Magnesium in PDB 1snf: Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate

All present enzymatic activity of Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate:
3.6.1.23;

The structure of Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate, PDB code: 1snf was solved by M.R.Sawaya, S.Chan, B.Segelke, T.Lekin, H.Krupka, U.S.Cho, M.-Y.Kim, M.So, C.-Y.Kim, C.M.Naranjo, Y.C.Rogers, M.S.Park, G.S.Waldo, I.Pashkov, D.Cascio, T.O.Yeates, J.L.Perry, T.C.Terwilliger, D.Eisenberg, Tbstructural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.89 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.228, 77.496, 93.949, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.5

The binding sites of Magnesium atom in the Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate (pdb code 1snf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate, PDB code: 1snf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2171 b:51.6 occ:1.00 O A:HOH2244 1.8 38.5 1.0 O B:HOH3248 2.1 37.8 1.0 O B:HOH3239 2.1 33.0 1.0 O A:HOH2243 2.7 42.2 1.0 OP1 B:UMP2170 3.1 67.5 1.0 O A:HOH2194 3.7 25.8 1.0 O A:HOH2204 3.9 32.2 1.0 OE1 A:GLN113 4.1 25.0 1.0 OD1 A:ASP28 4.2 24.1 1.0 OD2 A:ASP28 4.4 27.2 1.0 P B:UMP2170 4.4 67.1 1.0 OD2 B:ASP83 4.5 12.6 1.0 OD2 A:ASP24 4.5 22.5 1.0 OP2 B:UMP2170 4.6 65.4 1.0 CG A:ASP28 4.7 22.2 1.0 CD A:GLN113 5.0 26.0 1.0

Magnesium binding site 2 out of 3 in the Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3171 b:43.6 occ:1.00 O C:HOH3255 1.9 37.1 1.0 O B:HOH3241 2.0 30.7 1.0 O B:HOH3247 2.0 46.4 1.0 O B:HOH3244 2.3 37.9 1.0 OP3 C:UMP3170 2.4 64.0 1.0 O C:HOH3212 3.3 33.2 1.0 P C:UMP3170 3.6 63.3 1.0 OP2 C:UMP3170 3.8 61.9 1.0 O C:HOH3191 3.8 15.4 1.0 OD2 C:ASP83 4.1 18.4 1.0 OE1 B:GLN113 4.4 28.0 1.0 O5' C:UMP3170 4.5 57.6 1.0 OD1 B:ASP28 4.6 24.8 1.0 OD2 B:ASP24 4.6 22.1 1.0 O B:HOH3199 4.7 25.8 1.0 O B:HOH3242 4.7 40.3 1.0 OD2 B:ASP28 4.7 29.0 1.0 OP1 C:UMP3170 4.8 62.1 1.0 NH1 B:ARG64 4.8 38.4 1.0 C5' C:UMP3170 4.8 50.5 1.0 CD B:GLN113 5.0 24.2 1.0 CG C:ASP83 5.0 13.7 1.0

Magnesium binding site 3 out of 3 in the Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Deoxyuridine 5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1171 b:45.9 occ:1.00 O A:HOH2198 2.0 39.5 1.0 O C:HOH3236 2.0 37.4 1.0 O C:HOH3227 2.1 37.4 1.0 O A:HOH2224 2.2 36.0 1.0 O A:HOH2247 2.3 39.4 1.0 O C:HOH3229 2.4 31.5 1.0 OP3 A:UMP1170 3.6 59.1 1.0 O A:HOH2189 4.2 22.3 1.0 OP1 A:UMP1170 4.2 56.0 1.0 O C:HOH3235 4.2 18.1 1.0 OD1 C:ASP28 4.3 25.2 1.0 OD2 C:ASP28 4.4 24.2 1.0 OD2 C:ASP24 4.5 22.2 1.0 P A:UMP1170 4.5 58.4 1.0 OD2 A:ASP83 4.5 19.3 1.0 OE1 C:GLN113 4.6 25.5 1.0 CG C:ASP28 4.8 22.4 1.0 C5' A:UMP1170 4.9 47.5 1.0 NH2 C:ARG64 4.9 27.5 1.0 O A:HOH2240 5.0 39.4 1.0

S.Chan, B.Segelke, T.Lekin, H.Krupka, U.S.Cho, M.-Y.Kim, M.So, C.-Y.Kim, C.M.Naranjo, Y.C.Rogers, M.S.Park, G.S.Waldo, I.Pashkov, D.Cascio, J.L.Perry, M.R.Sawaya. Crystal Structure of the Mycobacterium Tuberculosis Dutpase: Insights Into the Catalytic Mechanism. J.Mol.Biol. V. 341 503 2004.
ISSN: ISSN 0022-2836
PubMed: 15276840
DOI: 10.1016/J.JMB.2004.06.028