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Magnesium in PDB 5lpg: Structure of NUDT15 in Complex with 6-Thio-Gmp

Enzymatic activity of Structure of NUDT15 in Complex with 6-Thio-Gmp

All present enzymatic activity of Structure of NUDT15 in Complex with 6-Thio-Gmp:
3.6.1.55;

Protein crystallography data

The structure of Structure of NUDT15 in Complex with 6-Thio-Gmp, PDB code: 5lpg was solved by G.Masuyer, M.Carter, D.Rehling, P.Stenmark, T.Helleday, A.-S.Jemth, N.C.K.Valerie, E.Homan, P.Herr, L.Bevc, B.D.G.Page, A.Hagenkort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.502, 49.050, 135.560, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of NUDT15 in Complex with 6-Thio-Gmp (pdb code 5lpg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of NUDT15 in Complex with 6-Thio-Gmp, PDB code: 5lpg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5lpg

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Magnesium binding site 1 out of 5 in the Structure of NUDT15 in Complex with 6-Thio-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of NUDT15 in Complex with 6-Thio-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:37.2
occ:1.00
 O A:HOH1210 2.0 32.4 1.0
O A:HOH1211 2.1 29.9 1.0
O A:HOH1228 2.1 32.1 1.0
OE2 A:GLU67 2.1 41.9 1.0
OE1 A:GLU63 2.2 27.6 1.0
O A:HOH1263 2.4 35.9 1.0
CD A:GLU63 3.1 32.7 1.0
CD A:GLU67 3.2 39.6 1.0
OE2 A:GLU63 3.3 27.8 1.0
O A:GLY47 3.6 28.7 1.0
O A:HOH1237 3.7 39.1 1.0
CG A:GLU67 3.8 34.1 1.0
OE1 A:GLU67 4.1 40.6 1.0
OE1 A:GLU113 4.2 45.1 1.0
OE1 A:GLU66 4.4 32.9 1.0
CG A:GLU63 4.5 26.8 1.0
O3A A:71V1102 4.5 89.1 1.0
O2A A:71V1102 4.5 71.2 1.0
C A:GLY47 4.6 27.3 1.0
OE2 A:GLU113 4.6 44.8 1.0
CA A:GLY48 4.7 28.5 1.0
CD A:GLU113 4.9 45.0 1.0
CB A:GLU63 4.9 25.3 1.0

Magnesium binding site 2 out of 5 in 5lpg

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Magnesium binding site 2 out of 5 in the Structure of NUDT15 in Complex with 6-Thio-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of NUDT15 in Complex with 6-Thio-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1101

b:35.5
occ:1.00
 O B:HOH1230 2.0 29.9 1.0
O B:HOH1215 2.1 29.4 1.0
O B:HOH1209 2.1 34.6 1.0
OE1 B:GLU63 2.1 26.1 1.0
O B:HOH1267 2.2 29.9 1.0
OE2 B:GLU67 2.2 31.4 1.0
CD B:GLU63 3.1 28.1 1.0
MG B:MG1102 3.2 30.9 1.0
CD B:GLU67 3.2 32.0 1.0
MG B:MG1103 3.3 31.5 1.0
OE2 B:GLU63 3.4 27.5 1.0
CG B:GLU67 3.6 32.3 1.0
MG B:MG1104 3.7 42.3 1.0
O B:HOH1254 3.7 31.5 1.0
O B:HOH1283 3.7 33.6 1.0
O B:HOH1243 3.8 37.1 1.0
O B:HOH1277 3.9 52.1 1.0
O B:GLY47 4.0 24.9 1.0
OE1 B:GLU113 4.0 33.9 1.0
OE1 B:GLU66 4.1 34.3 1.0
OE2 B:GLU113 4.3 34.9 1.0
OE1 B:GLU67 4.3 27.0 1.0
CG B:GLU63 4.5 26.2 1.0
O B:HOH1220 4.5 40.2 1.0
CD B:GLU113 4.6 36.6 1.0
CB B:GLU63 4.9 28.3 1.0
C B:GLY47 4.9 25.3 1.0
O B:HOH1227 4.9 27.4 1.0
CA B:GLY48 4.9 25.9 1.0
O B:HOH1257 4.9 30.6 1.0

Magnesium binding site 3 out of 5 in 5lpg

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Magnesium binding site 3 out of 5 in the Structure of NUDT15 in Complex with 6-Thio-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of NUDT15 in Complex with 6-Thio-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:30.9
occ:1.00
 O B:HOH1215 1.9 29.4 1.0
O B:HOH1257 2.1 30.6 1.0
O B:HOH1227 2.1 27.4 1.0
O B:GLY47 2.1 24.9 1.0
O B:HOH1254 2.2 31.5 1.0
OE2 B:GLU67 2.2 31.4 1.0
CD B:GLU67 3.1 32.0 1.0
MG B:MG1101 3.2 35.5 1.0
MG B:MG1103 3.2 31.5 1.0
C B:GLY47 3.3 25.3 1.0
OE1 B:GLU67 3.4 27.0 1.0
O B:HOH1209 3.7 34.6 1.0
OE1 B:GLU63 3.8 26.1 1.0
CA B:GLY48 3.9 25.9 1.0
O B:HOH1264 4.0 35.9 1.0
N B:GLY48 4.1 25.5 1.0
O B:HOH1248 4.1 34.9 1.0
O B:HOH1278 4.3 37.9 1.0
NH1 B:ARG34 4.3 52.8 1.0
N B:GLY47 4.3 25.3 1.0
O B:HOH1270 4.4 34.3 1.0
CA B:GLY47 4.4 26.7 1.0
O B:HOH1283 4.5 33.6 1.0
CG B:GLU67 4.5 32.3 1.0
O B:HOH1243 4.6 37.1 1.0
OE1 B:GLN44 4.6 36.9 1.0
CD B:GLU63 4.6 28.1 1.0
O B:HOH1267 4.8 29.9 1.0
O B:HOH1230 5.0 29.9 1.0

Magnesium binding site 4 out of 5 in 5lpg

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Magnesium binding site 4 out of 5 in the Structure of NUDT15 in Complex with 6-Thio-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of NUDT15 in Complex with 6-Thio-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:31.5
occ:1.00
 O B:HOH1215 1.7 29.4 1.0
O B:HOH1243 1.7 37.1 1.0
O B:HOH1283 1.8 33.6 1.0
O B:HOH1264 1.9 35.9 1.0
O B:HOH1267 3.2 29.9 1.0
MG B:MG1102 3.2 30.9 1.0
O B:HOH1257 3.3 30.6 1.0
MG B:MG1101 3.3 35.5 1.0
MG B:MG1104 3.3 42.3 1.0
CA B:GLY48 3.4 25.9 1.0
N B:HIS49 3.8 25.8 1.0
ND1 B:HIS49 3.9 43.9 1.0
O B:HOH1254 3.9 31.5 1.0
OE2 B:GLU63 4.0 27.5 1.0
O A:HOH1271 4.0 34.6 1.0
O B:HOH1209 4.0 34.6 1.0
O B:GLY47 4.1 24.9 1.0
OE1 B:GLU63 4.1 26.1 1.0
C B:GLY48 4.2 26.8 1.0
O B:HOH1277 4.2 52.1 1.0
O B:HOH1271 4.3 44.4 1.0
CD B:GLU63 4.3 28.1 1.0
OE2 B:GLU67 4.4 31.4 1.0
O B:HOH1214 4.5 30.1 1.0
O B:HOH1270 4.5 34.3 1.0
N B:GLY48 4.6 25.5 1.0
CE1 B:HIS49 4.6 46.4 1.0
C B:GLY47 4.7 25.3 1.0
CG B:HIS49 5.0 40.3 1.0

Magnesium binding site 5 out of 5 in 5lpg

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Magnesium binding site 5 out of 5 in the Structure of NUDT15 in Complex with 6-Thio-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of NUDT15 in Complex with 6-Thio-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:42.3
occ:1.00
 O B:HOH1214 1.9 30.1 1.0
O B:HOH1243 2.0 37.1 1.0
OE2 B:GLU63 2.1 27.5 1.0
O B:HOH1220 2.2 40.2 1.0
O B:HOH1267 2.2 29.9 1.0
O A:HOH1271 2.3 34.6 1.0
CD B:GLU63 3.2 28.1 1.0
MG B:MG1103 3.3 31.5 1.0
O B:HOH1283 3.5 33.6 1.0
MG B:MG1101 3.7 35.5 1.0
OE1 B:GLU63 3.7 26.1 1.0
NH1 B:ARG62 3.8 33.7 1.0
O B:HOH1215 3.8 29.4 1.0
OE2 B:GLU51 4.1 46.5 1.0
N B:HIS49 4.1 25.8 1.0
OE1 B:GLU66 4.3 34.3 1.0
O B:HIS49 4.4 23.9 1.0
NH2 B:ARG62 4.4 31.8 1.0
CG B:GLU63 4.5 26.2 1.0
CA B:GLY48 4.6 25.9 1.0
CZ B:ARG62 4.6 30.2 1.0
O B:HOH1230 4.6 29.9 1.0
O B:HOH1277 4.7 52.1 1.0
C B:GLY48 4.8 26.8 1.0
CB B:HIS49 4.8 32.6 1.0
O B:HOH1264 4.9 35.9 1.0
CA B:HIS49 4.9 29.3 1.0

Reference:

N.C.Valerie, A.Hagenkort, B.D.Page, G.Masuyer, D.Rehling, M.Carter, L.Bevc, P.Herr, E.Homan, N.G.Sheppard, P.Stenmark, A.S.Jemth, T.Helleday. NUDT15 Hydrolyzes 6-Thio-Deoxygtp to Mediate the Anticancer Efficacy of 6-Thioguanine. Cancer Res. V. 76 5501 2016.
ISSN: ESSN 1538-7445
PubMed: 27530327
DOI: 10.1158/0008-5472.CAN-16-0584
Page generated: Mon Dec 14 20:48:47 2020

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