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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

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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

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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

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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

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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

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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

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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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