Atomistry » Magnesium » PDB 5lmn-5ltt » 5lpg
Atomistry »
  Magnesium »
    PDB 5lmn-5ltt »
      5lpg »

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

Go back to Magnesium Binding Sites List in 5lpg
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

Go back to Magnesium Binding Sites List in 5lpg
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

Go back to Magnesium Binding Sites List in 5lpg
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

Go back to Magnesium Binding Sites List in 5lpg
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

Go back to Magnesium Binding Sites List in 5lpg
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: Sun Sep 29 20:22:05 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy