Calcium in PDB 3gij: DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
Enzymatic activity of DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
All present enzymatic activity of DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs:
2.7.7.7;
Protein crystallography data
The structure of DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs, PDB code: 3gij
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 /
2.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.264,
107.409,
97.867,
90.00,
100.54,
90.00
|
R / Rfree (%)
|
20.9 /
25.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
(pdb code 3gij). 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(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs, PDB code: 3gij:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 3gij
Go back to
Calcium Binding Sites List in 3gij
Calcium binding site 1 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
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(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca415
b:57.7
occ:1.00
|
OP1
|
D:2DA814
|
2.3
|
57.2
|
0.8
|
OD2
|
A:ASP7
|
2.3
|
58.5
|
1.0
|
OE2
|
A:GLU106
|
2.3
|
60.0
|
1.0
|
O
|
D:HOH502
|
2.3
|
38.5
|
1.0
|
OP2
|
D:2DA814
|
2.4
|
56.7
|
0.2
|
O
|
D:HOH717
|
2.4
|
81.6
|
1.0
|
O
|
A:HOH501
|
2.5
|
17.2
|
1.0
|
P
|
D:2DA814
|
3.1
|
54.7
|
0.2
|
NZ
|
A:LYS159
|
3.2
|
60.1
|
1.0
|
OP1
|
D:2DA814
|
3.2
|
55.2
|
0.2
|
CG
|
A:ASP7
|
3.2
|
53.2
|
1.0
|
P
|
D:2DA814
|
3.3
|
54.3
|
0.8
|
OD1
|
A:ASP7
|
3.4
|
50.2
|
1.0
|
O2A
|
A:DGT414
|
3.4
|
39.8
|
1.0
|
CD
|
A:GLU106
|
3.5
|
58.9
|
1.0
|
O5'
|
D:2DA814
|
3.6
|
57.0
|
0.8
|
O5'
|
D:2DA814
|
3.7
|
55.1
|
0.2
|
C5'
|
D:2DA814
|
3.8
|
57.8
|
0.8
|
OP2
|
D:2DA814
|
4.0
|
55.2
|
0.8
|
OE1
|
A:GLU106
|
4.2
|
60.8
|
1.0
|
O1A
|
A:DGT414
|
4.2
|
36.4
|
1.0
|
C3'
|
D:2DA814
|
4.2
|
53.4
|
0.2
|
C3'
|
D:2DA814
|
4.2
|
57.5
|
0.8
|
CE
|
A:LYS159
|
4.3
|
59.6
|
1.0
|
C5'
|
D:2DA814
|
4.4
|
54.5
|
0.2
|
PA
|
A:DGT414
|
4.4
|
33.0
|
1.0
|
C4'
|
D:2DA814
|
4.5
|
58.1
|
0.8
|
CA
|
A:CA416
|
4.6
|
43.0
|
1.0
|
CB
|
A:ASP7
|
4.6
|
52.8
|
1.0
|
CG
|
A:GLU106
|
4.6
|
56.9
|
1.0
|
CE
|
A:LYS152
|
4.7
|
65.0
|
1.0
|
O3'
|
D:DG813
|
4.7
|
55.5
|
1.0
|
OD1
|
A:ASP105
|
4.7
|
56.5
|
1.0
|
C4'
|
D:2DA814
|
4.7
|
53.9
|
0.2
|
CZ
|
A:PHE5
|
4.7
|
48.3
|
1.0
|
O1G
|
A:DGT414
|
4.8
|
40.9
|
1.0
|
OD1
|
A:ASP156
|
5.0
|
64.5
|
1.0
|
OD2
|
A:ASP105
|
5.0
|
48.9
|
1.0
|
|
Calcium binding site 2 out
of 6 in 3gij
Go back to
Calcium Binding Sites List in 3gij
Calcium binding site 2 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
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(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca416
b:43.0
occ:1.00
|
O
|
A:PHE8
|
2.3
|
49.2
|
1.0
|
OD2
|
A:ASP105
|
2.3
|
48.9
|
1.0
|
O2A
|
A:DGT414
|
2.3
|
39.8
|
1.0
|
OD1
|
A:ASP7
|
2.3
|
50.2
|
1.0
|
O1B
|
A:DGT414
|
2.3
|
41.0
|
1.0
|
O1G
|
A:DGT414
|
2.3
|
40.9
|
1.0
|
PG
|
A:DGT414
|
3.1
|
40.0
|
1.0
|
CG
|
A:ASP7
|
3.4
|
53.2
|
1.0
|
PB
|
A:DGT414
|
3.4
|
34.5
|
1.0
|
O
|
A:HOH501
|
3.4
|
17.2
|
1.0
|
C
|
A:PHE8
|
3.4
|
50.3
|
1.0
|
CG
|
A:ASP105
|
3.5
|
53.6
|
1.0
|
PA
|
A:DGT414
|
3.5
|
33.0
|
1.0
|
O
|
A:HOH721
|
3.7
|
47.4
|
1.0
|
O3B
|
A:DGT414
|
3.8
|
38.9
|
1.0
|
NZ
|
A:LYS159
|
3.9
|
60.1
|
1.0
|
O3A
|
A:DGT414
|
3.9
|
37.1
|
1.0
|
N
|
A:PHE8
|
3.9
|
51.2
|
1.0
|
C5'
|
A:DGT414
|
4.0
|
34.0
|
1.0
|
OD2
|
A:ASP7
|
4.0
|
58.5
|
1.0
|
C
|
A:ASP7
|
4.1
|
52.1
|
1.0
|
OD1
|
A:ASP105
|
4.2
|
56.5
|
1.0
|
O3G
|
A:DGT414
|
4.2
|
38.8
|
1.0
|
CA
|
A:PHE8
|
4.3
|
50.3
|
1.0
|
O2G
|
A:DGT414
|
4.3
|
37.8
|
1.0
|
CB
|
A:ASP7
|
4.3
|
52.8
|
1.0
|
O5'
|
A:DGT414
|
4.3
|
34.2
|
1.0
|
N
|
A:ASP9
|
4.3
|
50.2
|
1.0
|
CA
|
A:ASP9
|
4.4
|
50.8
|
1.0
|
N
|
A:TYR10
|
4.4
|
51.6
|
1.0
|
O
|
D:HOH502
|
4.4
|
38.5
|
1.0
|
CE
|
A:LYS159
|
4.5
|
59.6
|
1.0
|
C
|
A:ASP9
|
4.5
|
51.1
|
1.0
|
CB
|
A:ASP105
|
4.6
|
54.1
|
1.0
|
CA
|
A:ASP7
|
4.6
|
52.5
|
1.0
|
O
|
A:ASP7
|
4.6
|
52.2
|
1.0
|
CA
|
A:CA415
|
4.6
|
57.7
|
1.0
|
O2B
|
A:DGT414
|
4.6
|
39.2
|
1.0
|
N
|
A:PHE11
|
4.7
|
52.5
|
1.0
|
O1A
|
A:DGT414
|
4.7
|
36.4
|
1.0
|
CB
|
A:PHE8
|
4.9
|
50.9
|
1.0
|
O
|
A:ASP105
|
4.9
|
55.0
|
1.0
|
|
Calcium binding site 3 out
of 6 in 3gij
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Calcium Binding Sites List in 3gij
Calcium binding site 3 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
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(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca417
b:59.4
occ:1.00
|
O
|
A:ALA181
|
2.3
|
59.6
|
1.0
|
O
|
A:ILE186
|
2.3
|
58.6
|
1.0
|
O
|
A:HOH512
|
2.4
|
66.9
|
1.0
|
O
|
D:HOH516
|
2.4
|
38.2
|
1.0
|
O
|
D:HOH514
|
2.5
|
45.2
|
1.0
|
C
|
A:ALA181
|
3.5
|
59.1
|
1.0
|
C
|
A:ILE186
|
3.5
|
58.3
|
1.0
|
OP1
|
D:DG813
|
4.0
|
39.6
|
1.0
|
CA
|
A:GLY187
|
4.2
|
59.3
|
1.0
|
CA
|
A:ALA181
|
4.2
|
59.5
|
1.0
|
N
|
A:GLY187
|
4.3
|
58.5
|
1.0
|
OP2
|
D:DG813
|
4.3
|
44.4
|
1.0
|
O
|
A:VAL183
|
4.3
|
58.4
|
1.0
|
N
|
A:ASP182
|
4.4
|
58.8
|
1.0
|
CA
|
A:ASP182
|
4.5
|
58.6
|
1.0
|
CB
|
A:ALA181
|
4.5
|
59.4
|
1.0
|
CA
|
A:ILE186
|
4.6
|
58.2
|
1.0
|
C
|
A:GLY187
|
4.6
|
60.3
|
1.0
|
P
|
D:DG813
|
4.7
|
42.3
|
1.0
|
CB
|
A:ILE186
|
4.7
|
57.9
|
1.0
|
O
|
A:GLY187
|
4.8
|
60.1
|
1.0
|
C
|
A:ASP182
|
4.8
|
58.1
|
1.0
|
N
|
A:ILE186
|
4.9
|
57.9
|
1.0
|
|
Calcium binding site 4 out
of 6 in 3gij
Go back to
Calcium Binding Sites List in 3gij
Calcium binding site 4 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
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(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1415
b:68.9
occ:1.00
|
O
|
B:HOH1501
|
2.1
|
44.9
|
1.0
|
OE2
|
B:GLU1106
|
2.3
|
69.2
|
1.0
|
OD2
|
B:ASP1007
|
2.3
|
65.1
|
1.0
|
O
|
B:HOH1502
|
2.8
|
64.8
|
1.0
|
OP1
|
H:2DA1814
|
3.0
|
70.1
|
1.0
|
CD
|
B:GLU1106
|
3.0
|
68.7
|
1.0
|
CG
|
B:ASP1007
|
3.0
|
58.0
|
1.0
|
OD1
|
B:ASP1007
|
3.1
|
59.3
|
1.0
|
O2A
|
B:DGT1414
|
3.3
|
57.3
|
1.0
|
CG
|
B:GLU1106
|
3.4
|
66.7
|
1.0
|
O5'
|
H:2DA1814
|
3.6
|
68.0
|
1.0
|
P
|
H:2DA1814
|
3.8
|
68.1
|
1.0
|
OE1
|
B:GLU1106
|
4.0
|
69.4
|
1.0
|
CA
|
B:CA1416
|
4.0
|
57.5
|
1.0
|
O1A
|
B:DGT1414
|
4.2
|
58.1
|
1.0
|
C5'
|
H:2DA1814
|
4.2
|
66.6
|
1.0
|
PA
|
B:DGT1414
|
4.3
|
57.0
|
1.0
|
O1G
|
B:DGT1414
|
4.3
|
57.5
|
1.0
|
C3'
|
H:2DA1814
|
4.3
|
64.2
|
1.0
|
OD1
|
B:ASP1105
|
4.4
|
63.3
|
1.0
|
CB
|
B:ASP1007
|
4.4
|
56.5
|
1.0
|
CZ
|
B:PHE1005
|
4.5
|
50.5
|
1.0
|
NZ
|
B:LYS1159
|
4.5
|
69.4
|
1.0
|
OD2
|
B:ASP1105
|
4.6
|
59.9
|
1.0
|
OP2
|
H:2DA1814
|
4.6
|
69.7
|
1.0
|
CE
|
B:LYS1152
|
4.7
|
60.5
|
1.0
|
C4'
|
H:2DA1814
|
4.7
|
64.7
|
1.0
|
NZ
|
B:LYS1152
|
4.8
|
61.0
|
1.0
|
O
|
B:HOH1503
|
4.8
|
74.0
|
1.0
|
CG
|
B:ASP1105
|
4.9
|
63.5
|
1.0
|
CE
|
B:LYS1159
|
4.9
|
69.6
|
1.0
|
O5'
|
B:DGT1414
|
4.9
|
56.8
|
1.0
|
CB
|
B:GLU1106
|
4.9
|
65.7
|
1.0
|
|
Calcium binding site 5 out
of 6 in 3gij
Go back to
Calcium Binding Sites List in 3gij
Calcium binding site 5 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
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(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1416
b:57.5
occ:1.00
|
O
|
B:PHE1008
|
2.3
|
55.0
|
1.0
|
OD2
|
B:ASP1105
|
2.3
|
59.9
|
1.0
|
O1B
|
B:DGT1414
|
2.3
|
57.0
|
1.0
|
OD1
|
B:ASP1007
|
2.3
|
59.3
|
1.0
|
O2A
|
B:DGT1414
|
2.3
|
57.3
|
1.0
|
O1G
|
B:DGT1414
|
2.3
|
57.5
|
1.0
|
PG
|
B:DGT1414
|
3.0
|
57.0
|
1.0
|
CG
|
B:ASP1007
|
3.2
|
58.0
|
1.0
|
CG
|
B:ASP1105
|
3.5
|
63.5
|
1.0
|
C
|
B:PHE1008
|
3.5
|
54.4
|
1.0
|
PB
|
B:DGT1414
|
3.5
|
54.6
|
1.0
|
PA
|
B:DGT1414
|
3.7
|
57.0
|
1.0
|
OD2
|
B:ASP1007
|
3.7
|
65.1
|
1.0
|
O3B
|
B:DGT1414
|
3.9
|
56.5
|
1.0
|
O2G
|
B:DGT1414
|
3.9
|
56.3
|
1.0
|
CA
|
B:CA1415
|
4.0
|
68.9
|
1.0
|
N
|
B:PHE1008
|
4.0
|
55.0
|
1.0
|
C5'
|
B:DGT1414
|
4.0
|
55.5
|
1.0
|
OD1
|
B:ASP1105
|
4.1
|
63.3
|
1.0
|
O
|
B:HOH1501
|
4.2
|
44.9
|
1.0
|
O3A
|
B:DGT1414
|
4.2
|
56.7
|
1.0
|
O3G
|
B:DGT1414
|
4.2
|
56.6
|
1.0
|
O5'
|
B:DGT1414
|
4.3
|
56.8
|
1.0
|
C
|
B:ASP1007
|
4.3
|
55.5
|
1.0
|
CA
|
B:PHE1008
|
4.3
|
54.8
|
1.0
|
NZ
|
B:LYS1159
|
4.3
|
69.4
|
1.0
|
CB
|
B:ASP1007
|
4.4
|
56.5
|
1.0
|
N
|
B:ASP1009
|
4.4
|
54.3
|
1.0
|
N
|
B:TYR1010
|
4.4
|
53.5
|
1.0
|
CA
|
B:ASP1009
|
4.5
|
54.3
|
1.0
|
CB
|
B:ASP1105
|
4.5
|
64.2
|
1.0
|
C
|
B:ASP1009
|
4.7
|
53.8
|
1.0
|
O2B
|
B:DGT1414
|
4.7
|
55.7
|
1.0
|
CA
|
B:ASP1007
|
4.7
|
55.9
|
1.0
|
O
|
B:ASP1007
|
4.7
|
55.6
|
1.0
|
O1A
|
B:DGT1414
|
4.8
|
58.1
|
1.0
|
O
|
B:ASP1105
|
4.8
|
65.0
|
1.0
|
N
|
B:PHE1011
|
4.8
|
52.3
|
1.0
|
CB
|
B:PHE1008
|
4.9
|
54.7
|
1.0
|
CE
|
B:LYS1159
|
5.0
|
69.6
|
1.0
|
|
Calcium binding site 6 out
of 6 in 3gij
Go back to
Calcium Binding Sites List in 3gij
Calcium binding site 6 out
of 6 in the DPO4 Extension Ternary Complex with Oxog(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs
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(Syn)-A(Anti) and Oxog(Anti)- A(Syn) Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1417
b:69.6
occ:1.00
|
OP1
|
H:DG1813
|
2.3
|
66.7
|
1.0
|
O
|
B:HOH1516
|
2.5
|
62.6
|
1.0
|
O
|
B:VAL1183
|
2.7
|
61.6
|
1.0
|
O
|
B:ILE1186
|
2.8
|
61.2
|
1.0
|
O
|
B:HOH1515
|
2.8
|
51.5
|
1.0
|
O
|
B:ALA1181
|
2.9
|
64.9
|
1.0
|
C
|
B:VAL1183
|
3.4
|
61.8
|
1.0
|
P
|
H:DG1813
|
3.7
|
61.1
|
1.0
|
C
|
B:ILE1186
|
3.8
|
61.2
|
1.0
|
CA
|
B:PRO1184
|
3.8
|
61.2
|
1.0
|
N
|
B:PRO1184
|
3.9
|
61.4
|
1.0
|
C
|
B:ASP1182
|
3.9
|
63.4
|
1.0
|
N
|
B:ILE1186
|
3.9
|
60.9
|
1.0
|
C
|
B:ALA1181
|
4.0
|
64.7
|
1.0
|
N
|
B:GLY1185
|
4.1
|
61.0
|
1.0
|
N
|
B:VAL1183
|
4.1
|
62.7
|
1.0
|
O
|
B:ASP1182
|
4.1
|
63.3
|
1.0
|
OP2
|
H:DG1813
|
4.2
|
62.4
|
1.0
|
O
|
H:HOH1514
|
4.2
|
65.9
|
1.0
|
CA
|
B:ILE1186
|
4.3
|
61.0
|
1.0
|
CA
|
B:ASP1182
|
4.3
|
63.8
|
1.0
|
C
|
B:PRO1184
|
4.3
|
61.0
|
1.0
|
O5'
|
H:DG1813
|
4.4
|
62.8
|
1.0
|
CA
|
B:VAL1183
|
4.4
|
62.0
|
1.0
|
O
|
B:HOH1512
|
4.4
|
85.6
|
1.0
|
CB
|
B:ILE1186
|
4.5
|
61.1
|
1.0
|
N
|
B:ASP1182
|
4.6
|
64.2
|
1.0
|
O3'
|
H:DA1812
|
4.8
|
60.6
|
1.0
|
N
|
B:GLY1187
|
4.8
|
61.4
|
1.0
|
C
|
B:GLY1185
|
4.9
|
60.7
|
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
|