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Calcium in PDB 2asd: Oxog-Modified Insertion Ternary Complex

Enzymatic activity of Oxog-Modified Insertion Ternary Complex

All present enzymatic activity of Oxog-Modified Insertion Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of Oxog-Modified Insertion Ternary Complex, PDB code: 2asd was solved by O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.955, 101.109, 84.124, 90.00, 97.14, 90.00
R / Rfree (%) 22.5 / 25.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Oxog-Modified Insertion Ternary Complex (pdb code 2asd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Oxog-Modified Insertion Ternary Complex, PDB code: 2asd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2asd

Go back to Calcium Binding Sites List in 2asd
Calcium binding site 1 out of 7 in the Oxog-Modified Insertion Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Oxog-Modified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca418

b:27.0
occ:1.00
 O D:HOH693 1.9 20.0 0.0
O D:HOH694 2.3 33.7 1.0
O D:HOH696 2.4 31.9 1.0
O E:HOH691 2.4 36.0 1.0
O D:HOH695 2.5 34.8 1.0
O D:HOH692 2.5 44.1 1.0
N2 D:DG805 4.3 12.6 1.0
O D:HOH537 4.5 34.7 1.0
N3 D:DG805 4.6 12.3 1.0
O4' E:DA917 4.7 9.3 1.0
O4' D:DG806 4.7 12.4 1.0
N3 E:DA916 4.8 11.3 1.0
C4' E:DA917 4.9 10.6 1.0
C4' D:DG806 4.9 12.9 1.0
O D:HOH503 4.9 31.9 1.0
C5' D:DG806 4.9 12.7 1.0
C2 D:DG805 5.0 12.9 1.0

Calcium binding site 2 out of 7 in 2asd

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Calcium binding site 2 out of 7 in the Oxog-Modified Insertion Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Oxog-Modified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:17.8
occ:1.00
 O A:HOH520 2.3 26.4 1.0
OE2 A:GLU106 2.3 17.5 1.0
OP1 D:DDG813 2.3 17.2 1.0
O A:HOH519 2.3 18.0 1.0
OD2 A:ASP7 2.4 12.0 1.0
O A:HOH521 2.5 29.6 1.0
CD A:GLU106 3.2 14.9 1.0
CG A:ASP7 3.4 12.3 1.0
P D:DDG813 3.5 16.5 1.0
O5' D:DDG813 3.8 16.6 1.0
CG A:GLU106 3.8 13.5 1.0
NZ A:LYS159 3.8 18.1 1.0
OD1 A:ASP7 3.9 12.8 1.0
O2A A:DCP414 4.0 13.4 1.0
NZ A:LYS152 4.0 15.1 1.0
OE1 A:GLU106 4.1 16.0 1.0
C5' D:DDG813 4.1 15.3 1.0
OP2 D:DDG813 4.3 16.6 1.0
CZ A:PHE5 4.6 12.3 1.0
CB A:ASP7 4.6 11.5 1.0
CE A:LYS152 4.7 15.4 1.0
O3' D:DA812 4.7 15.5 1.0
O A:HOH533 4.8 43.4 1.0
OD1 A:ASP105 4.8 11.0 1.0
O1A A:DCP414 4.9 14.2 1.0
CA A:CA416 4.9 12.8 1.0
CE A:LYS159 4.9 18.5 1.0
C3' D:DDG813 4.9 15.2 1.0
O A:HOH531 4.9 41.2 1.0

Calcium binding site 3 out of 7 in 2asd

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Calcium binding site 3 out of 7 in the Oxog-Modified Insertion Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Oxog-Modified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:12.8
occ:1.00
 O A:PHE8 2.3 11.7 1.0
O1G A:DCP414 2.3 15.2 1.0
OD2 A:ASP105 2.3 12.2 1.0
OD1 A:ASP7 2.3 12.8 1.0
O1B A:DCP414 2.3 13.9 1.0
O2A A:DCP414 2.3 13.4 1.0
PB A:DCP414 3.5 14.8 1.0
CG A:ASP105 3.5 12.3 1.0
CG A:ASP7 3.5 12.3 1.0
C A:PHE8 3.5 11.4 1.0
PG A:DCP414 3.5 21.6 1.0
PA A:DCP414 3.6 14.0 1.0
O A:HOH519 3.6 18.0 1.0
O3A A:DCP414 3.9 13.3 1.0
O3B A:DCP414 3.9 16.6 1.0
OD2 A:ASP7 4.0 12.0 1.0
N A:PHE8 4.0 11.6 1.0
C5' A:DCP414 4.0 11.2 1.0
OD1 A:ASP105 4.1 11.0 1.0
O5' A:DCP414 4.3 12.1 1.0
O3G A:DCP414 4.3 15.7 1.0
C A:ASP7 4.3 11.5 1.0
CA A:PHE8 4.3 11.5 1.0
NZ A:LYS159 4.3 18.1 1.0
O A:HOH520 4.4 26.4 1.0
N A:ASP9 4.5 11.2 1.0
O2G A:DCP414 4.5 18.3 1.0
CB A:ASP105 4.6 11.4 1.0
CA A:ASP9 4.6 11.1 1.0
N A:TYR10 4.6 10.7 1.0
CB A:ASP7 4.6 11.5 1.0
O2B A:DCP414 4.7 12.3 1.0
O A:ASP7 4.7 11.3 1.0
O1A A:DCP414 4.7 14.2 1.0
C A:ASP9 4.7 10.9 1.0
N A:PHE11 4.7 9.3 1.0
CE A:LYS159 4.8 18.5 1.0
CA A:ASP7 4.8 11.5 1.0
CA A:CA415 4.9 17.8 1.0
CB A:PHE11 4.9 8.7 1.0
CB A:PHE8 4.9 11.4 1.0

Calcium binding site 4 out of 7 in 2asd

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Calcium binding site 4 out of 7 in the Oxog-Modified Insertion Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Oxog-Modified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:14.8
occ:1.00
 O A:HOH687 2.2 26.5 1.0
O A:HOH689 2.3 36.9 1.0
O A:ALA181 2.3 13.9 1.0
O A:HOH690 2.3 22.3 1.0
O A:ILE186 2.3 13.6 1.0
O D:HOH688 2.4 26.4 1.0
O A:HOH685 2.5 20.0 0.0
O A:HOH686 2.9 20.0 0.0
C A:ALA181 3.4 13.3 1.0
C A:ILE186 3.6 13.6 1.0
CA A:GLY187 4.2 14.3 1.0
N A:GLY187 4.3 13.9 1.0
CA A:ALA181 4.3 12.8 1.0
OP2 D:DA812 4.4 12.0 1.0
N A:ASP182 4.4 13.4 1.0
OP1 D:DA812 4.4 11.6 1.0
CA A:ASP182 4.5 13.9 1.0
CB A:ALA181 4.6 12.8 1.0
O A:VAL183 4.6 12.6 1.0
C A:GLY187 4.6 14.6 1.0
O A:HOH1701 4.7 36.0 1.0
CA A:ILE186 4.7 13.4 1.0
O A:GLY187 4.7 14.7 1.0
CB A:ILE186 4.8 13.4 1.0
O D:HOH568 4.9 52.9 1.0
OD1 A:ASP182 4.9 19.6 1.0
P D:DA812 5.0 12.5 1.0

Calcium binding site 5 out of 7 in 2asd

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Calcium binding site 5 out of 7 in the Oxog-Modified Insertion Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Oxog-Modified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:22.0
occ:1.00
 O B:ALA1181 2.3 20.5 1.0
O B:HOH1508 2.3 51.3 1.0
O H:HOH1512 2.3 34.9 1.0
O B:HOH1510 2.3 46.3 1.0
O B:HOH1509 2.4 44.2 1.0
O H:HOH1511 2.4 32.1 1.0
O B:ILE1186 2.6 18.4 1.0
C B:ALA1181 3.4 19.7 1.0
C B:ILE1186 3.8 18.3 1.0
CA B:ALA1181 4.2 19.9 1.0
CA B:GLY1187 4.2 19.5 1.0
CB B:ALA1181 4.4 19.9 1.0
N B:ASP1182 4.4 19.2 1.0
OP2 H:DA1812 4.4 13.7 1.0
N B:GLY1187 4.5 18.9 1.0
OP1 H:DA1812 4.5 13.1 1.0
CA B:ASP1182 4.6 18.9 1.0
O B:VAL1183 4.7 16.6 1.0
C B:GLY1187 4.7 20.1 1.0
CA B:ILE1186 5.0 18.0 1.0
P H:DA1812 5.0 13.7 1.0

Calcium binding site 6 out of 7 in 2asd

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Calcium binding site 6 out of 7 in the Oxog-Modified Insertion Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Oxog-Modified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:11.1
occ:1.00
 OD2 B:ASP1007 2.3 11.2 1.0
OD2 B:ASP1105 2.3 12.5 1.0
O B:PHE1008 2.3 11.6 1.0
O1B B:DCP1414 2.3 10.8 1.0
O2A B:DCP1414 2.3 10.8 1.0
O1G B:DCP1414 2.3 14.2 1.0
PB B:DCP1414 3.4 13.1 1.0
CG B:ASP1105 3.5 13.2 1.0
CG B:ASP1007 3.5 12.3 1.0
C B:PHE1008 3.5 11.5 1.0
PA B:DCP1414 3.5 12.5 1.0
PG B:DCP1414 3.5 20.8 1.0
O B:HOH1503 3.6 20.1 1.0
O3A B:DCP1414 3.8 12.9 1.0
O3B B:DCP1414 3.8 14.7 1.0
OD1 B:ASP1105 4.0 13.5 1.0
N B:PHE1008 4.0 11.2 1.0
OD1 B:ASP1007 4.0 12.7 1.0
C5' B:DCP1414 4.0 9.5 1.0
O B:HOH1622 4.0 28.4 1.0
NZ B:LYS1159 4.2 19.4 1.0
O3G B:DCP1414 4.2 14.2 1.0
O5' B:DCP1414 4.2 11.2 1.0
O B:HOH1505 4.3 28.6 1.0
CA B:PHE1008 4.3 11.5 1.0
C B:ASP1007 4.3 11.1 1.0
N B:ASP1009 4.5 11.1 1.0
CB B:ASP1105 4.6 13.6 1.0
CA B:ASP1009 4.6 11.2 1.0
O2B B:DCP1414 4.7 11.5 1.0
CB B:ASP1007 4.7 11.2 1.0
N B:TYR1010 4.7 10.7 1.0
O2G B:DCP1414 4.7 19.5 1.0
O B:ASP1007 4.7 10.7 1.0
O1A B:DCP1414 4.7 12.6 1.0
C B:ASP1009 4.8 10.7 1.0
CA B:CA1417 4.8 25.2 1.0
CA B:ASP1007 4.8 10.9 1.0
N B:PHE1011 4.9 9.8 1.0
O B:ASP1105 4.9 12.7 1.0
CB B:PHE1008 4.9 11.6 1.0
CB B:PHE1011 4.9 9.2 1.0
CE B:LYS1159 5.0 19.1 1.0

Calcium binding site 7 out of 7 in 2asd

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Calcium binding site 7 out of 7 in the Oxog-Modified Insertion Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Oxog-Modified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:25.2
occ:1.00
 O B:HOH1503 2.3 20.1 1.0
O B:HOH1505 2.4 28.6 1.0
O B:HOH1504 2.4 31.4 1.0
OD1 B:ASP1007 2.5 12.7 1.0
OE2 B:GLU1106 2.5 17.4 1.0
OP1 H:DDG1813 2.6 20.9 1.0
CD B:GLU1106 3.3 18.1 1.0
CG B:ASP1007 3.5 12.3 1.0
P H:DDG1813 3.7 20.7 1.0
NZ B:LYS1159 3.7 19.4 1.0
NZ B:LYS1152 3.8 16.7 1.0
CG B:GLU1106 3.8 15.2 1.0
O2A B:DCP1414 3.8 10.8 1.0
OD2 B:ASP1007 3.8 11.2 1.0
O5' H:DDG1813 3.9 18.7 1.0
C5' H:DDG1813 4.0 16.4 1.0
OE1 B:GLU1106 4.1 21.0 1.0
CE B:LYS1152 4.3 16.6 1.0
OP2 H:DDG1813 4.4 20.2 1.0
CZ B:PHE1005 4.5 11.2 1.0
CB B:ASP1007 4.7 11.2 1.0
O1A B:DCP1414 4.7 12.6 1.0
CE B:LYS1159 4.8 19.1 1.0
O H:HOH1506 4.8 40.0 1.0
CA B:CA1416 4.8 11.1 1.0
OD1 B:ASP1105 4.8 13.5 1.0
C3' H:DDG1813 4.8 14.3 1.0
PA B:DCP1414 4.9 12.5 1.0
CE2 B:PHE1005 5.0 10.9 1.0
O3' H:DA1812 5.0 20.0 1.0

Reference:

O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, D.J.Patel. Stepwise Translocation of DPO4 Polymerase During Error-Free Bypass of An Oxog Lesion Plos Biol. V. 4 1 2006.
ISSN: ISSN 1544-9173
PubMed: 16379496
DOI: 10.1371/JOURNAL.PBIO.0040011
Page generated: Tue Jul 8 04:21:41 2025

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