Magnesium in PDB 4to1: Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex
Protein crystallography data
The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex, PDB code: 4to1
was solved by
X.Ji,
C.Tang,
Q.Zhao,
W.Wang,
Y.Xiong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.55
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.204,
141.586,
98.187,
90.00,
115.79,
90.00
|
R / Rfree (%)
|
22.1 /
23.5
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex
(pdb code 4to1). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex, PDB code: 4to1:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 4to1
Go back to
Magnesium Binding Sites List in 4to1
Magnesium binding site 1 out
of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg703
b:28.6
occ:1.00
|
O3G
|
C:GTP706
|
1.9
|
24.7
|
1.0
|
O3G
|
A:DTP702
|
1.9
|
20.4
|
1.0
|
O1B
|
A:DTP702
|
2.0
|
19.1
|
1.0
|
O
|
C:HOH808
|
2.0
|
32.8
|
1.0
|
O2B
|
C:GTP706
|
2.0
|
21.4
|
1.0
|
O1A
|
C:GTP706
|
2.2
|
16.9
|
1.0
|
PG
|
C:GTP706
|
3.2
|
24.6
|
1.0
|
PB
|
C:GTP706
|
3.2
|
20.4
|
1.0
|
PB
|
A:DTP702
|
3.3
|
19.6
|
1.0
|
PG
|
A:DTP702
|
3.3
|
23.1
|
1.0
|
O3B
|
C:GTP706
|
3.5
|
21.9
|
1.0
|
PA
|
C:GTP706
|
3.5
|
18.7
|
1.0
|
NZ
|
B:LYS116
|
3.6
|
62.2
|
1.0
|
O3B
|
A:DTP702
|
3.6
|
21.1
|
1.0
|
O3A
|
C:GTP706
|
3.8
|
20.5
|
1.0
|
O3'
|
C:GTP706
|
3.8
|
19.4
|
1.0
|
NZ
|
A:LYS523
|
3.9
|
51.4
|
1.0
|
O2G
|
C:GTP706
|
4.0
|
25.9
|
1.0
|
O2G
|
A:DTP702
|
4.1
|
21.1
|
1.0
|
O1G
|
C:GTP706
|
4.2
|
24.6
|
1.0
|
C5'
|
C:GTP706
|
4.2
|
20.0
|
1.0
|
O2B
|
A:DTP702
|
4.2
|
20.7
|
1.0
|
O3A
|
A:DTP702
|
4.3
|
18.7
|
1.0
|
O5'
|
C:GTP706
|
4.4
|
19.5
|
1.0
|
O1G
|
A:DTP702
|
4.4
|
21.1
|
1.0
|
O1B
|
C:GTP706
|
4.5
|
23.4
|
1.0
|
C3'
|
C:GTP706
|
4.5
|
20.2
|
1.0
|
O2A
|
C:GTP706
|
4.7
|
17.3
|
1.0
|
CE
|
B:LYS116
|
4.9
|
60.7
|
1.0
|
C4'
|
C:GTP706
|
4.9
|
20.1
|
1.0
|
CE
|
A:LYS523
|
5.0
|
50.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 4to1
Go back to
Magnesium Binding Sites List in 4to1
Magnesium binding site 2 out
of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg704
b:48.7
occ:1.00
|
O2G
|
B:DTP702
|
1.7
|
23.0
|
1.0
|
O1G
|
D:GTP704
|
1.8
|
26.8
|
1.0
|
O1B
|
B:DTP702
|
2.0
|
17.9
|
1.0
|
O
|
A:HOH805
|
2.2
|
48.0
|
1.0
|
O1B
|
D:GTP704
|
2.2
|
20.3
|
1.0
|
O2A
|
D:GTP704
|
2.3
|
18.8
|
1.0
|
PG
|
B:DTP702
|
3.1
|
22.5
|
1.0
|
PG
|
D:GTP704
|
3.2
|
25.7
|
1.0
|
PB
|
B:DTP702
|
3.2
|
17.9
|
1.0
|
PB
|
D:GTP704
|
3.4
|
20.1
|
1.0
|
O3B
|
B:DTP702
|
3.5
|
20.8
|
1.0
|
NZ
|
B:LYS523
|
3.6
|
82.3
|
1.0
|
O3B
|
D:GTP704
|
3.6
|
21.6
|
1.0
|
O1G
|
B:DTP702
|
3.7
|
19.4
|
1.0
|
NZ
|
A:LYS116
|
3.7
|
80.7
|
1.0
|
PA
|
D:GTP704
|
3.7
|
20.4
|
1.0
|
O3A
|
D:GTP704
|
4.0
|
22.1
|
1.0
|
O3'
|
D:GTP704
|
4.0
|
21.9
|
1.0
|
O2G
|
D:GTP704
|
4.1
|
26.5
|
1.0
|
O3G
|
D:GTP704
|
4.1
|
26.3
|
1.0
|
O
|
B:HOH804
|
4.1
|
61.5
|
1.0
|
O3G
|
B:DTP702
|
4.2
|
23.2
|
1.0
|
O2B
|
B:DTP702
|
4.2
|
19.3
|
1.0
|
O3A
|
B:DTP702
|
4.3
|
18.4
|
1.0
|
C5'
|
D:GTP704
|
4.4
|
22.1
|
1.0
|
O5'
|
D:GTP704
|
4.6
|
21.4
|
1.0
|
C3'
|
D:GTP704
|
4.6
|
21.5
|
1.0
|
O2B
|
D:GTP704
|
4.7
|
23.4
|
1.0
|
CE
|
B:LYS523
|
4.7
|
84.2
|
1.0
|
O1A
|
D:GTP704
|
4.9
|
19.9
|
1.0
|
CE
|
A:LYS116
|
5.0
|
79.1
|
1.0
|
C4'
|
D:GTP704
|
5.0
|
21.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 4to1
Go back to
Magnesium Binding Sites List in 4to1
Magnesium binding site 3 out
of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg702
b:32.2
occ:1.00
|
O1B
|
C:DCP701
|
1.8
|
23.5
|
1.0
|
O2B
|
D:GTP701
|
1.9
|
23.8
|
1.0
|
O3G
|
D:GTP701
|
1.9
|
22.9
|
1.0
|
O2G
|
C:DCP701
|
2.0
|
23.8
|
1.0
|
O1A
|
D:GTP701
|
2.1
|
23.7
|
1.0
|
O
|
D:HOH802
|
2.2
|
50.6
|
1.0
|
PB
|
D:GTP701
|
3.1
|
22.6
|
1.0
|
PG
|
D:GTP701
|
3.2
|
24.1
|
1.0
|
PB
|
C:DCP701
|
3.3
|
21.8
|
1.0
|
PG
|
C:DCP701
|
3.3
|
24.1
|
1.0
|
PA
|
D:GTP701
|
3.4
|
23.9
|
1.0
|
O3B
|
D:GTP701
|
3.5
|
22.1
|
1.0
|
NZ
|
D:LYS116
|
3.5
|
64.0
|
1.0
|
O3A
|
D:GTP701
|
3.6
|
23.2
|
1.0
|
O3B
|
C:DCP701
|
3.7
|
24.2
|
1.0
|
NZ
|
C:LYS523
|
3.8
|
69.9
|
1.0
|
O3'
|
D:GTP701
|
3.9
|
28.1
|
1.0
|
O1G
|
C:DCP701
|
4.0
|
25.5
|
1.0
|
C5'
|
D:GTP701
|
4.0
|
27.6
|
1.0
|
O1G
|
D:GTP701
|
4.1
|
23.4
|
1.0
|
O5'
|
D:GTP701
|
4.2
|
25.4
|
1.0
|
O2G
|
D:GTP701
|
4.2
|
23.9
|
1.0
|
O2B
|
C:DCP701
|
4.2
|
21.3
|
1.0
|
O3A
|
C:DCP701
|
4.3
|
21.8
|
1.0
|
O
|
D:HOH803
|
4.4
|
35.4
|
1.0
|
C3'
|
D:GTP701
|
4.4
|
29.0
|
1.0
|
O3G
|
C:DCP701
|
4.5
|
29.0
|
1.0
|
O1B
|
D:GTP701
|
4.5
|
22.0
|
1.0
|
O2A
|
D:GTP701
|
4.6
|
22.8
|
1.0
|
C4'
|
D:GTP701
|
4.7
|
29.5
|
1.0
|
O
|
D:HOH801
|
4.8
|
53.8
|
1.0
|
CE
|
D:LYS116
|
4.8
|
62.4
|
1.0
|
CE
|
C:LYS523
|
5.0
|
70.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 4to1
Go back to
Magnesium Binding Sites List in 4to1
Magnesium binding site 4 out
of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg703
b:15.9
occ:1.00
|
O1G
|
C:GTP704
|
1.8
|
28.3
|
1.0
|
O1B
|
D:DCP702
|
1.9
|
18.1
|
1.0
|
O2G
|
D:DCP702
|
1.9
|
17.9
|
1.0
|
O1B
|
C:GTP704
|
2.0
|
25.8
|
1.0
|
O1A
|
C:GTP704
|
2.2
|
26.9
|
1.0
|
O
|
C:HOH821
|
2.2
|
74.7
|
1.0
|
PG
|
C:GTP704
|
3.1
|
30.2
|
1.0
|
PB
|
C:GTP704
|
3.1
|
26.4
|
1.0
|
PB
|
D:DCP702
|
3.3
|
18.1
|
1.0
|
PG
|
D:DCP702
|
3.3
|
18.0
|
1.0
|
O3B
|
C:GTP704
|
3.3
|
28.0
|
1.0
|
PA
|
C:GTP704
|
3.4
|
25.4
|
1.0
|
NZ
|
C:LYS116
|
3.5
|
92.6
|
1.0
|
O3A
|
C:GTP704
|
3.6
|
25.4
|
1.0
|
O3B
|
D:DCP702
|
3.7
|
18.3
|
1.0
|
NZ
|
D:LYS523
|
3.8
|
96.6
|
1.0
|
O3G
|
C:GTP704
|
4.0
|
31.2
|
1.0
|
O1G
|
D:DCP702
|
4.1
|
16.4
|
1.0
|
O3'
|
C:GTP704
|
4.1
|
23.5
|
1.0
|
O2G
|
C:GTP704
|
4.1
|
28.5
|
1.0
|
C5'
|
C:GTP704
|
4.2
|
24.7
|
1.0
|
O2B
|
D:DCP702
|
4.3
|
17.4
|
1.0
|
O3A
|
D:DCP702
|
4.3
|
17.9
|
1.0
|
O5'
|
C:GTP704
|
4.3
|
25.1
|
1.0
|
O3G
|
D:DCP702
|
4.4
|
19.5
|
1.0
|
O2B
|
C:GTP704
|
4.5
|
26.3
|
1.0
|
O
|
C:HOH822
|
4.5
|
53.4
|
1.0
|
O2A
|
C:GTP704
|
4.5
|
25.5
|
1.0
|
C3'
|
C:GTP704
|
4.7
|
23.7
|
1.0
|
CE
|
C:LYS116
|
4.8
|
88.7
|
1.0
|
CE
|
D:LYS523
|
4.9
|
0.3
|
1.0
|
C4'
|
C:GTP704
|
5.0
|
24.1
|
1.0
|
|
Reference:
X.Ji,
C.Tang,
Q.Zhao,
W.Wang,
Y.Xiong.
Structural Basis of Cellular Dntp Regulation By SAMHD1. Proc.Natl.Acad.Sci.Usa V. 111 E4305 2014.
ISSN: ESSN 1091-6490
PubMed: 25267621
DOI: 10.1073/PNAS.1412289111
Page generated: Tue Aug 20 04:08:35 2024
|