Magnesium in PDB 2pun: 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: 2pun 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)	51.17 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	214.730, 83.620, 51.170, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.5

The binding sites of Magnesium atom in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding (pdb code 2pun). 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: 2pun:
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:Mg401 b:39.4 occ:1.00 O2G A:ACP999 2.1 36.0 1.0 O2B A:ACP999 2.1 37.3 1.0 OE1 A:GLU252 2.3 29.6 1.0 OD2 A:ASP250 2.5 35.1 1.0 O A:HOH1086 2.5 33.6 1.0 PG A:ACP999 3.0 33.6 1.0 CD A:GLU252 3.2 29.1 1.0 PB A:ACP999 3.2 34.9 1.0 CG A:ASP250 3.4 32.3 1.0 O1G A:ACP999 3.4 34.3 1.0 O A:HOH1062 3.5 43.3 1.0 C3B A:ACP999 3.5 35.3 1.0 OD1 A:ASP250 3.6 33.2 1.0 ND2 A:ASN44 3.7 37.4 1.0 OE2 A:GLU252 3.7 31.1 1.0 O A:HOH1025 3.8 26.9 1.0 O1B A:ACP999 3.9 32.7 1.0 NZ A:LYS61 4.2 35.8 1.0 O A:HOH1121 4.2 30.4 1.0 O A:HOH1178 4.2 28.2 1.0 CG A:GLU252 4.2 28.9 1.0 O3G A:ACP999 4.4 36.0 1.0 O3A A:ACP999 4.5 33.6 1.0 CB A:ASP250 4.8 29.1 1.0 O A:HOH1039 4.9 22.4 1.0 CG A:ASN44 4.9 38.7 1.0 CB A:GLU252 4.9 27.9 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:Mg401 b:47.1 occ:1.00 O2B B:ACP999 1.9 50.3 1.0 OE1 B:GLU252 2.3 35.9 1.0 O2G B:ACP999 2.3 56.0 1.0 OD2 B:ASP250 2.4 40.7 1.0 CG B:ASP250 3.0 34.4 1.0 OD1 B:ASP250 3.1 37.9 1.0 PG B:ACP999 3.1 55.0 1.0 CD B:GLU252 3.2 31.6 1.0 PB B:ACP999 3.2 51.3 1.0 O1G B:ACP999 3.4 56.2 1.0 C3B B:ACP999 3.4 53.5 1.0 O B:HOH1161 3.5 32.4 1.0 OE2 B:GLU252 3.8 33.8 1.0 NZ B:LYS61 4.0 36.4 1.0 CG B:GLU252 4.1 29.1 1.0 O1B B:ACP999 4.1 50.6 1.0 ND2 B:ASN44 4.1 37.3 1.0 O3A B:ACP999 4.3 49.5 1.0 O B:HOH1010 4.3 22.8 1.0 CB B:ASP250 4.4 30.7 1.0 O3G B:ACP999 4.6 56.2 1.0 O2A B:ACP999 5.0 48.5 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