960 4.7 12.5 1.0 NE2 A:HIS264 4.7 7.8 1.0 CB A:GLU176 4.7 8.5 1.0 CD B:LYS98 4.8 16.9 1.0 CG2 A:ILE145 4.8 13.8 1.0 CD1 A:ILE145 4.8 14.2 1.0 CA A:GLU176 4.8 9.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Rubisco-Like Protein From Geobacillus Kaustophilus Liganded with MG2+ Ions


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 A Rubisco-Like Protein From Geobacillus Kaustophilus Liganded with MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:11.8 occ:1.00 OQ2 B:KCX173 2.1 7.8 1.0 OE1 B:GLU176 2.2 8.0 1.0 OD1 B:ASP175 2.2 8.1 1.0 O B:HOH1245 2.3 9.7 1.0 O B:HOH1243 2.3 9.7 1.0 O B:HOH1244 2.3 12.8 1.0 CX B:KCX173 3.1 9.3 1.0 CD B:GLU176 3.1 8.6 1.0 CG B:ASP175 3.3 11.3 1.0 OQ1 B:KCX173 3.4 8.8 1.0 OE2 B:GLU176 3.4 10.6 1.0 N B:GLU176 3.8 8.2 1.0 O B:HOH961 3.9 11.8 1.0 OD2 B:ASP175 3.9 12.0 1.0 CA B:ASP175 4.2 8.7 1.0 NZ B:KCX173 4.3 7.1 1.0 CB B:ASP175 4.3 8.7 1.0 CG B:GLU176 4.5 8.6 1.0 C B:ASP175 4.5 7.8 1.0 O B:HOH974 4.5 16.8 1.0 O B:HOH989 4.5 11.1 1.0 NE2 B:HIS264 4.6 5.8 1.0 O B:HOH1168 4.6 27.2 1.0 CB B:GLU176 4.7 7.2 1.0 CD1 B:ILE145 4.7 8.0 1.0 CG2 B:ILE145 4.8 6.7 1.0 CD A:LYS98 4.8 12.5 1.0 CA B:GLU176 4.8 8.3 1.0

H.J.Imker, A.A.Fedorov, E.V.Fedorov, S.C.Almo, J.A.Gerlt. Mechanistic Diversity in the Rubisco Superfamily: the "Enolase" in the Methionine Salvage Pathway in Geobacillus Kaustophilus. Biochemistry V. 46 4077 2007.
ISSN: ISSN 0006-2960
PubMed: 17352497
DOI: 10.1021/BI7000483