Magnesium in PDB 4bgb: Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri

The structure of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri, PDB code: 4bgb was solved by M.Schacherl, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.147 / 1.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.790, 108.540, 117.350, 90.00, 90.00, 90.00
R / Rfree (%)	15.76 / 18.28

The structure of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri also contains other interesting chemical elements:

Potassium	(K)	5 atoms
Calcium	(Ca)	1 atom

The binding sites of Magnesium atom in the Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (pdb code 4bgb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri, PDB code: 4bgb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1358 b:18.2 occ:0.57 O A:HOH2125 2.4 43.0 1.0 O2B A:ADP1352 2.5 17.1 0.5 O A:HOH2123 2.6 29.8 1.0 OD2 A:ASP165 2.6 26.8 1.0 O A:HOH2127 2.8 36.0 1.0 O A:HOH2202 2.9 25.9 1.0 O A:HOH2102 3.0 42.0 1.0 O A:HOH2103 3.4 38.2 1.0 O A:HOH2223 3.5 37.0 1.0 PB A:ADP1352 3.6 29.3 0.5 CG A:ASP165 3.7 22.2 1.0 O A:HOH2126 3.8 18.1 1.0 O1B A:ADP1352 3.9 30.7 0.5 O3A A:ADP1352 4.4 28.4 0.5 CB A:ASP165 4.5 19.5 1.0 O1A A:ADP1352 4.5 48.5 0.5 OD1 A:ASP165 4.5 24.3 1.0 CA A:GLY167 4.5 23.5 1.0 O2A A:ADP1352 4.5 21.9 0.5 O2A A:ADP1352 4.6 45.7 0.5 N A:GLY167 4.6 22.2 1.0 O A:ASP165 4.6 20.4 1.0 O A:HOH2128 4.7 32.1 1.0 O3B A:ADP1352 4.7 24.4 0.5 OE2 A:GLU326 4.7 19.8 1.0 O A:MET169 4.8 20.5 0.5 O1B A:ADP1352 4.9 31.7 0.5 O A:MET169 4.9 18.8 0.5 C A:ASP165 5.0 20.1 1.0

Magnesium binding site 2 out of 4 in the Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1359 b:21.8 occ:1.00 OD1 B:ASP165 2.4 23.7 1.0 O B:HOH2005 2.6 28.9 1.0 O1B B:ADP1352 2.7 24.3 1.0 O2A B:ADP1352 2.7 17.4 1.0 O B:HOH2132 2.9 26.3 1.0 CG B:ASP165 3.5 22.3 1.0 O3A B:ADP1352 3.6 17.1 1.0 PA B:ADP1352 3.7 14.2 1.0 PB B:ADP1352 3.7 13.9 1.0 CA B:GLY167 3.9 13.5 1.0 CG B:GLU326 4.1 14.8 1.0 OD2 B:ASP165 4.2 23.3 1.0 N B:GLY167 4.2 13.5 1.0 OE2 B:GLU326 4.3 15.2 1.0 C1 B:GOL1356 4.3 22.1 0.5 O2B B:ADP1352 4.3 26.1 1.0 NE2 B:GLN44 4.4 22.3 0.5 O B:HOH2269 4.6 31.3 1.0 CB B:ASP165 4.6 16.7 1.0 O1A B:ADP1352 4.6 17.6 1.0 C2 B:GOL1356 4.6 21.5 0.5 CD B:GLU326 4.7 14.3 1.0 O B:HOH2134 4.7 27.5 1.0 CA B:GLY297 4.7 12.6 1.0 C B:VAL166 4.7 11.7 1.0 O B:HOH2133 4.7 28.3 1.0 O5' B:ADP1352 4.9 14.9 1.0 O B:VAL166 4.9 13.5 1.0 O3B B:ADP1352 4.9 16.6 1.0 O1 B:GOL1356 5.0 34.5 0.5 O B:HOH2006 5.0 17.4 1.0 OE1 B:GLN44 5.0 13.8 0.5

Magnesium binding site 3 out of 4 in the Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1360 b:28.2 occ:1.00 O1A B:ADP1352 2.2 17.6 1.0 O B:HOH2012 2.3 29.8 1.0 O B:HOH2004 2.3 30.0 0.4 O B:HOH2015 2.4 43.7 1.0 C3 B:GOL1356 2.5 29.7 0.5 O2 B:GOL1356 2.6 17.2 0.5 C2 B:GOL1356 2.8 21.5 0.5 O3 B:GOL1356 2.8 31.3 0.5 O B:HOH2014 3.0 38.6 1.0 O B:HOH2292 3.4 38.5 1.0 O B:HOH2291 3.6 33.4 1.0 PA B:ADP1352 3.7 14.2 1.0 OG1 B:THR48 4.0 11.3 0.5 OD1 B:ASP51 4.3 22.3 1.0 C1 B:GOL1356 4.3 22.1 0.5 O3B B:ADP1352 4.3 16.6 1.0 OD2 B:ASP51 4.4 23.1 1.0 O B:HOH2018 4.4 42.9 1.0 O3A B:ADP1352 4.5 17.1 1.0 CA B:GLY49 4.5 13.4 1.0 O2A B:ADP1352 4.6 17.4 1.0 CG B:ASP51 4.6 21.4 1.0 C5' B:ADP1352 4.6 14.3 1.0 N B:GLY49 4.6 13.5 1.0 O5' B:ADP1352 4.7 14.9 1.0 C B:GLY49 4.9 12.6 1.0 O B:GLY49 4.9 13.7 1.0 PB B:ADP1352 4.9 13.9 1.0

Magnesium binding site 4 out of 4 in the Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1361 b:26.8 occ:1.00 OE2 B:GLU217 2.3 21.8 0.5 O B:HOH2172 2.4 30.0 1.0 O3 B:GOL1355 2.5 48.1 1.0 O B:GLU215 2.6 28.2 1.0 OE1 B:GLU217 2.6 23.4 0.5 O2 B:GOL1355 2.7 55.6 1.0 CD B:GLU217 2.8 22.4 0.5 O B:HOH2177 3.1 47.7 1.0 C2 B:GOL1355 3.4 54.7 1.0 C3 B:GOL1355 3.5 52.2 1.0 C B:GLU215 3.7 25.3 1.0 CG B:GLU217 3.8 24.0 0.5 O B:HOH2171 3.9 34.8 1.0 CA B:GLY216 4.1 20.9 1.0 OE2 B:GLU217 4.1 25.2 0.5 C B:GLY216 4.1 21.3 1.0 CG B:GLU217 4.3 22.6 0.5 N B:GLY216 4.4 22.1 1.0 O B:GLY216 4.4 22.6 1.0 CD B:GLU217 4.5 24.6 0.5 N B:GLU217 4.5 20.4 0.5 N B:GLU217 4.5 21.0 0.5 C1 B:GOL1355 4.8 54.4 1.0 CA B:GLU215 4.9 25.9 1.0 CB B:GLU217 4.9 23.1 0.5 OD1 B:ASP268 4.9 20.0 1.0

M.Schacherl, S.M.Waltersperger, U.Baumann. Structural Characterization of the Ribonuclease H-Like Type Askha Superfamily Kinase MK0840 From Methanopyrus Kandleri Acta Crystallogr.,Sect.D V. 69 2440 2013.
ISSN: ISSN 0907-4449
PubMed: 24311585
DOI: 10.1107/S0907444913022683