Manganese in PDB 6oi7: Se-Met Structure of Apo- Escherichia Coli Dgtpase
Enzymatic activity of Se-Met Structure of Apo- Escherichia Coli Dgtpase
All present enzymatic activity of Se-Met Structure of Apo- Escherichia Coli Dgtpase:
3.1.5.1;
Protein crystallography data
The structure of Se-Met Structure of Apo- Escherichia Coli Dgtpase, PDB code: 6oi7
was solved by
G.Calero,
C.O.Barnes,
Y.Wu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.97 /
2.90
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
192.183,
192.183,
287.189,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
23.4
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Se-Met Structure of Apo- Escherichia Coli Dgtpase
(pdb code 6oi7). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
Se-Met Structure of Apo- Escherichia Coli Dgtpase, PDB code: 6oi7:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 6oi7
Go back to
Manganese Binding Sites List in 6oi7
Manganese binding site 1 out
of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn601
b:0.1
occ:0.93
|
NE2
|
A:HIS117
|
2.2
|
0.5
|
1.0
|
OD1
|
A:ASP268
|
2.5
|
0.4
|
1.0
|
CE1
|
A:HIS69
|
3.0
|
77.2
|
1.0
|
CD2
|
A:HIS117
|
3.1
|
0.8
|
1.0
|
OD1
|
A:ASP118
|
3.2
|
0.6
|
1.0
|
CE1
|
A:HIS117
|
3.3
|
0.2
|
1.0
|
ND1
|
A:HIS69
|
3.4
|
74.4
|
1.0
|
CG
|
A:ASP268
|
3.7
|
0.8
|
1.0
|
CG
|
A:ASP118
|
3.9
|
0.4
|
1.0
|
OD2
|
A:ASP118
|
4.0
|
0.1
|
1.0
|
OD2
|
A:ASP268
|
4.1
|
0.4
|
1.0
|
NE2
|
A:HIS69
|
4.2
|
78.8
|
1.0
|
CG
|
A:HIS117
|
4.3
|
99.1
|
1.0
|
ND1
|
A:HIS117
|
4.3
|
0.1
|
1.0
|
CG2
|
A:VAL73
|
4.6
|
63.6
|
1.0
|
OE1
|
A:GLN53
|
4.6
|
0.8
|
1.0
|
CG
|
A:HIS69
|
4.7
|
80.1
|
1.0
|
NH1
|
A:ARG66
|
4.8
|
0.3
|
1.0
|
CB
|
A:ASP268
|
4.9
|
97.7
|
1.0
|
|
Manganese binding site 2 out
of 6 in 6oi7
Go back to
Manganese Binding Sites List in 6oi7
Manganese binding site 2 out
of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn601
b:0.2
occ:0.67
|
NE2
|
B:HIS117
|
2.0
|
0.2
|
1.0
|
OD1
|
B:ASP268
|
2.4
|
0.8
|
1.0
|
CD2
|
B:HIS117
|
2.6
|
0.3
|
1.0
|
NE2
|
B:HIS69
|
2.7
|
0.8
|
1.0
|
CG
|
B:ASP268
|
3.2
|
0.9
|
1.0
|
CE1
|
B:HIS117
|
3.2
|
0.4
|
1.0
|
CD2
|
B:HIS69
|
3.4
|
0.1
|
1.0
|
OD2
|
B:ASP268
|
3.4
|
0.9
|
1.0
|
OD2
|
B:ASP118
|
3.5
|
0.1
|
1.0
|
CE1
|
B:HIS69
|
3.7
|
0.8
|
1.0
|
OD1
|
B:ASP118
|
3.9
|
0.2
|
1.0
|
CG
|
B:HIS117
|
3.9
|
0.7
|
1.0
|
CG
|
B:ASP118
|
4.0
|
0.7
|
1.0
|
ND1
|
B:HIS117
|
4.1
|
0.6
|
1.0
|
CB
|
B:ASP268
|
4.6
|
0.1
|
1.0
|
CG
|
B:HIS69
|
4.6
|
0.3
|
1.0
|
ND1
|
B:HIS69
|
4.7
|
0.2
|
1.0
|
CB
|
B:TYR272
|
4.7
|
1.0
|
1.0
|
OE1
|
B:GLN53
|
4.8
|
0.3
|
1.0
|
|
Manganese binding site 3 out
of 6 in 6oi7
Go back to
Manganese Binding Sites List in 6oi7
Manganese binding site 3 out
of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn601
b:0.8
occ:0.82
|
NE2
|
C:HIS117
|
2.2
|
96.7
|
1.0
|
CD2
|
C:HIS117
|
2.8
|
0.3
|
1.0
|
OD1
|
C:ASP268
|
2.8
|
94.2
|
1.0
|
CE1
|
C:HIS69
|
2.9
|
83.1
|
1.0
|
OD1
|
C:ASP118
|
3.1
|
0.9
|
1.0
|
CE1
|
C:HIS117
|
3.5
|
95.1
|
1.0
|
ND1
|
C:HIS69
|
3.5
|
88.8
|
1.0
|
CG
|
C:ASP268
|
3.6
|
99.4
|
1.0
|
OD2
|
C:ASP268
|
3.8
|
0.2
|
1.0
|
CG
|
C:ASP118
|
3.8
|
0.2
|
1.0
|
OD2
|
C:ASP118
|
3.9
|
0.7
|
1.0
|
NE2
|
C:HIS69
|
4.0
|
86.0
|
1.0
|
CG
|
C:HIS117
|
4.1
|
97.7
|
1.0
|
ND1
|
C:HIS117
|
4.4
|
0.7
|
1.0
|
OE1
|
C:GLN53
|
4.5
|
0.0
|
1.0
|
NH1
|
C:ARG66
|
4.5
|
1.0
|
1.0
|
CG
|
C:HIS69
|
4.8
|
85.2
|
1.0
|
NE2
|
C:GLN53
|
4.9
|
0.3
|
1.0
|
CG2
|
C:VAL73
|
4.9
|
61.9
|
1.0
|
|
Manganese binding site 4 out
of 6 in 6oi7
Go back to
Manganese Binding Sites List in 6oi7
Manganese binding site 4 out
of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn601
b:0.6
occ:0.97
|
NE2
|
D:HIS117
|
2.5
|
0.3
|
1.0
|
OD1
|
D:ASP268
|
2.6
|
0.3
|
1.0
|
CE1
|
D:HIS69
|
2.7
|
0.4
|
1.0
|
CD2
|
D:HIS117
|
3.3
|
0.1
|
1.0
|
CG
|
D:ASP268
|
3.4
|
0.4
|
1.0
|
ND1
|
D:HIS69
|
3.5
|
0.8
|
1.0
|
OD2
|
D:ASP118
|
3.5
|
0.1
|
1.0
|
OD2
|
D:ASP268
|
3.5
|
0.8
|
1.0
|
CE1
|
D:HIS117
|
3.7
|
0.4
|
1.0
|
NE2
|
D:HIS69
|
3.7
|
0.4
|
1.0
|
CG
|
D:ASP118
|
4.2
|
0.2
|
1.0
|
OD1
|
D:ASP118
|
4.4
|
0.8
|
1.0
|
CG
|
D:HIS117
|
4.5
|
0.4
|
1.0
|
ND1
|
D:HIS117
|
4.7
|
0.0
|
1.0
|
CG
|
D:HIS69
|
4.7
|
0.5
|
1.0
|
CD2
|
D:HIS69
|
4.8
|
0.8
|
1.0
|
CB
|
D:ASP268
|
4.8
|
0.4
|
1.0
|
OE1
|
D:GLN53
|
4.9
|
0.3
|
1.0
|
NH1
|
D:ARG66
|
4.9
|
0.8
|
1.0
|
|
Manganese binding site 5 out
of 6 in 6oi7
Go back to
Manganese Binding Sites List in 6oi7
Manganese binding site 5 out
of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn601
b:0.1
occ:0.76
|
NE2
|
E:HIS117
|
2.1
|
0.7
|
1.0
|
OD1
|
E:ASP268
|
2.7
|
0.8
|
1.0
|
CE1
|
E:HIS69
|
2.9
|
81.0
|
1.0
|
CD2
|
E:HIS117
|
3.0
|
0.4
|
1.0
|
CE1
|
E:HIS117
|
3.2
|
0.2
|
1.0
|
OD2
|
E:ASP118
|
3.2
|
0.1
|
1.0
|
ND1
|
E:HIS69
|
3.4
|
78.8
|
1.0
|
CG
|
E:ASP268
|
3.8
|
0.4
|
1.0
|
CG
|
E:ASP118
|
3.9
|
0.0
|
1.0
|
NE2
|
E:HIS69
|
4.0
|
84.1
|
1.0
|
OD1
|
E:ASP118
|
4.1
|
0.4
|
1.0
|
CG
|
E:HIS117
|
4.2
|
0.1
|
1.0
|
ND1
|
E:HIS117
|
4.2
|
0.3
|
1.0
|
OD2
|
E:ASP268
|
4.3
|
0.7
|
1.0
|
OE1
|
E:GLN53
|
4.7
|
0.1
|
1.0
|
CG2
|
E:VAL73
|
4.7
|
76.5
|
1.0
|
CG
|
E:HIS69
|
4.7
|
78.3
|
1.0
|
CB
|
E:ASP268
|
4.9
|
0.5
|
1.0
|
|
Manganese binding site 6 out
of 6 in 6oi7
Go back to
Manganese Binding Sites List in 6oi7
Manganese binding site 6 out
of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn601
b:0.6
occ:0.60
|
NE2
|
F:HIS117
|
2.1
|
0.1
|
1.0
|
OD1
|
F:ASP268
|
2.6
|
0.7
|
1.0
|
CD2
|
F:HIS117
|
2.7
|
0.1
|
1.0
|
NE2
|
F:HIS69
|
3.0
|
87.7
|
1.0
|
CE1
|
F:HIS117
|
3.3
|
0.0
|
1.0
|
CD2
|
F:HIS69
|
3.5
|
80.1
|
1.0
|
CG
|
F:ASP268
|
3.5
|
0.6
|
1.0
|
OD1
|
F:ASP118
|
3.6
|
0.1
|
1.0
|
OD2
|
F:ASP268
|
3.9
|
0.5
|
1.0
|
CG
|
F:HIS117
|
4.0
|
0.2
|
1.0
|
CE1
|
F:HIS69
|
4.2
|
93.1
|
1.0
|
ND1
|
F:HIS117
|
4.2
|
0.4
|
1.0
|
CG
|
F:ASP118
|
4.3
|
0.5
|
1.0
|
OD2
|
F:ASP118
|
4.3
|
0.5
|
1.0
|
CG2
|
F:VAL73
|
4.6
|
64.5
|
1.0
|
CB
|
F:ASP268
|
4.7
|
90.3
|
1.0
|
CG
|
F:HIS69
|
4.8
|
76.7
|
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
|