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Magnesium in PDB 4mz7: Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase

Protein crystallography data

The structure of Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase, PDB code: 4mz7 was solved by C.Zhu, W.Gao, K.Zhao, X.Qin, Y.Zhang, X.Peng, L.Zhang, Y.Dong, W.Zhang, P.Li, W.Wei, Y.Gong, X.F.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.404, 103.608, 92.134, 90.00, 121.98, 90.00
R / Rfree (%) 19.4 / 22.6

Other elements in 4mz7:

The structure of Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase (pdb code 4mz7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase, PDB code: 4mz7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4mz7

Go back to Magnesium Binding Sites List in 4mz7
Magnesium binding site 1 out of 2 in the Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:16.6
occ:1.00
O1G B:DTP805 2.0 10.2 1.0
O2G A:DGT704 2.1 14.0 1.0
O2B B:DTP805 2.1 8.6 1.0
O A:HOH1038 2.1 6.3 1.0
O1B A:DGT704 2.2 10.4 1.0
O1A A:DGT704 2.3 8.6 1.0
PB A:DGT704 3.2 12.6 1.0
PB B:DTP805 3.3 9.1 1.0
PG A:DGT704 3.3 15.6 1.0
PG B:DTP805 3.3 11.1 1.0
PA A:DGT704 3.5 10.2 1.0
O3B A:DGT704 3.5 14.3 1.0
O3B B:DTP805 3.6 11.0 1.0
O3A A:DGT704 3.7 10.7 1.0
NZ A:LYS116 3.9 14.1 1.0
O3' A:DGT704 3.9 8.5 1.0
O2G B:DTP805 4.0 12.2 1.0
O1B B:DTP805 4.1 9.6 1.0
C5' A:DGT704 4.2 8.5 1.0
O3G A:DGT704 4.2 15.1 1.0
O1G A:DGT704 4.2 16.0 1.0
O A:HOH871 4.3 23.1 1.0
O3A B:DTP805 4.3 8.9 1.0
O B:HOH1071 4.3 27.0 1.0
O5' A:DGT704 4.4 9.3 1.0
O3G B:DTP805 4.4 11.6 1.0
C3' A:DGT704 4.5 8.6 1.0
O A:HOH804 4.5 9.9 1.0
O2B A:DGT704 4.6 12.0 1.0
O2A A:DGT704 4.6 9.5 1.0
O A:HOH939 4.7 27.8 1.0
C4' A:DGT704 4.9 8.3 1.0
CE A:LYS116 5.0 14.8 1.0

Magnesium binding site 2 out of 2 in 4mz7

Go back to Magnesium Binding Sites List in 4mz7
Magnesium binding site 2 out of 2 in the Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:19.3
occ:1.00
O2G B:DGT801 2.0 20.2 1.0
O2B A:DGT703 2.1 12.3 1.0
O3G A:DGT703 2.1 15.2 1.0
O1B B:DGT801 2.1 14.7 1.0
O1A B:DGT801 2.2 12.3 1.0
O B:HOH1241 2.2 9.3 1.0
PB B:DGT801 3.1 17.8 1.0
PG B:DGT801 3.2 20.2 1.0
PB A:DGT703 3.2 11.6 1.0
PG A:DGT703 3.3 14.4 1.0
PA B:DGT801 3.4 13.6 1.0
O3B B:DGT801 3.5 19.1 1.0
O3A B:DGT801 3.6 15.4 1.0
O3B A:DGT703 3.6 14.7 1.0
NZ B:LYS116 3.8 19.2 1.0
O3' B:DGT801 4.0 10.2 1.0
O1G A:DGT703 4.1 13.5 1.0
O1B A:DGT703 4.1 11.6 1.0
C5' B:DGT801 4.2 9.7 1.0
O B:HOH1258 4.2 34.8 1.0
O1G B:DGT801 4.2 22.5 1.0
O3G B:DGT801 4.2 19.6 1.0
O A:HOH900 4.2 24.6 1.0
O B:HOH1033 4.3 30.7 1.0
O5' B:DGT801 4.3 10.9 1.0
O3A A:DGT703 4.3 11.3 1.0
O2B B:DGT801 4.5 19.2 1.0
O2G A:DGT703 4.5 15.9 1.0
C3' B:DGT801 4.5 10.3 1.0
O2A B:DGT801 4.5 13.7 1.0
O B:HOH916 4.6 12.6 1.0
C4' B:DGT801 4.9 10.0 1.0

Reference:

C.Zhu, W.Gao, K.Zhao, X.Qin, Y.Zhang, X.Peng, L.Zhang, Y.Dong, W.Zhang, P.Li, W.Wei, Y.Gong, X.F.Yu. Structural Insight Into Dgtp-Dependent Activation of Tetrameric SAMHD1 Deoxynucleoside Triphosphate Triphosphohydrolase Nat Commun V. 4 2722 2013.
ISSN: ESSN 2041-1723
PubMed: 24217394
DOI: 10.1038/NCOMMS3722
Page generated: Mon Dec 14 19:13:27 2020

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