Calcium in PDB 3gil: DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
Enzymatic activity of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
All present enzymatic activity of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair:
2.7.7.7;
Protein crystallography data
The structure of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair, PDB code: 3gil
was solved by
O.Rechkoblit,
L.Malinina,
D.J.Patel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.71
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.289,
110.682,
102.190,
90.00,
99.22,
90.00
|
R / Rfree (%)
|
20 /
25.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
(pdb code 3gil). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair, PDB code: 3gil:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 3gil
Go back to
Calcium Binding Sites List in 3gil
Calcium binding site 1 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca415
b:37.8
occ:1.00
|
O
|
A:HOH615
|
2.2
|
21.9
|
1.0
|
O2A
|
A:DGT414
|
2.3
|
38.1
|
1.0
|
OD2
|
A:ASP7
|
2.3
|
40.7
|
1.0
|
OE2
|
A:GLU106
|
2.3
|
41.4
|
1.0
|
OD1
|
A:ASP105
|
2.5
|
45.4
|
1.0
|
O
|
A:HOH614
|
2.9
|
54.8
|
1.0
|
CG
|
A:ASP7
|
3.1
|
44.4
|
1.0
|
CG
|
A:ASP105
|
3.2
|
45.7
|
1.0
|
OD2
|
A:ASP105
|
3.2
|
43.4
|
1.0
|
OD1
|
A:ASP7
|
3.4
|
43.7
|
1.0
|
CD
|
A:GLU106
|
3.4
|
45.8
|
1.0
|
CA
|
A:CA416
|
3.5
|
38.6
|
1.0
|
PA
|
A:DGT414
|
3.6
|
35.0
|
1.0
|
O1A
|
A:DGT414
|
3.9
|
36.7
|
1.0
|
CG
|
A:GLU106
|
4.0
|
45.1
|
1.0
|
CB
|
A:GLU106
|
4.0
|
46.0
|
1.0
|
OG
|
A:SER103
|
4.1
|
45.4
|
1.0
|
O
|
D:HOH536
|
4.1
|
39.4
|
1.0
|
O5'
|
A:DGT414
|
4.2
|
36.2
|
1.0
|
C5'
|
A:DGT414
|
4.3
|
35.9
|
1.0
|
CB
|
A:ASP7
|
4.3
|
42.8
|
1.0
|
OE1
|
A:GLU106
|
4.4
|
45.5
|
1.0
|
O
|
A:HOH520
|
4.5
|
44.0
|
1.0
|
CB
|
A:ASP105
|
4.6
|
45.8
|
1.0
|
C
|
A:ASP105
|
4.7
|
45.7
|
1.0
|
O
|
A:ASP105
|
4.7
|
46.1
|
1.0
|
O1G
|
A:DGT414
|
4.8
|
40.3
|
1.0
|
N
|
A:GLU106
|
4.8
|
46.0
|
1.0
|
O3A
|
A:DGT414
|
4.9
|
35.8
|
1.0
|
OP1
|
D:2DT814
|
5.0
|
44.1
|
1.0
|
CA
|
A:ASP7
|
5.0
|
42.8
|
1.0
|
|
Calcium binding site 2 out
of 6 in 3gil
Go back to
Calcium Binding Sites List in 3gil
Calcium binding site 2 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca416
b:38.6
occ:1.00
|
OD1
|
A:ASP7
|
2.3
|
43.7
|
1.0
|
O1B
|
A:DGT414
|
2.3
|
37.0
|
1.0
|
O
|
A:PHE8
|
2.3
|
41.2
|
1.0
|
O2A
|
A:DGT414
|
2.3
|
38.1
|
1.0
|
O1G
|
A:DGT414
|
2.3
|
40.3
|
1.0
|
OD2
|
A:ASP105
|
2.3
|
43.4
|
1.0
|
PG
|
A:DGT414
|
3.2
|
43.4
|
1.0
|
PB
|
A:DGT414
|
3.2
|
35.1
|
1.0
|
CG
|
A:ASP7
|
3.3
|
44.4
|
1.0
|
PA
|
A:DGT414
|
3.3
|
35.0
|
1.0
|
O3A
|
A:DGT414
|
3.4
|
35.8
|
1.0
|
CG
|
A:ASP105
|
3.5
|
45.7
|
1.0
|
C
|
A:PHE8
|
3.5
|
42.4
|
1.0
|
CA
|
A:CA415
|
3.5
|
37.8
|
1.0
|
O
|
A:HOH595
|
3.6
|
22.8
|
1.0
|
OD2
|
A:ASP7
|
3.7
|
40.7
|
1.0
|
O3B
|
A:DGT414
|
3.8
|
39.0
|
1.0
|
C5'
|
A:DGT414
|
4.1
|
35.9
|
1.0
|
OD1
|
A:ASP105
|
4.1
|
45.4
|
1.0
|
O5'
|
A:DGT414
|
4.2
|
36.2
|
1.0
|
N
|
A:PHE8
|
4.2
|
42.7
|
1.0
|
O3G
|
A:DGT414
|
4.2
|
40.2
|
1.0
|
C
|
A:ASP7
|
4.3
|
42.7
|
1.0
|
O2G
|
A:DGT414
|
4.4
|
42.1
|
1.0
|
O
|
A:HOH615
|
4.4
|
21.9
|
1.0
|
CA
|
A:PHE8
|
4.4
|
42.9
|
1.0
|
O
|
A:ASP7
|
4.4
|
42.7
|
1.0
|
N
|
A:TYR10
|
4.5
|
44.0
|
1.0
|
CE
|
A:LYS159
|
4.5
|
51.2
|
1.0
|
N
|
A:ASP9
|
4.5
|
42.4
|
1.0
|
O2B
|
A:DGT414
|
4.6
|
36.9
|
1.0
|
CA
|
A:ASP9
|
4.6
|
43.0
|
1.0
|
O1A
|
A:DGT414
|
4.6
|
36.7
|
1.0
|
CB
|
A:ASP7
|
4.6
|
42.8
|
1.0
|
CB
|
A:ASP105
|
4.7
|
45.8
|
1.0
|
C
|
A:ASP9
|
4.7
|
43.5
|
1.0
|
NZ
|
A:LYS159
|
4.8
|
52.5
|
1.0
|
N
|
A:PHE11
|
4.9
|
44.2
|
1.0
|
CA
|
A:ASP7
|
5.0
|
42.8
|
1.0
|
|
Calcium binding site 3 out
of 6 in 3gil
Go back to
Calcium Binding Sites List in 3gil
Calcium binding site 3 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca417
b:60.3
occ:1.00
|
O
|
A:HOH619
|
2.2
|
30.6
|
1.0
|
O
|
A:HOH616
|
2.3
|
33.5
|
1.0
|
O
|
A:ALA181
|
2.3
|
59.2
|
1.0
|
O
|
A:ILE186
|
2.3
|
59.6
|
1.0
|
O
|
D:HOH617
|
2.3
|
30.4
|
1.0
|
C
|
A:ALA181
|
3.4
|
58.9
|
1.0
|
C
|
A:ILE186
|
3.5
|
59.2
|
1.0
|
O
|
A:HOH618
|
3.6
|
65.0
|
1.0
|
CA
|
A:ALA181
|
4.0
|
58.7
|
1.0
|
CA
|
A:GLY187
|
4.0
|
59.9
|
1.0
|
CB
|
A:ALA181
|
4.1
|
58.7
|
1.0
|
N
|
A:GLY187
|
4.2
|
59.7
|
1.0
|
C
|
A:GLY187
|
4.4
|
60.0
|
1.0
|
N
|
A:ASP182
|
4.5
|
58.7
|
1.0
|
O
|
A:GLY187
|
4.5
|
60.1
|
1.0
|
OP2
|
D:DG813
|
4.7
|
41.6
|
1.0
|
CA
|
A:ILE186
|
4.7
|
58.9
|
1.0
|
CA
|
A:ASP182
|
4.8
|
58.7
|
1.0
|
CB
|
A:ILE186
|
4.8
|
59.0
|
1.0
|
O
|
A:VAL183
|
4.9
|
57.9
|
1.0
|
OP1
|
D:DG813
|
4.9
|
42.4
|
1.0
|
|
Calcium binding site 4 out
of 6 in 3gil
Go back to
Calcium Binding Sites List in 3gil
Calcium binding site 4 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1415
b:47.5
occ:1.00
|
OE2
|
B:GLU1106
|
2.3
|
50.2
|
1.0
|
O2A
|
B:DGT1414
|
2.3
|
40.9
|
1.0
|
OD2
|
B:ASP1007
|
2.3
|
46.6
|
1.0
|
OD1
|
B:ASP1105
|
2.5
|
45.9
|
1.0
|
O
|
B:HOH621
|
2.6
|
42.4
|
1.0
|
CG
|
B:ASP1007
|
3.0
|
43.9
|
1.0
|
CG
|
B:GLU1106
|
3.0
|
49.9
|
1.0
|
CD
|
B:GLU1106
|
3.0
|
51.4
|
1.0
|
OD1
|
B:ASP1007
|
3.1
|
42.1
|
1.0
|
OD2
|
B:ASP1105
|
3.1
|
43.5
|
1.0
|
CG
|
B:ASP1105
|
3.2
|
47.4
|
1.0
|
CA
|
B:CA1416
|
3.4
|
40.4
|
1.0
|
PA
|
B:DGT1414
|
3.6
|
32.2
|
1.0
|
O1A
|
B:DGT1414
|
4.0
|
33.7
|
1.0
|
C5'
|
B:DGT1414
|
4.0
|
28.5
|
1.0
|
O5'
|
B:DGT1414
|
4.2
|
31.0
|
1.0
|
OE1
|
B:GLU1106
|
4.3
|
51.0
|
1.0
|
CB
|
B:ASP1007
|
4.3
|
43.3
|
1.0
|
CB
|
B:GLU1106
|
4.4
|
48.8
|
1.0
|
O1G
|
B:DGT1414
|
4.4
|
38.6
|
1.0
|
OG
|
B:SER1103
|
4.5
|
49.9
|
1.0
|
O
|
B:ASP1105
|
4.6
|
47.6
|
1.0
|
C
|
B:ASP1105
|
4.6
|
48.0
|
1.0
|
CB
|
B:ASP1105
|
4.7
|
48.0
|
1.0
|
NZ
|
B:LYS1159
|
4.8
|
54.3
|
1.0
|
N
|
B:GLU1106
|
4.8
|
48.2
|
1.0
|
NZ
|
B:LYS1152
|
4.9
|
48.3
|
1.0
|
OP1
|
H:2DT1814
|
4.9
|
48.4
|
1.0
|
CA
|
B:ASP1007
|
4.9
|
43.1
|
1.0
|
CA
|
B:GLU1106
|
5.0
|
48.5
|
1.0
|
O3A
|
B:DGT1414
|
5.0
|
34.2
|
1.0
|
|
Calcium binding site 5 out
of 6 in 3gil
Go back to
Calcium Binding Sites List in 3gil
Calcium binding site 5 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1416
b:40.4
occ:1.00
|
O2A
|
B:DGT1414
|
2.3
|
40.9
|
1.0
|
OD1
|
B:ASP1007
|
2.3
|
42.1
|
1.0
|
O1B
|
B:DGT1414
|
2.3
|
37.6
|
1.0
|
O
|
B:PHE1008
|
2.3
|
41.4
|
1.0
|
OD2
|
B:ASP1105
|
2.3
|
43.5
|
1.0
|
O1G
|
B:DGT1414
|
2.3
|
38.6
|
1.0
|
PG
|
B:DGT1414
|
3.0
|
36.4
|
1.0
|
O
|
B:HOH597
|
3.1
|
33.9
|
1.0
|
PB
|
B:DGT1414
|
3.3
|
32.6
|
1.0
|
PA
|
B:DGT1414
|
3.3
|
32.2
|
1.0
|
CA
|
B:CA1415
|
3.4
|
47.5
|
1.0
|
CG
|
B:ASP1007
|
3.4
|
43.9
|
1.0
|
CG
|
B:ASP1105
|
3.5
|
47.4
|
1.0
|
C
|
B:PHE1008
|
3.5
|
42.5
|
1.0
|
O3A
|
B:DGT1414
|
3.5
|
34.2
|
1.0
|
OD2
|
B:ASP1007
|
3.8
|
46.6
|
1.0
|
O3B
|
B:DGT1414
|
3.8
|
35.9
|
1.0
|
O2G
|
B:DGT1414
|
3.9
|
35.9
|
1.0
|
C5'
|
B:DGT1414
|
3.9
|
28.5
|
1.0
|
OD1
|
B:ASP1105
|
4.0
|
45.9
|
1.0
|
N
|
B:PHE1008
|
4.0
|
43.0
|
1.0
|
O5'
|
B:DGT1414
|
4.1
|
31.0
|
1.0
|
NZ
|
B:LYS1159
|
4.2
|
54.3
|
1.0
|
O3G
|
B:DGT1414
|
4.2
|
34.0
|
1.0
|
CA
|
B:PHE1008
|
4.3
|
42.9
|
1.0
|
C
|
B:ASP1007
|
4.4
|
43.0
|
1.0
|
N
|
B:ASP1009
|
4.5
|
42.5
|
1.0
|
O1A
|
B:DGT1414
|
4.5
|
33.7
|
1.0
|
N
|
B:TYR1010
|
4.5
|
42.5
|
1.0
|
O2B
|
B:DGT1414
|
4.6
|
32.5
|
1.0
|
CA
|
B:ASP1009
|
4.6
|
42.7
|
1.0
|
CB
|
B:ASP1007
|
4.7
|
43.3
|
1.0
|
CB
|
B:ASP1105
|
4.7
|
48.0
|
1.0
|
O
|
B:ASP1007
|
4.8
|
42.6
|
1.0
|
C
|
B:ASP1009
|
4.8
|
42.6
|
1.0
|
N
|
B:PHE1011
|
4.9
|
41.8
|
1.0
|
O
|
B:HOH621
|
4.9
|
42.4
|
1.0
|
CA
|
B:ASP1007
|
5.0
|
43.1
|
1.0
|
|
Calcium binding site 6 out
of 6 in 3gil
Go back to
Calcium Binding Sites List in 3gil
Calcium binding site 6 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1417
b:64.8
occ:1.00
|
O
|
B:ILE1186
|
2.3
|
65.1
|
1.0
|
OP1
|
H:DG1813
|
2.3
|
60.0
|
1.0
|
O
|
B:HOH627
|
2.5
|
56.9
|
1.0
|
O
|
B:HOH626
|
2.6
|
45.7
|
1.0
|
O
|
H:HOH625
|
2.7
|
42.9
|
1.0
|
O
|
B:ALA1181
|
2.8
|
63.5
|
1.0
|
O
|
B:VAL1183
|
3.4
|
62.4
|
1.0
|
C
|
B:ILE1186
|
3.4
|
65.0
|
1.0
|
P
|
H:DG1813
|
3.8
|
51.7
|
1.0
|
N
|
B:ILE1186
|
3.9
|
64.0
|
1.0
|
C
|
B:ALA1181
|
4.0
|
63.3
|
1.0
|
C
|
B:VAL1183
|
4.1
|
62.4
|
1.0
|
CA
|
B:ILE1186
|
4.1
|
64.4
|
1.0
|
CB
|
B:ILE1186
|
4.4
|
64.4
|
1.0
|
N
|
B:VAL1183
|
4.5
|
62.3
|
1.0
|
N
|
B:GLY1187
|
4.5
|
65.7
|
1.0
|
OP2
|
H:DG1813
|
4.5
|
53.0
|
1.0
|
N
|
B:GLY1185
|
4.5
|
63.2
|
1.0
|
C
|
B:ASP1182
|
4.5
|
62.6
|
1.0
|
CA
|
B:PRO1184
|
4.6
|
62.5
|
1.0
|
O5'
|
H:DG1813
|
4.6
|
50.3
|
1.0
|
N
|
B:PRO1184
|
4.6
|
62.3
|
1.0
|
CA
|
B:ASP1182
|
4.7
|
63.0
|
1.0
|
O3'
|
H:DA1812
|
4.7
|
49.4
|
1.0
|
CA
|
B:GLY1187
|
4.7
|
66.0
|
1.0
|
N
|
B:ASP1182
|
4.8
|
63.1
|
1.0
|
C
|
B:PRO1184
|
4.8
|
62.8
|
1.0
|
O
|
B:HOH624
|
4.9
|
60.9
|
1.0
|
CA
|
B:VAL1183
|
4.9
|
62.3
|
1.0
|
O
|
B:ASP1182
|
4.9
|
62.5
|
1.0
|
C
|
B:GLY1185
|
4.9
|
63.5
|
1.0
|
CA
|
B:ALA1181
|
5.0
|
63.3
|
1.0
|
|
Reference:
O.Rechkoblit,
L.Malinina,
Y.Cheng,
N.E.Geacintov,
S.Broyde,
D.J.Patel.
Impact of Conformational Heterogeneity of Oxog Lesions and Their Pairing Partners on Bypass Fidelity By Y Family Polymerases. Structure V. 17 725 2009.
ISSN: ISSN 0969-2126
PubMed: 19446528
DOI: 10.1016/J.STR.2009.03.011
Page generated: Sat Jul 13 10:41:03 2024
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