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

The structure of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri, PDB code: 4bga 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)	73.568 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.570, 111.670, 87.880, 90.00, 89.55, 90.00
R / Rfree (%)	15.42 / 20.8

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

Potassium

(K)

8 atoms

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

Magnesium binding site 1 out of 3 in the Nucleotide-Bound Open 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 Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1354 b:50.5 occ:1.00 O1B B:ADP1355 2.3 77.4 1.0 O2A B:ADP1355 2.8 58.9 1.0 OD1 B:ASP165 3.1 31.4 1.0 PB B:ADP1355 3.7 99.7 1.0 CG B:ASP165 3.9 32.4 1.0 OE2 B:GLU326 3.9 43.7 1.0 PA B:ADP1355 4.0 62.8 1.0 OD2 B:ASP165 4.0 46.6 1.0 O3A B:ADP1355 4.1 53.0 1.0 O B:HOH2032 4.2 25.5 1.0 O2B B:ADP1355 4.5 36.8 1.0 CA B:GLY167 4.5 23.6 1.0 O B:HOH2024 4.6 36.8 1.0 CA B:GLY297 4.7 12.9 1.0 O3B B:ADP1355 4.8 72.6 1.0 O B:HOH2027 4.8 43.4 1.0 O1A B:ADP1355 4.9 52.2 1.0 N B:GLY167 4.9 20.9 1.0 N B:GLY298 5.0 22.6 1.0

Magnesium binding site 2 out of 3 in the Nucleotide-Bound Open 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 Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1363 b:55.4 occ:1.00 O1A C:ADP1364 2.4 49.3 1.0 O C:HOH2051 3.2 46.1 1.0 OD1 C:ASP165 3.3 34.0 1.0 PA C:ADP1364 3.5 97.1 1.0 O2A C:ADP1364 3.6 32.2 1.0 OE2 C:GLU326 3.7 38.1 1.0 OD2 C:ASP165 3.7 43.7 1.0 CG C:ASP165 3.9 32.0 1.0 O1B C:ADP1364 4.0 98.6 1.0 CA C:GLY297 4.6 26.3 1.0 O3A C:ADP1364 4.6 82.2 1.0 O5' C:ADP1364 4.6 56.3 1.0 CA C:GLY167 4.6 29.9 1.0 O C:HOH2029 4.7 34.0 1.0 N C:GLY298 4.8 28.2 1.0 PB C:ADP1364 4.9 0.7 1.0 CD C:GLU326 4.9 40.7 1.0

Magnesium binding site 3 out of 3 in the Nucleotide-Bound Open 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 Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1355 b:52.9 occ:1.00 O1B D:ADP1356 2.4 75.9 1.0 O2A D:ADP1356 2.8 49.9 1.0 OD1 D:ASP165 3.2 31.4 1.0 PB D:ADP1356 3.7 90.5 1.0 OD2 D:ASP165 3.8 45.3 1.0 CG D:ASP165 3.9 31.8 1.0 OE2 D:GLU326 3.9 33.8 1.0 PA D:ADP1356 4.0 74.1 1.0 O3B D:ADP1356 4.1 82.7 1.0 O3A D:ADP1356 4.2 43.6 1.0 O D:HOH2018 4.2 23.9 1.0 CA D:GLY167 4.6 20.3 1.0 CA D:GLY297 4.7 18.0 1.0 O1A D:ADP1356 4.8 54.8 1.0 N D:GLY298 4.8 17.6 1.0 O2B D:ADP1356 4.9 49.0 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