Manganese in PDB 6oix: Structure of Escherichia Coli Dgtpase Bound to Gtp
Enzymatic activity of Structure of Escherichia Coli Dgtpase Bound to Gtp
All present enzymatic activity of Structure of Escherichia Coli Dgtpase Bound to Gtp:
3.1.5.1;
Protein crystallography data
The structure of Structure of Escherichia Coli Dgtpase Bound to Gtp, PDB code: 6oix
was solved by
C.O.Barnes,
Y.Wu,
G.Calero,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.75 /
3.15
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
191.587,
191.587,
292.870,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19 /
20.8
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Structure of Escherichia Coli Dgtpase Bound to Gtp
(pdb code 6oix). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
Structure of Escherichia Coli Dgtpase Bound to Gtp, PDB code: 6oix:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 6oix
Go back to
Manganese Binding Sites List in 6oix
Manganese binding site 1 out
of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Structure of Escherichia Coli Dgtpase Bound to Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn602
b:0.4
occ:1.00
|
OD1
|
A:ASP268
|
2.8
|
0.3
|
1.0
|
NE2
|
A:HIS69
|
2.8
|
99.4
|
1.0
|
NE2
|
A:HIS117
|
3.0
|
97.0
|
0.8
|
O3'
|
A:GTP601
|
3.4
|
0.9
|
0.9
|
CD2
|
A:HIS69
|
3.5
|
98.1
|
1.0
|
CD2
|
A:HIS117
|
3.7
|
96.5
|
0.8
|
CG
|
A:ASP268
|
3.7
|
1.0
|
1.0
|
OD2
|
A:ASP268
|
3.9
|
0.7
|
1.0
|
CE1
|
A:HIS69
|
3.9
|
0.8
|
1.0
|
OD1
|
A:ASP118
|
4.0
|
0.0
|
1.0
|
CE1
|
A:HIS117
|
4.1
|
95.8
|
0.8
|
O1B
|
A:GTP601
|
4.3
|
0.9
|
0.9
|
NE2
|
A:GLN53
|
4.4
|
0.4
|
1.0
|
CG
|
A:ASP118
|
4.5
|
0.5
|
1.0
|
OD2
|
A:ASP118
|
4.6
|
0.6
|
1.0
|
C3'
|
A:GTP601
|
4.6
|
0.6
|
0.9
|
CG
|
A:HIS69
|
4.7
|
96.4
|
1.0
|
CG
|
A:HIS117
|
4.9
|
93.0
|
0.8
|
ND1
|
A:HIS69
|
4.9
|
0.1
|
1.0
|
|
Manganese binding site 2 out
of 6 in 6oix
Go back to
Manganese Binding Sites List in 6oix
Manganese binding site 2 out
of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Structure of Escherichia Coli Dgtpase Bound to Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn602
b:0.0
occ:1.00
|
NE2
|
B:HIS117
|
2.8
|
0.4
|
0.8
|
OD1
|
B:ASP268
|
2.9
|
0.8
|
1.0
|
NE2
|
B:HIS69
|
3.2
|
0.1
|
1.0
|
CD2
|
B:HIS117
|
3.4
|
0.4
|
0.8
|
OD2
|
B:ASP118
|
3.7
|
0.3
|
1.0
|
OD1
|
B:ASP118
|
3.7
|
0.6
|
1.0
|
CG
|
B:ASP268
|
3.8
|
0.3
|
1.0
|
CD2
|
B:HIS69
|
3.8
|
0.6
|
1.0
|
OD2
|
B:ASP268
|
3.9
|
0.4
|
1.0
|
CG
|
B:ASP118
|
4.0
|
0.4
|
1.0
|
CE1
|
B:HIS117
|
4.0
|
0.7
|
0.8
|
C5'
|
B:GTP601
|
4.1
|
0.3
|
1.0
|
O
|
B:HOH702
|
4.1
|
90.6
|
1.0
|
O3'
|
B:GTP601
|
4.1
|
0.8
|
1.0
|
CE1
|
B:HIS69
|
4.3
|
0.0
|
1.0
|
C4'
|
B:GTP601
|
4.6
|
0.9
|
1.0
|
CG
|
B:HIS117
|
4.7
|
0.1
|
0.8
|
OE1
|
B:GLN53
|
4.7
|
0.3
|
1.0
|
C3'
|
B:GTP601
|
4.8
|
0.2
|
1.0
|
O3A
|
B:GTP601
|
4.9
|
0.9
|
1.0
|
O5'
|
B:GTP601
|
4.9
|
0.4
|
1.0
|
NH1
|
B:ARG66
|
5.0
|
0.0
|
1.0
|
|
Manganese binding site 3 out
of 6 in 6oix
Go back to
Manganese Binding Sites List in 6oix
Manganese binding site 3 out
of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Structure of Escherichia Coli Dgtpase Bound to Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn602
b:0.7
occ:1.00
|
NE2
|
C:HIS117
|
2.9
|
93.7
|
0.8
|
OD1
|
C:ASP268
|
3.0
|
0.7
|
1.0
|
NE2
|
C:HIS69
|
3.2
|
90.2
|
1.0
|
O3'
|
C:GTP601
|
3.3
|
0.7
|
0.9
|
O1B
|
C:GTP601
|
3.4
|
0.6
|
0.9
|
CD2
|
C:HIS117
|
3.7
|
93.6
|
0.8
|
CG
|
C:ASP268
|
3.8
|
0.3
|
1.0
|
CD2
|
C:HIS69
|
3.9
|
89.9
|
1.0
|
OD1
|
C:ASP118
|
3.9
|
0.3
|
1.0
|
OD2
|
C:ASP118
|
3.9
|
1.0
|
1.0
|
OD2
|
C:ASP268
|
3.9
|
0.5
|
1.0
|
CE1
|
C:HIS117
|
4.0
|
93.2
|
0.8
|
CE1
|
C:HIS69
|
4.2
|
91.4
|
1.0
|
CG
|
C:ASP118
|
4.3
|
0.2
|
1.0
|
NE2
|
C:GLN53
|
4.3
|
0.2
|
1.0
|
C3'
|
C:GTP601
|
4.5
|
0.7
|
0.9
|
C4'
|
C:GTP601
|
4.8
|
0.7
|
0.9
|
PB
|
C:GTP601
|
4.8
|
0.4
|
0.9
|
CG
|
C:HIS117
|
4.9
|
90.1
|
0.8
|
NH1
|
C:ARG66
|
5.0
|
0.5
|
1.0
|
O5'
|
C:GTP601
|
5.0
|
0.6
|
0.9
|
|
Manganese binding site 4 out
of 6 in 6oix
Go back to
Manganese Binding Sites List in 6oix
Manganese binding site 4 out
of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Structure of Escherichia Coli Dgtpase Bound to Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn602
b:0.4
occ:1.00
|
OD1
|
D:ASP268
|
2.6
|
0.8
|
1.0
|
NE2
|
D:HIS117
|
2.8
|
0.6
|
1.0
|
NE2
|
D:HIS69
|
3.0
|
0.3
|
1.0
|
O3'
|
D:GTP601
|
3.4
|
0.5
|
1.0
|
CG
|
D:ASP268
|
3.5
|
0.1
|
1.0
|
CD2
|
D:HIS117
|
3.7
|
0.1
|
1.0
|
OD2
|
D:ASP268
|
3.7
|
0.7
|
1.0
|
CD2
|
D:HIS69
|
3.8
|
0.0
|
1.0
|
O1B
|
D:GTP601
|
3.9
|
0.4
|
1.0
|
CE1
|
D:HIS117
|
3.9
|
0.8
|
1.0
|
OD2
|
D:ASP118
|
4.0
|
0.4
|
1.0
|
CE1
|
D:HIS69
|
4.0
|
0.1
|
1.0
|
OD1
|
D:ASP118
|
4.1
|
0.3
|
1.0
|
CG
|
D:ASP118
|
4.4
|
0.1
|
1.0
|
NE2
|
D:GLN53
|
4.4
|
0.1
|
1.0
|
C3'
|
D:GTP601
|
4.6
|
0.3
|
1.0
|
O3A
|
D:GTP601
|
4.8
|
0.7
|
1.0
|
C4'
|
D:GTP601
|
4.8
|
0.1
|
1.0
|
CG
|
D:HIS117
|
4.9
|
0.5
|
1.0
|
CB
|
D:ASP268
|
4.9
|
0.8
|
1.0
|
PB
|
D:GTP601
|
4.9
|
0.8
|
1.0
|
CG
|
D:HIS69
|
4.9
|
0.2
|
1.0
|
|
Manganese binding site 5 out
of 6 in 6oix
Go back to
Manganese Binding Sites List in 6oix
Manganese binding site 5 out
of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Structure of Escherichia Coli Dgtpase Bound to Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn602
b:0.3
occ:1.00
|
OD1
|
E:ASP268
|
3.0
|
0.5
|
1.0
|
NE2
|
E:HIS117
|
3.2
|
0.3
|
0.9
|
O1B
|
E:GTP601
|
3.2
|
1.0
|
0.9
|
O3'
|
E:GTP601
|
3.6
|
0.1
|
0.9
|
NE2
|
E:HIS69
|
3.7
|
99.0
|
1.0
|
CG
|
E:ASP268
|
3.8
|
0.1
|
1.0
|
OD2
|
E:ASP268
|
3.8
|
0.4
|
1.0
|
C5'
|
E:GTP601
|
3.8
|
0.6
|
0.9
|
CD2
|
E:HIS117
|
3.8
|
0.3
|
0.9
|
OD1
|
E:ASP118
|
3.9
|
0.9
|
1.0
|
OD2
|
E:ASP118
|
4.2
|
0.1
|
1.0
|
C4'
|
E:GTP601
|
4.2
|
0.2
|
0.9
|
CE1
|
E:HIS117
|
4.3
|
0.8
|
0.9
|
CD2
|
E:HIS69
|
4.4
|
98.3
|
1.0
|
PB
|
E:GTP601
|
4.4
|
0.4
|
0.9
|
CG
|
E:ASP118
|
4.4
|
0.8
|
1.0
|
C3'
|
E:GTP601
|
4.5
|
0.4
|
0.9
|
NE2
|
E:GLN53
|
4.6
|
0.2
|
1.0
|
CE1
|
E:HIS69
|
4.7
|
99.8
|
1.0
|
O3B
|
E:GTP601
|
4.7
|
0.4
|
0.9
|
O5'
|
E:GTP601
|
4.9
|
0.8
|
0.9
|
O3A
|
E:GTP601
|
4.9
|
0.7
|
0.9
|
NH1
|
E:ARG66
|
4.9
|
0.0
|
1.0
|
|
Manganese binding site 6 out
of 6 in 6oix
Go back to
Manganese Binding Sites List in 6oix
Manganese binding site 6 out
of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Structure of Escherichia Coli Dgtpase Bound to Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn602
b:0.4
occ:1.00
|
O1B
|
F:GTP601
|
3.0
|
0.6
|
0.9
|
OD1
|
F:ASP268
|
3.2
|
0.5
|
1.0
|
NE2
|
F:HIS69
|
3.3
|
1.0
|
1.0
|
NE2
|
F:HIS117
|
3.3
|
95.4
|
0.8
|
C5'
|
F:GTP601
|
3.5
|
0.6
|
0.9
|
O3'
|
F:GTP601
|
3.7
|
0.7
|
0.9
|
C4'
|
F:GTP601
|
3.9
|
0.4
|
0.9
|
CD2
|
F:HIS69
|
3.9
|
99.5
|
1.0
|
OD1
|
F:ASP118
|
4.0
|
0.4
|
1.0
|
OD2
|
F:ASP118
|
4.0
|
0.8
|
1.0
|
NE2
|
F:GLN53
|
4.1
|
0.9
|
1.0
|
CD2
|
F:HIS117
|
4.1
|
95.9
|
0.8
|
CG
|
F:ASP268
|
4.1
|
0.5
|
1.0
|
CE1
|
F:HIS69
|
4.2
|
0.6
|
1.0
|
PB
|
F:GTP601
|
4.2
|
0.8
|
0.9
|
OD2
|
F:ASP268
|
4.2
|
0.6
|
1.0
|
CE1
|
F:HIS117
|
4.3
|
93.8
|
0.8
|
CG
|
F:ASP118
|
4.4
|
0.6
|
1.0
|
C3'
|
F:GTP601
|
4.4
|
0.3
|
0.9
|
O3A
|
F:GTP601
|
4.5
|
1.0
|
0.9
|
NH2
|
F:ARG66
|
4.7
|
0.1
|
1.0
|
O5'
|
F:GTP601
|
4.7
|
0.3
|
0.9
|
CD
|
F:GLN53
|
5.0
|
0.7
|
1.0
|
O2B
|
F:GTP601
|
5.0
|
0.3
|
0.9
|
OE1
|
F:GLN53
|
5.0
|
0.9
|
1.0
|
|
Reference:
C.O.Barnes,
Y.Wu,
J.Song,
G.Lin,
E.L.Baxter,
A.S.Brewster,
V.Nagarajan,
A.Holmes,
S.M.Soltis,
N.K.Sauter,
J.Ahn,
A.E.Cohen,
G.Calero.
The Crystal Structure of Dgtpase Reveals the Molecular Basis of Dgtp Selectivity. Proc.Natl.Acad.Sci.Usa V. 116 9333 2019.
ISSN: ESSN 1091-6490
PubMed: 31019074
DOI: 10.1073/PNAS.1814999116
Page generated: Sun Oct 6 05:43:05 2024
|