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Calcium in PDB 2rdj: Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms

Enzymatic activity of Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms

All present enzymatic activity of Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms:
2.7.7.7;

Protein crystallography data

The structure of Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms, PDB code: 2rdj was solved by J.H.Y.Wong, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.11 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.993, 102.510, 106.109, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms (pdb code 2rdj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms, PDB code: 2rdj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2rdj

Go back to Calcium Binding Sites List in 2rdj
Calcium binding site 1 out of 4 in the Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca353

b:35.7
occ:1.00
 O1P A:TMP355 2.3 41.8 1.0
OD1 A:ASP7 2.3 36.2 1.0
O C:HOH25 2.3 33.8 1.0
OD2 A:ASP105 2.3 37.9 1.0
O A:PHE8 2.3 30.0 1.0
O A:HOH426 2.3 35.5 1.0
P A:TMP355 3.3 40.3 1.0
O5' A:TMP355 3.4 43.2 1.0
CG A:ASP7 3.4 34.3 1.0
CG A:ASP105 3.5 35.8 1.0
C A:PHE8 3.5 29.3 1.0
O2P A:TMP355 3.8 39.7 1.0
OD2 A:ASP7 3.9 37.8 1.0
O3' C:DT14 4.0 46.4 1.0
N A:PHE8 4.1 30.6 1.0
C5' A:TMP355 4.1 45.2 1.0
O A:HOH427 4.2 35.1 1.0
OD1 A:ASP105 4.3 36.2 1.0
O A:HOH358 4.3 27.8 1.0
CB A:ASP105 4.3 32.7 1.0
CA A:PHE8 4.3 29.6 1.0
N A:TYR10 4.3 28.7 1.0
C A:ASP7 4.4 31.3 1.0
O A:HOH445 4.4 38.0 1.0
N A:PHE11 4.5 26.7 1.0
N A:ASP9 4.5 29.0 1.0
CA A:ASP9 4.5 29.0 1.0
NZ A:LYS159 4.6 37.5 1.0
C A:ASP9 4.6 28.8 1.0
CB A:ASP7 4.7 31.1 1.0
O A:ASP105 4.7 32.9 1.0
O3P A:TMP355 4.7 41.5 1.0
CB A:PHE11 4.7 26.0 1.0
O A:ASP7 4.9 31.7 1.0
CA A:ASP7 4.9 31.5 1.0
CB A:PHE8 4.9 29.4 1.0
CA A:TYR10 5.0 28.8 1.0

Calcium binding site 2 out of 4 in 2rdj

Go back to Calcium Binding Sites List in 2rdj
Calcium binding site 2 out of 4 in the Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca354

b:40.2
occ:1.00
 O A:HOH421 2.2 52.4 1.0
O A:HOH420 2.3 40.4 1.0
O A:HOH431 2.3 42.0 1.0
O A:ILE186 2.3 39.8 1.0
O A:ALA181 2.3 41.6 1.0
O A:HOH497 2.3 37.1 1.0
O C:HOH17 2.4 39.3 1.0
C A:ALA181 3.5 41.6 1.0
C A:ILE186 3.5 40.2 1.0
CA A:GLY187 4.1 40.6 1.0
N A:GLY187 4.2 39.9 1.0
CA A:ALA181 4.3 41.4 1.0
OP1 C:DA13 4.4 38.0 1.0
CB A:ALA181 4.5 41.4 1.0
N A:ASP182 4.5 41.9 1.0
OP2 C:DA13 4.5 40.6 1.0
CA A:ASP182 4.6 42.5 1.0
C A:GLY187 4.6 40.8 1.0
O A:VAL183 4.6 40.4 1.0
CA A:ILE186 4.7 40.2 1.0
O A:GLY187 4.8 40.2 1.0
CB A:ILE186 5.0 39.9 1.0
P C:DA13 5.0 35.9 1.0

Calcium binding site 3 out of 4 in 2rdj

Go back to Calcium Binding Sites List in 2rdj
Calcium binding site 3 out of 4 in the Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca353

b:45.5
occ:1.00
 O B:PHE8 2.2 38.5 1.0
OD2 B:ASP105 2.3 44.2 1.0
O B:HOH368 2.3 53.5 1.0
O E:HOH26 2.5 40.3 1.0
OP1 E:DT14 2.5 48.8 1.0
OD1 B:ASP7 2.6 39.5 1.0
CG B:ASP105 3.4 38.9 1.0
C B:PHE8 3.5 37.9 1.0
O B:HOH381 3.6 46.0 1.0
P E:DT14 3.6 50.9 1.0
CG B:ASP7 3.7 41.1 1.0
O5' E:DT14 3.8 48.2 1.0
OD1 B:ASP105 3.8 37.9 1.0
N B:TYR10 3.9 38.7 1.0
OD2 B:ASP7 4.1 45.9 1.0
C5' E:DT14 4.2 45.2 1.0
N B:PHE8 4.3 37.5 1.0
N B:PHE11 4.3 36.5 1.0
CA B:ASP9 4.3 38.5 1.0
C B:ASP9 4.3 37.9 1.0
N B:ASP9 4.3 37.9 1.0
O B:HOH376 4.4 45.5 1.0
CA B:PHE8 4.4 37.1 1.0
OP2 E:DT14 4.5 50.6 1.0
CB B:ASP105 4.6 37.0 1.0
CA B:TYR10 4.6 38.8 1.0
C B:ASP7 4.7 38.7 1.0
NZ B:LYS159 4.7 52.4 1.0
O3' E:DA13 4.8 49.3 1.0
CB B:PHE11 4.8 34.3 1.0
O B:ASP105 4.9 38.2 1.0
CB B:ASP7 4.9 39.6 1.0

Calcium binding site 4 out of 4 in 2rdj

Go back to Calcium Binding Sites List in 2rdj
Calcium binding site 4 out of 4 in the Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Snapshots of A Y-Family Dna Polymerase in Replication: DPO4 in Apo and Binary/Ternary Complex Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca354

b:45.0
occ:1.00
 O B:HOH402 2.2 39.7 1.0
O B:HOH406 2.3 44.9 1.0
O B:ALA181 2.3 43.3 1.0
O E:HOH15 2.4 45.8 1.0
O B:ILE186 2.4 41.8 1.0
C B:ALA181 3.5 42.8 1.0
C B:ILE186 3.6 40.6 1.0
CA B:GLY187 4.2 40.1 1.0
N B:GLY187 4.4 39.9 1.0
CA B:ALA181 4.4 42.9 1.0
N B:ASP182 4.5 43.0 1.0
OP2 E:DA12 4.5 49.9 1.0
OP1 E:DA12 4.6 47.1 1.0
O B:VAL183 4.6 40.5 1.0
CA B:ASP182 4.6 42.6 1.0
CB B:ALA181 4.7 42.5 1.0
CA B:ILE186 4.7 40.5 1.0
C B:GLY187 4.8 40.1 1.0
CB B:ILE186 4.9 40.6 1.0

Reference:

J.H.Wong, K.A.Fiala, Z.Suo, H.Ling. Snapshots of A Y-Family Dna Polymerase in Replication: Substrate-Induced Conformational Transitions and Implications For Fidelity of DPO4. J.Mol.Biol. V. 379 317 2008.
ISSN: ISSN 0022-2836
PubMed: 18448122
DOI: 10.1016/J.JMB.2008.03.038
Page generated: Sat Dec 12 03:52:02 2020

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