Magnesium in PDB 3vnp: Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus

The structure of Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus, PDB code: 3vnp was solved by P.P.Karthe, T.S.Kumarevel, S.Kuramitsu, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.978, 58.704, 94.393, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus (pdb code 3vnp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus, PDB code: 3vnp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus


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 Hypothetical Protein (GK2848) From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:23.0 occ:1.00 ND1 A:HIS64 2.3 29.7 1.0 NE2 A:HIS86 2.4 28.1 1.0 O C:HOH326 2.4 35.0 1.0 NE2 C:HIS81 2.5 26.5 1.0 CE1 A:HIS64 3.1 29.2 1.0 CD2 A:HIS86 3.3 27.3 1.0 CE1 C:HIS81 3.4 23.9 1.0 CE1 A:HIS86 3.4 28.2 1.0 CG A:HIS64 3.4 28.1 1.0 CD2 C:HIS81 3.5 23.9 1.0 CB A:HIS64 3.8 27.1 1.0 O C:HOH328 3.9 62.7 1.0 OE1 C:GLN58 3.9 41.0 1.0 OH C:TYR158 3.9 40.8 1.0 O A:GLN65 4.3 28.3 1.0 NE2 A:HIS64 4.3 29.3 1.0 CD2 A:HIS64 4.5 28.4 1.0 CG A:HIS86 4.5 27.0 1.0 ND1 A:HIS86 4.5 27.5 1.0 ND1 C:HIS81 4.5 25.1 1.0 CG C:HIS81 4.6 23.9 1.0 CD C:GLN58 4.9 38.2 1.0 N A:GLN65 4.9 26.0 1.0 CE C:MET98 4.9 28.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus


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 Hypothetical Protein (GK2848) From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:19.9 occ:1.00 ND1 B:HIS64 2.3 24.9 1.0 NE2 B:HIS86 2.3 30.0 1.0 O A:HOH320 2.5 54.0 1.0 NE2 A:HIS81 2.5 27.4 1.0 CD2 B:HIS86 3.1 30.7 1.0 CE1 B:HIS64 3.1 26.4 1.0 CD2 A:HIS81 3.1 26.2 1.0 CE1 B:HIS86 3.4 30.7 1.0 CG B:HIS64 3.4 26.2 1.0 OE1 A:GLN58 3.6 32.5 1.0 CE1 A:HIS81 3.7 27.6 1.0 CB B:HIS64 3.9 25.3 1.0 OH A:TYR158 4.2 43.0 1.0 O B:GLN65 4.2 30.0 1.0 NE2 B:HIS64 4.3 27.5 1.0 CG B:HIS86 4.3 31.3 1.0 CG A:HIS81 4.4 26.5 1.0 ND1 B:HIS86 4.4 31.6 1.0 CD2 B:HIS64 4.5 27.5 1.0 ND1 A:HIS81 4.6 27.6 1.0 CE A:MET98 4.6 28.7 1.0 CD A:GLN58 4.7 29.9 1.0 N B:GLN65 5.0 26.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:21.5 occ:1.00 ND1 C:HIS64 2.3 22.9 1.0 NE2 C:HIS86 2.3 24.8 1.0 NE2 B:HIS81 2.5 26.2 1.0 O B:HOH316 2.6 44.2 1.0 CE1 C:HIS64 3.1 22.6 1.0 CD2 C:HIS86 3.3 24.6 1.0 CE1 B:HIS81 3.3 24.2 1.0 CE1 C:HIS86 3.3 24.9 1.0 CG C:HIS64 3.4 21.8 1.0 CD2 B:HIS81 3.5 22.9 1.0 O C:HOH315 3.5 40.8 1.0 OE1 B:GLN58 3.7 33.9 1.0 CB C:HIS64 3.8 20.6 1.0 OH B:TYR158 4.1 43.2 1.0 O C:GLN65 4.3 20.8 1.0 NE2 C:HIS64 4.3 24.7 1.0 CD2 C:HIS64 4.4 21.2 1.0 ND1 C:HIS86 4.4 26.1 1.0 CG C:HIS86 4.5 25.4 1.0 ND1 B:HIS81 4.5 24.1 1.0 CG B:HIS81 4.6 23.3 1.0 CD B:GLN58 4.7 31.4 1.0 O B:HOH328 4.8 50.2 1.0 CE B:MET98 4.8 22.2 1.0 N C:GLN65 4.8 20.8 1.0

P.P.Karthe, T.S.Kumarevel, S.Kuramitsu, S.Yokoyama. Crystal Structure of Hypothetical Protein (GK2848) From Geobacillus Kaustophilus To Be Published.