Magnesium in PDB 1sjn: Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Alpha, Beta-Imido-Dutp

All present enzymatic activity of Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Alpha, Beta-Imido-Dutp:
3.6.1.23;

The structure of Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Alpha, Beta-Imido-Dutp, PDB code: 1sjn 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)	60.86 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.521, 78.506, 94.509, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.8

The binding sites of Magnesium atom in the Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Alpha, Beta-Imido-Dutp (pdb code 1sjn). 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 Alpha, Beta-Imido-Dutp, PDB code: 1sjn:
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 Alpha, Beta-Imido-Dutp


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 Alpha, Beta-Imido-Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg171 b:24.4 occ:1.00 O1B B:DUP3170 2.0 24.3 1.0 O1G B:DUP3170 2.1 27.7 1.0 O1A B:DUP3170 2.1 20.4 1.0 O B:HOH3212 2.1 24.6 1.0 O A:HOH1218 2.2 23.0 1.0 O A:HOH1221 2.2 24.2 1.0 PB B:DUP3170 3.1 23.4 1.0 PA B:DUP3170 3.2 22.1 1.0 PG B:DUP3170 3.3 27.9 1.0 O3B B:DUP3170 3.5 25.6 1.0 N3A B:DUP3170 3.6 21.9 1.0 O B:HOH3214 3.9 33.8 1.0 O3G B:DUP3170 3.9 31.0 1.0 NH2 C:ARG140 4.0 33.5 1.0 NE A:ARG64 4.1 18.0 1.0 O B:HOH3233 4.2 34.1 1.0 OD1 A:ASP28 4.2 21.7 1.0 OD2 A:ASP28 4.2 25.1 1.0 NH2 A:ARG64 4.3 17.9 1.0 O2A B:DUP3170 4.3 19.6 1.0 O5' B:DUP3170 4.3 20.6 1.0 C5' B:DUP3170 4.4 21.9 1.0 O2G B:DUP3170 4.4 27.9 1.0 O2B B:DUP3170 4.5 22.1 1.0 CG A:ASP28 4.7 24.1 1.0 CZ A:ARG64 4.7 16.5 1.0 CB A:ALA20 5.0 38.0 1.0 NE2 A:GLN113 5.0 41.6 1.0

Magnesium binding site 2 out of 3 in the Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Alpha, Beta-Imido-Dutp


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 Alpha, Beta-Imido-Dutp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg171 b:40.0 occ:1.00 O1A B:DUP2170 1.7 24.1 0.7 O2B B:DUP2170 1.9 47.4 0.3 O B:HOH3174 1.9 31.4 1.0 O1B B:DUP2170 2.0 29.1 0.7 O2G B:DUP2170 2.0 49.7 0.3 O1G B:DUP2170 2.0 31.4 0.7 O B:HOH3207 2.0 30.4 1.0 O3B B:DUP2170 2.1 49.2 0.3 O B:HOH3239 2.1 33.1 1.0 PB B:DUP2170 2.2 49.4 0.3 O2A B:DUP2170 2.4 35.1 0.3 PG B:DUP2170 2.6 50.3 0.3 N3A B:DUP2170 2.7 41.0 0.3 PA B:DUP2170 3.0 35.0 0.3 PB B:DUP2170 3.1 29.4 0.7 PA B:DUP2170 3.2 28.6 0.7 PG B:DUP2170 3.3 34.9 0.7 O3B B:DUP2170 3.5 31.1 0.7 O3G B:DUP2170 3.6 50.7 0.3 N3A B:DUP2170 3.6 27.8 0.7 O1G B:DUP2170 3.7 52.1 0.3 O1B B:DUP2170 3.7 49.5 0.3 O B:HOH3236 3.8 38.9 1.0 O5' B:DUP2170 3.8 33.0 0.3 O3G B:DUP2170 4.1 33.7 0.7 O2A B:DUP2170 4.2 24.4 0.7 O5' B:DUP2170 4.2 22.9 0.7 O B:HOH3178 4.3 25.1 1.0 OD1 B:ASP28 4.3 26.1 1.0 O2G B:DUP2170 4.3 34.3 0.7 O1A B:DUP2170 4.3 35.7 0.3 NE B:ARG64 4.5 24.7 1.0 O2B B:DUP2170 4.5 26.6 0.7 OD2 B:ASP28 4.5 29.1 1.0 C5' B:DUP2170 4.6 31.4 0.3 C5' B:DUP2170 4.6 20.2 0.7 NH2 B:ARG64 4.8 27.2 1.0 NE2 B:GLN113 4.9 27.6 1.0 CG B:ASP28 4.9 26.6 1.0 OE1 B:GLN113 5.0 30.2 1.0

Magnesium binding site 3 out of 3 in the Mycobacterium Tuberculosis Dutpase Complexed with Magnesium and Alpha, Beta-Imido-Dutp


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 Alpha, Beta-Imido-Dutp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg171 b:21.8 occ:1.00 O1A A:DUP1170 2.0 20.6 1.0 O1G A:DUP1170 2.0 22.2 1.0 O1B A:DUP1170 2.0 20.8 1.0 O C:HOH192 2.1 22.8 1.0 O C:HOH217 2.1 24.4 1.0 O A:HOH1220 2.1 21.8 1.0 PB A:DUP1170 3.1 22.2 1.0 PG A:DUP1170 3.2 23.8 1.0 PA A:DUP1170 3.3 21.2 1.0 O3B A:DUP1170 3.6 23.7 1.0 N3A A:DUP1170 3.6 21.7 1.0 NH2 B:ARG140 3.9 27.1 1.0 O3G A:DUP1170 3.9 24.8 1.0 OD1 C:ASP28 4.2 34.1 1.0 NE C:ARG64 4.3 21.9 1.0 OD2 C:ASP28 4.3 38.9 1.0 O C:HOH201 4.3 28.0 1.0 O A:HOH1186 4.3 29.4 1.0 O5' A:DUP1170 4.3 19.7 1.0 C5' A:DUP1170 4.3 22.0 1.0 O A:HOH1202 4.3 34.4 1.0 O2A A:DUP1170 4.4 22.4 1.0 O2G A:DUP1170 4.4 22.2 1.0 OE1 C:GLN113 4.4 28.3 1.0 NH2 C:ARG64 4.4 24.3 1.0 O2B A:DUP1170 4.5 20.2 1.0 CG C:ASP28 4.7 31.0 1.0 O A:HOH1217 4.7 31.5 1.0 NE2 C:GLN113 4.7 27.8 1.0 CD C:GLN113 4.8 24.3 1.0 CZ C:ARG64 4.9 25.3 1.0 CB C:ALA20 4.9 34.5 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