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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

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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

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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

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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

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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

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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

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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: Tue Jul 8 12:43:49 2025

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