Calcium in PDB 3gv5: Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Enzymatic activity of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
All present enzymatic activity of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp:
2.7.7.7;
Protein crystallography data
The structure of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp, PDB code: 3gv5
was solved by
K.N.Kirouac,
H.Ling,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.57 /
2.00
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
140.160,
71.750,
127.420,
90.00,
112.53,
90.00
|
R / Rfree (%)
|
20.5 /
25.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
(pdb code 3gv5). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp, PDB code: 3gv5:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 3gv5
Go back to
Calcium Binding Sites List in 3gv5
Calcium binding site 1 out
of 8 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca421
b:35.1
occ:1.00
|
O
|
B:SER296
|
2.4
|
49.0
|
1.0
|
O
|
T:HOH157
|
2.4
|
11.8
|
1.0
|
NE2
|
B:GLN300
|
2.5
|
55.5
|
1.0
|
O
|
B:HOH647
|
2.7
|
21.2
|
1.0
|
C
|
B:SER296
|
3.5
|
51.4
|
1.0
|
CD
|
B:GLN300
|
3.6
|
61.4
|
1.0
|
CG
|
B:GLN300
|
3.9
|
59.5
|
1.0
|
CA
|
B:SER296
|
4.1
|
51.3
|
1.0
|
O
|
B:PRO298
|
4.1
|
52.8
|
1.0
|
O
|
B:LEU295
|
4.6
|
51.8
|
1.0
|
OP1
|
T:DA844
|
4.6
|
64.1
|
1.0
|
N
|
B:GLY297
|
4.6
|
50.7
|
1.0
|
OE1
|
B:GLN300
|
4.7
|
59.3
|
1.0
|
O
|
B:HOH512
|
4.8
|
25.0
|
1.0
|
O
|
T:HOH42
|
4.8
|
22.3
|
1.0
|
CB
|
B:SER296
|
4.9
|
51.3
|
1.0
|
CA
|
B:GLY297
|
4.9
|
51.9
|
1.0
|
|
Calcium binding site 2 out
of 8 in 3gv5
Go back to
Calcium Binding Sites List in 3gv5
Calcium binding site 2 out
of 8 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca423
b:28.6
occ:1.00
|
O
|
B:LYS237
|
2.4
|
67.7
|
1.0
|
O
|
P:HOH312
|
2.4
|
19.2
|
1.0
|
O
|
P:HOH648
|
2.4
|
27.0
|
1.0
|
O
|
B:HOH712
|
2.4
|
26.8
|
1.0
|
O
|
B:HOH546
|
2.6
|
28.1
|
1.0
|
C
|
B:LYS237
|
3.5
|
67.9
|
1.0
|
OP1
|
P:DA872
|
4.2
|
49.4
|
1.0
|
CA
|
B:GLU238
|
4.3
|
68.6
|
1.0
|
N
|
B:GLU238
|
4.3
|
68.0
|
1.0
|
O
|
P:HOH682
|
4.4
|
33.6
|
1.0
|
O
|
B:ILE242
|
4.5
|
62.8
|
1.0
|
CB
|
B:LYS237
|
4.5
|
68.3
|
1.0
|
CA
|
B:LYS237
|
4.5
|
67.9
|
1.0
|
OP2
|
P:DA872
|
4.7
|
49.4
|
1.0
|
O
|
B:ILE239
|
4.7
|
69.1
|
1.0
|
OP2
|
P:DG873
|
4.8
|
49.6
|
1.0
|
C
|
B:GLU238
|
4.8
|
68.5
|
1.0
|
P
|
P:DA872
|
4.9
|
49.7
|
1.0
|
|
Calcium binding site 3 out
of 8 in 3gv5
Go back to
Calcium Binding Sites List in 3gv5
Calcium binding site 3 out
of 8 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca424
b:13.5
occ:1.00
|
OD1
|
B:ASP126
|
2.2
|
61.7
|
1.0
|
O3B
|
B:ADI425
|
2.2
|
22.0
|
1.0
|
O
|
B:LEU35
|
2.3
|
49.2
|
1.0
|
OD1
|
B:ASP34
|
2.3
|
51.7
|
1.0
|
O1A
|
B:ADI425
|
2.3
|
16.7
|
1.0
|
O
|
P:HOH279
|
2.7
|
24.7
|
1.0
|
PA
|
B:ADI425
|
3.4
|
20.9
|
1.0
|
CG
|
B:ASP126
|
3.4
|
55.6
|
1.0
|
PB
|
B:ADI425
|
3.4
|
26.4
|
1.0
|
C
|
B:LEU35
|
3.4
|
49.6
|
1.0
|
CG
|
B:ASP34
|
3.5
|
50.8
|
1.0
|
O3A
|
B:ADI425
|
3.7
|
23.4
|
1.0
|
O5'
|
B:ADI425
|
3.8
|
22.6
|
1.0
|
O2B
|
B:ADI425
|
3.9
|
23.8
|
1.0
|
N
|
B:LEU35
|
4.0
|
48.8
|
1.0
|
OD2
|
B:ASP126
|
4.0
|
58.5
|
1.0
|
OD2
|
B:ASP34
|
4.2
|
52.7
|
1.0
|
CA
|
B:LEU35
|
4.2
|
50.1
|
1.0
|
C
|
B:ASP34
|
4.3
|
48.7
|
1.0
|
C5'
|
B:ADI425
|
4.4
|
22.2
|
1.0
|
O
|
B:HOH644
|
4.4
|
24.6
|
1.0
|
N
|
B:ASP36
|
4.4
|
49.9
|
1.0
|
CB
|
B:ASP126
|
4.4
|
51.6
|
1.0
|
N
|
B:CYS37
|
4.5
|
51.0
|
1.0
|
CA
|
B:ASP36
|
4.6
|
50.5
|
1.0
|
CB
|
B:ASP34
|
4.7
|
48.1
|
1.0
|
O
|
B:ASP34
|
4.7
|
46.9
|
1.0
|
O1B
|
B:ADI425
|
4.7
|
24.0
|
1.0
|
C
|
B:ASP36
|
4.7
|
49.7
|
1.0
|
O3'
|
P:DG873
|
4.7
|
57.9
|
1.0
|
O2A
|
B:ADI425
|
4.7
|
15.5
|
1.0
|
CB
|
B:LEU35
|
4.8
|
51.1
|
1.0
|
CA
|
B:ASP34
|
4.8
|
48.4
|
1.0
|
N
|
B:PHE38
|
4.9
|
48.4
|
1.0
|
O
|
B:ASP126
|
4.9
|
48.8
|
1.0
|
OE2
|
B:GLU127
|
4.9
|
53.9
|
1.0
|
|
Calcium binding site 4 out
of 8 in 3gv5
Go back to
Calcium Binding Sites List in 3gv5
Calcium binding site 4 out
of 8 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Ca1
b:31.1
occ:1.00
|
O
|
T:HOH757
|
2.4
|
29.7
|
1.0
|
O
|
P:HOH751
|
2.5
|
16.9
|
1.0
|
O
|
P:HOH754
|
2.5
|
16.0
|
1.0
|
O
|
B:HOH523
|
2.8
|
19.3
|
1.0
|
N7
|
P:DA872
|
3.6
|
48.8
|
1.0
|
N6
|
B:ADI425
|
4.0
|
21.6
|
1.0
|
O
|
T:HOH336
|
4.1
|
27.0
|
1.0
|
N6
|
P:DA872
|
4.4
|
47.5
|
1.0
|
C8
|
P:DA872
|
4.4
|
48.9
|
1.0
|
C5
|
P:DA872
|
4.5
|
50.2
|
1.0
|
N7
|
P:DG873
|
4.6
|
48.0
|
1.0
|
O6
|
P:DG873
|
4.7
|
44.6
|
1.0
|
OP1
|
T:DA838
|
4.7
|
83.7
|
1.0
|
C6
|
P:DA872
|
4.8
|
50.4
|
1.0
|
C6
|
B:ADI425
|
4.9
|
20.3
|
1.0
|
|
Calcium binding site 5 out
of 8 in 3gv5
Go back to
Calcium Binding Sites List in 3gv5
Calcium binding site 5 out
of 8 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca421
b:14.3
occ:1.00
|
O3B
|
D:ADI424
|
2.1
|
27.7
|
1.0
|
O
|
D:LEU35
|
2.3
|
49.6
|
1.0
|
OD2
|
D:ASP126
|
2.3
|
59.5
|
1.0
|
OD1
|
D:ASP34
|
2.3
|
55.8
|
1.0
|
O
|
D:HOH638
|
2.4
|
23.1
|
1.0
|
O1A
|
D:ADI424
|
2.4
|
19.3
|
1.0
|
CG
|
D:ASP126
|
3.3
|
56.3
|
1.0
|
PB
|
D:ADI424
|
3.4
|
29.7
|
1.0
|
C
|
D:LEU35
|
3.4
|
51.6
|
1.0
|
PA
|
D:ADI424
|
3.5
|
23.6
|
1.0
|
CG
|
D:ASP34
|
3.5
|
53.5
|
1.0
|
CA
|
D:CA422
|
3.5
|
43.5
|
1.0
|
O
|
D:HOH436
|
3.6
|
33.6
|
1.0
|
OD1
|
D:ASP126
|
3.7
|
59.7
|
1.0
|
O3A
|
D:ADI424
|
3.8
|
27.8
|
1.0
|
N
|
D:LEU35
|
3.9
|
51.1
|
1.0
|
O5'
|
D:ADI424
|
3.9
|
27.0
|
1.0
|
OD2
|
D:ASP34
|
4.1
|
57.8
|
1.0
|
O2B
|
D:ADI424
|
4.2
|
28.7
|
1.0
|
CA
|
D:LEU35
|
4.2
|
52.1
|
1.0
|
C
|
D:ASP34
|
4.2
|
50.9
|
1.0
|
C5'
|
D:ADI424
|
4.3
|
26.6
|
1.0
|
N
|
D:ASP36
|
4.4
|
51.1
|
1.0
|
N
|
D:CYS37
|
4.5
|
51.8
|
1.0
|
O1B
|
D:ADI424
|
4.6
|
26.9
|
1.0
|
CB
|
D:ASP126
|
4.6
|
53.8
|
1.0
|
CB
|
D:ASP34
|
4.6
|
50.2
|
1.0
|
CA
|
D:ASP36
|
4.7
|
51.5
|
1.0
|
O
|
D:HOH480
|
4.7
|
34.7
|
1.0
|
C
|
D:ASP36
|
4.7
|
51.1
|
1.0
|
CA
|
D:ASP34
|
4.8
|
50.1
|
1.0
|
O
|
D:ASP34
|
4.8
|
48.7
|
1.0
|
N
|
D:PHE38
|
4.8
|
48.7
|
1.0
|
O2A
|
D:ADI424
|
4.9
|
22.4
|
1.0
|
O3'
|
E:DG873
|
4.9
|
48.3
|
1.0
|
CB
|
D:LEU35
|
5.0
|
52.7
|
1.0
|
O
|
D:ASP126
|
5.0
|
51.4
|
1.0
|
|
Calcium binding site 6 out
of 8 in 3gv5
Go back to
Calcium Binding Sites List in 3gv5
Calcium binding site 6 out
of 8 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca422
b:43.5
occ:1.00
|
O
|
D:HOH638
|
2.0
|
23.1
|
1.0
|
OE2
|
D:GLU127
|
2.1
|
52.9
|
1.0
|
O
|
D:HOH436
|
2.6
|
33.6
|
1.0
|
OD2
|
D:ASP34
|
2.6
|
57.8
|
1.0
|
OD1
|
D:ASP34
|
2.9
|
55.8
|
1.0
|
CG
|
D:ASP34
|
3.1
|
53.5
|
1.0
|
CD
|
D:GLU127
|
3.1
|
50.9
|
1.0
|
O
|
D:HOH480
|
3.3
|
34.7
|
1.0
|
O3'
|
E:DG873
|
3.4
|
48.3
|
1.0
|
CA
|
D:CA421
|
3.5
|
14.3
|
1.0
|
CG
|
D:GLU127
|
3.7
|
49.0
|
1.0
|
C3'
|
E:DG873
|
3.8
|
46.2
|
1.0
|
OD1
|
D:ASP126
|
4.0
|
59.7
|
1.0
|
O3B
|
D:ADI424
|
4.1
|
27.7
|
1.0
|
OE1
|
D:GLU127
|
4.1
|
50.3
|
1.0
|
C5'
|
E:DG873
|
4.3
|
44.9
|
1.0
|
C4'
|
E:DG873
|
4.4
|
45.9
|
1.0
|
OD2
|
D:ASP126
|
4.5
|
59.5
|
1.0
|
CB
|
D:ASP34
|
4.6
|
50.2
|
1.0
|
C5'
|
D:ADI424
|
4.6
|
26.6
|
1.0
|
CG
|
D:ASP126
|
4.7
|
56.3
|
1.0
|
O5'
|
D:ADI424
|
4.8
|
27.0
|
1.0
|
NZ
|
D:LYS207
|
4.9
|
53.7
|
1.0
|
O1A
|
D:ADI424
|
5.0
|
19.3
|
1.0
|
|
Calcium binding site 7 out
of 8 in 3gv5
Go back to
Calcium Binding Sites List in 3gv5
Calcium binding site 7 out
of 8 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca423
b:36.9
occ:1.00
|
O
|
D:HOH527
|
2.5
|
14.4
|
1.0
|
O
|
D:HOH505
|
2.7
|
18.1
|
1.0
|
NE2
|
D:GLN144
|
2.8
|
45.0
|
1.0
|
O
|
D:HOH521
|
3.9
|
20.1
|
1.0
|
CD
|
D:GLN144
|
4.1
|
49.9
|
1.0
|
O
|
D:HOH508
|
4.6
|
23.3
|
1.0
|
OE1
|
D:GLN144
|
4.8
|
52.0
|
1.0
|
CB
|
D:GLN144
|
4.8
|
50.5
|
1.0
|
CG
|
D:GLN144
|
5.0
|
49.6
|
1.0
|
|
Calcium binding site 8 out
of 8 in 3gv5
Go back to
Calcium Binding Sites List in 3gv5
Calcium binding site 8 out
of 8 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Ddadp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca1
b:19.3
occ:1.00
|
O
|
D:HOH525
|
2.3
|
8.5
|
1.0
|
OP2
|
F:DT842
|
2.3
|
31.3
|
1.0
|
OE2
|
D:GLU304
|
2.4
|
51.9
|
1.0
|
O
|
D:HOH565
|
2.5
|
18.6
|
1.0
|
O
|
F:HOH150
|
2.5
|
10.4
|
1.0
|
P
|
F:DT842
|
3.3
|
32.8
|
1.0
|
CD
|
D:GLU304
|
3.6
|
50.9
|
1.0
|
OP1
|
F:DT842
|
3.6
|
30.9
|
1.0
|
O3'
|
F:DC841
|
4.1
|
30.9
|
1.0
|
O
|
D:GLU305
|
4.2
|
51.5
|
1.0
|
OE1
|
D:GLU304
|
4.3
|
51.3
|
1.0
|
N
|
D:GLU305
|
4.3
|
51.1
|
1.0
|
O
|
D:GLU97
|
4.4
|
47.1
|
1.0
|
O
|
D:HOH438
|
4.4
|
9.2
|
1.0
|
CB
|
D:GLU304
|
4.4
|
49.9
|
1.0
|
CA
|
D:GLU304
|
4.5
|
49.4
|
1.0
|
CG
|
D:GLU304
|
4.6
|
49.8
|
1.0
|
O5'
|
F:DT842
|
4.7
|
33.1
|
1.0
|
C3'
|
F:DC841
|
4.7
|
31.4
|
1.0
|
CA
|
D:ASP98
|
4.7
|
18.3
|
1.0
|
O
|
D:HOH619
|
4.8
|
38.0
|
1.0
|
O
|
D:HOH646
|
4.8
|
25.1
|
1.0
|
O
|
D:HOH651
|
4.8
|
31.7
|
1.0
|
C
|
D:GLU304
|
4.9
|
50.9
|
1.0
|
N
|
D:LEU99
|
5.0
|
44.4
|
1.0
|
|
Reference:
K.N.Kirouac,
H.Ling.
Structural Basis of Error-Prone Replication and Stalling at A Thymine Base By Human Dna Polymerase Iota Embo J. V. 28 1644 2009.
ISSN: ISSN 0261-4189
PubMed: 19440206
DOI: 10.1038/EMBOJ.2009.122
Page generated: Sat Jul 13 10:48:45 2024
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