Atomistry » Calcium » PDB 3gif-3gy5 » 3gv5
Atomistry »
  Calcium »
    PDB 3gif-3gy5 »
      3gv5 »

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: Tue Jul 8 12:49:48 2025

Last articles

Mg in 5MH5
Mg in 5MGY
Mg in 5MFM
Mg in 5MH1
Mg in 5MGA
Mg in 5M73
Mg in 5MFL
Mg in 5MF4
Mg in 5MF5
Mg in 5MCP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy