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Calcium in PDB 3gil: DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair

Enzymatic activity of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair

All present enzymatic activity of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair:
2.7.7.7;

Protein crystallography data

The structure of DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair, PDB code: 3gil 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 / 2.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.289, 110.682, 102.190, 90.00, 99.22, 90.00
R / Rfree (%) 20 / 25.9

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair (pdb code 3gil). 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(Anti)-T(Anti) Pair, PDB code: 3gil:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3gil

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Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair


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(Anti)-T(Anti) Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:37.8
occ:1.00
 O A:HOH615 2.2 21.9 1.0
O2A A:DGT414 2.3 38.1 1.0
OD2 A:ASP7 2.3 40.7 1.0
OE2 A:GLU106 2.3 41.4 1.0
OD1 A:ASP105 2.5 45.4 1.0
O A:HOH614 2.9 54.8 1.0
CG A:ASP7 3.1 44.4 1.0
CG A:ASP105 3.2 45.7 1.0
OD2 A:ASP105 3.2 43.4 1.0
OD1 A:ASP7 3.4 43.7 1.0
CD A:GLU106 3.4 45.8 1.0
CA A:CA416 3.5 38.6 1.0
PA A:DGT414 3.6 35.0 1.0
O1A A:DGT414 3.9 36.7 1.0
CG A:GLU106 4.0 45.1 1.0
CB A:GLU106 4.0 46.0 1.0
OG A:SER103 4.1 45.4 1.0
O D:HOH536 4.1 39.4 1.0
O5' A:DGT414 4.2 36.2 1.0
C5' A:DGT414 4.3 35.9 1.0
CB A:ASP7 4.3 42.8 1.0
OE1 A:GLU106 4.4 45.5 1.0
O A:HOH520 4.5 44.0 1.0
CB A:ASP105 4.6 45.8 1.0
C A:ASP105 4.7 45.7 1.0
O A:ASP105 4.7 46.1 1.0
O1G A:DGT414 4.8 40.3 1.0
N A:GLU106 4.8 46.0 1.0
O3A A:DGT414 4.9 35.8 1.0
OP1 D:2DT814 5.0 44.1 1.0
CA A:ASP7 5.0 42.8 1.0

Calcium binding site 2 out of 6 in 3gil

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Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair


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(Anti)-T(Anti) Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:38.6
occ:1.00
 OD1 A:ASP7 2.3 43.7 1.0
O1B A:DGT414 2.3 37.0 1.0
O A:PHE8 2.3 41.2 1.0
O2A A:DGT414 2.3 38.1 1.0
O1G A:DGT414 2.3 40.3 1.0
OD2 A:ASP105 2.3 43.4 1.0
PG A:DGT414 3.2 43.4 1.0
PB A:DGT414 3.2 35.1 1.0
CG A:ASP7 3.3 44.4 1.0
PA A:DGT414 3.3 35.0 1.0
O3A A:DGT414 3.4 35.8 1.0
CG A:ASP105 3.5 45.7 1.0
C A:PHE8 3.5 42.4 1.0
CA A:CA415 3.5 37.8 1.0
O A:HOH595 3.6 22.8 1.0
OD2 A:ASP7 3.7 40.7 1.0
O3B A:DGT414 3.8 39.0 1.0
C5' A:DGT414 4.1 35.9 1.0
OD1 A:ASP105 4.1 45.4 1.0
O5' A:DGT414 4.2 36.2 1.0
N A:PHE8 4.2 42.7 1.0
O3G A:DGT414 4.2 40.2 1.0
C A:ASP7 4.3 42.7 1.0
O2G A:DGT414 4.4 42.1 1.0
O A:HOH615 4.4 21.9 1.0
CA A:PHE8 4.4 42.9 1.0
O A:ASP7 4.4 42.7 1.0
N A:TYR10 4.5 44.0 1.0
CE A:LYS159 4.5 51.2 1.0
N A:ASP9 4.5 42.4 1.0
O2B A:DGT414 4.6 36.9 1.0
CA A:ASP9 4.6 43.0 1.0
O1A A:DGT414 4.6 36.7 1.0
CB A:ASP7 4.6 42.8 1.0
CB A:ASP105 4.7 45.8 1.0
C A:ASP9 4.7 43.5 1.0
NZ A:LYS159 4.8 52.5 1.0
N A:PHE11 4.9 44.2 1.0
CA A:ASP7 5.0 42.8 1.0

Calcium binding site 3 out of 6 in 3gil

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Calcium binding site 3 out of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair


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(Anti)-T(Anti) Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:60.3
occ:1.00
 O A:HOH619 2.2 30.6 1.0
O A:HOH616 2.3 33.5 1.0
O A:ALA181 2.3 59.2 1.0
O A:ILE186 2.3 59.6 1.0
O D:HOH617 2.3 30.4 1.0
C A:ALA181 3.4 58.9 1.0
C A:ILE186 3.5 59.2 1.0
O A:HOH618 3.6 65.0 1.0
CA A:ALA181 4.0 58.7 1.0
CA A:GLY187 4.0 59.9 1.0
CB A:ALA181 4.1 58.7 1.0
N A:GLY187 4.2 59.7 1.0
C A:GLY187 4.4 60.0 1.0
N A:ASP182 4.5 58.7 1.0
O A:GLY187 4.5 60.1 1.0
OP2 D:DG813 4.7 41.6 1.0
CA A:ILE186 4.7 58.9 1.0
CA A:ASP182 4.8 58.7 1.0
CB A:ILE186 4.8 59.0 1.0
O A:VAL183 4.9 57.9 1.0
OP1 D:DG813 4.9 42.4 1.0

Calcium binding site 4 out of 6 in 3gil

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Calcium binding site 4 out of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair


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(Anti)-T(Anti) Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:47.5
occ:1.00
 OE2 B:GLU1106 2.3 50.2 1.0
O2A B:DGT1414 2.3 40.9 1.0
OD2 B:ASP1007 2.3 46.6 1.0
OD1 B:ASP1105 2.5 45.9 1.0
O B:HOH621 2.6 42.4 1.0
CG B:ASP1007 3.0 43.9 1.0
CG B:GLU1106 3.0 49.9 1.0
CD B:GLU1106 3.0 51.4 1.0
OD1 B:ASP1007 3.1 42.1 1.0
OD2 B:ASP1105 3.1 43.5 1.0
CG B:ASP1105 3.2 47.4 1.0
CA B:CA1416 3.4 40.4 1.0
PA B:DGT1414 3.6 32.2 1.0
O1A B:DGT1414 4.0 33.7 1.0
C5' B:DGT1414 4.0 28.5 1.0
O5' B:DGT1414 4.2 31.0 1.0
OE1 B:GLU1106 4.3 51.0 1.0
CB B:ASP1007 4.3 43.3 1.0
CB B:GLU1106 4.4 48.8 1.0
O1G B:DGT1414 4.4 38.6 1.0
OG B:SER1103 4.5 49.9 1.0
O B:ASP1105 4.6 47.6 1.0
C B:ASP1105 4.6 48.0 1.0
CB B:ASP1105 4.7 48.0 1.0
NZ B:LYS1159 4.8 54.3 1.0
N B:GLU1106 4.8 48.2 1.0
NZ B:LYS1152 4.9 48.3 1.0
OP1 H:2DT1814 4.9 48.4 1.0
CA B:ASP1007 4.9 43.1 1.0
CA B:GLU1106 5.0 48.5 1.0
O3A B:DGT1414 5.0 34.2 1.0

Calcium binding site 5 out of 6 in 3gil

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Calcium binding site 5 out of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair


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(Anti)-T(Anti) Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:40.4
occ:1.00
 O2A B:DGT1414 2.3 40.9 1.0
OD1 B:ASP1007 2.3 42.1 1.0
O1B B:DGT1414 2.3 37.6 1.0
O B:PHE1008 2.3 41.4 1.0
OD2 B:ASP1105 2.3 43.5 1.0
O1G B:DGT1414 2.3 38.6 1.0
PG B:DGT1414 3.0 36.4 1.0
O B:HOH597 3.1 33.9 1.0
PB B:DGT1414 3.3 32.6 1.0
PA B:DGT1414 3.3 32.2 1.0
CA B:CA1415 3.4 47.5 1.0
CG B:ASP1007 3.4 43.9 1.0
CG B:ASP1105 3.5 47.4 1.0
C B:PHE1008 3.5 42.5 1.0
O3A B:DGT1414 3.5 34.2 1.0
OD2 B:ASP1007 3.8 46.6 1.0
O3B B:DGT1414 3.8 35.9 1.0
O2G B:DGT1414 3.9 35.9 1.0
C5' B:DGT1414 3.9 28.5 1.0
OD1 B:ASP1105 4.0 45.9 1.0
N B:PHE1008 4.0 43.0 1.0
O5' B:DGT1414 4.1 31.0 1.0
NZ B:LYS1159 4.2 54.3 1.0
O3G B:DGT1414 4.2 34.0 1.0
CA B:PHE1008 4.3 42.9 1.0
C B:ASP1007 4.4 43.0 1.0
N B:ASP1009 4.5 42.5 1.0
O1A B:DGT1414 4.5 33.7 1.0
N B:TYR1010 4.5 42.5 1.0
O2B B:DGT1414 4.6 32.5 1.0
CA B:ASP1009 4.6 42.7 1.0
CB B:ASP1007 4.7 43.3 1.0
CB B:ASP1105 4.7 48.0 1.0
O B:ASP1007 4.8 42.6 1.0
C B:ASP1009 4.8 42.6 1.0
N B:PHE1011 4.9 41.8 1.0
O B:HOH621 4.9 42.4 1.0
CA B:ASP1007 5.0 43.1 1.0

Calcium binding site 6 out of 6 in 3gil

Go back to Calcium Binding Sites List in 3gil
Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with Oxog(Anti)-T(Anti) Pair


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(Anti)-T(Anti) Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:64.8
occ:1.00
 O B:ILE1186 2.3 65.1 1.0
OP1 H:DG1813 2.3 60.0 1.0
O B:HOH627 2.5 56.9 1.0
O B:HOH626 2.6 45.7 1.0
O H:HOH625 2.7 42.9 1.0
O B:ALA1181 2.8 63.5 1.0
O B:VAL1183 3.4 62.4 1.0
C B:ILE1186 3.4 65.0 1.0
P H:DG1813 3.8 51.7 1.0
N B:ILE1186 3.9 64.0 1.0
C B:ALA1181 4.0 63.3 1.0
C B:VAL1183 4.1 62.4 1.0
CA B:ILE1186 4.1 64.4 1.0
CB B:ILE1186 4.4 64.4 1.0
N B:VAL1183 4.5 62.3 1.0
N B:GLY1187 4.5 65.7 1.0
OP2 H:DG1813 4.5 53.0 1.0
N B:GLY1185 4.5 63.2 1.0
C B:ASP1182 4.5 62.6 1.0
CA B:PRO1184 4.6 62.5 1.0
O5' H:DG1813 4.6 50.3 1.0
N B:PRO1184 4.6 62.3 1.0
CA B:ASP1182 4.7 63.0 1.0
O3' H:DA1812 4.7 49.4 1.0
CA B:GLY1187 4.7 66.0 1.0
N B:ASP1182 4.8 63.1 1.0
C B:PRO1184 4.8 62.8 1.0
O B:HOH624 4.9 60.9 1.0
CA B:VAL1183 4.9 62.3 1.0
O B:ASP1182 4.9 62.5 1.0
C B:GLY1185 4.9 63.5 1.0
CA B:ALA1181 5.0 63.3 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

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