Magnesium in PDB 2pul: Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding

All present enzymatic activity of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding:
2.7.1.100;

The structure of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding, PDB code: 2pul was solved by S.-Y.Ku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.80 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	214.150, 83.470, 51.260, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24

The binding sites of Magnesium atom in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding (pdb code 2pul). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding, PDB code: 2pul:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:35.7 occ:1.00 O2B A:ACP999 2.1 31.6 1.0 OE1 A:GLU252 2.2 27.3 1.0 O2G A:ACP999 2.2 35.1 1.0 OD2 A:ASP250 2.3 26.7 1.0 O A:HOH1212 2.3 29.0 1.0 CD A:GLU252 3.0 27.2 1.0 PG A:ACP999 3.1 35.5 1.0 CG A:ASP250 3.2 23.4 1.0 PB A:ACP999 3.3 31.3 1.0 O1G A:ACP999 3.4 34.0 1.0 OD1 A:ASP250 3.4 25.9 1.0 O A:HOH1179 3.5 38.8 1.0 OE2 A:GLU252 3.6 28.1 1.0 C3B A:ACP999 3.6 33.5 1.0 ND2 A:ASN44 3.7 30.5 1.0 O1B A:ACP999 4.0 30.0 1.0 NZ A:LYS61 4.1 26.9 1.0 CG A:GLU252 4.1 23.2 1.0 O A:HOH1213 4.4 40.7 1.0 O3A A:ACP999 4.5 28.1 1.0 O A:HOH1210 4.5 25.7 1.0 O3G A:ACP999 4.5 37.2 1.0 CB A:ASP250 4.5 21.8 1.0 CB A:GLU252 4.8 22.4 1.0 O A:HOH1197 4.9 36.9 1.0 CG A:ASN44 5.0 33.6 1.0

Magnesium binding site 2 out of 2 in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:47.6 occ:1.00 O2B B:ACP999 2.2 45.7 1.0 OE1 B:GLU252 2.2 36.1 1.0 OD2 B:ASP250 2.3 29.3 1.0 O2G B:ACP999 2.3 49.7 1.0 OD1 B:ASP250 2.7 27.4 1.0 CG B:ASP250 2.8 25.5 1.0 CD B:GLU252 3.0 34.6 1.0 PG B:ACP999 3.5 47.7 1.0 PB B:ACP999 3.5 45.8 1.0 OE2 B:GLU252 3.6 37.3 1.0 C3B B:ACP999 3.8 46.9 1.0 CG B:GLU252 3.9 27.8 1.0 ND2 B:ASN44 3.9 35.0 1.0 NZ B:LYS61 4.0 29.6 1.0 O1G B:ACP999 4.1 48.7 1.0 O B:HOH1263 4.1 37.4 1.0 O B:HOH1000 4.2 44.1 1.0 CB B:ASP250 4.2 22.2 1.0 O B:HOH1001 4.2 40.6 1.0 CB B:GLU252 4.3 23.1 1.0 O1B B:ACP999 4.5 44.6 1.0 O3A B:ACP999 4.5 45.5 1.0 O3G B:ACP999 4.7 48.9 1.0 CE B:LYS61 4.9 30.7 1.0

S.-Y.Ku, P.Yip, K.A.Cornell, M.K.Riscoe, J.-B.Behr, G.Guillerm, P.L.Howell. Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding J.Biol.Chem. V. 282 22195 2007.
ISSN: ISSN 0021-9258
PubMed: 17522047
DOI: 10.1074/JBC.M611045200