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

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

Go back to 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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy