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Calcium in PDB 2atl: Unmodified Insertion Ternary Complex

Enzymatic activity of Unmodified Insertion Ternary Complex

All present enzymatic activity of Unmodified Insertion Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of Unmodified Insertion Ternary Complex, PDB code: 2atl 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.584, 101.758, 112.286, 90.00, 94.72, 90.00
R / Rfree (%) 22.4 / 27.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Unmodified Insertion Ternary Complex (pdb code 2atl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Unmodified Insertion Ternary Complex, PDB code: 2atl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2atl

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Calcium binding site 1 out of 8 in the Unmodified 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 Unmodified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca418

b:46.0
occ:1.00
 O D:HOH510 2.2 2.0 1.0
O D:HOH513 2.5 8.8 1.0
O D:HOH512 3.4 6.2 1.0
O E:HOH511 3.6 13.8 1.0
N2 D:DG805 3.8 17.7 1.0
N3 D:DG805 3.9 17.7 1.0
O E:HOH509 4.1 14.8 1.0
C2 D:DG805 4.2 17.4 1.0
O4' E:DA917 4.3 2.0 1.0
N3 E:DA916 4.3 4.1 1.0
C2 E:DA916 4.6 4.2 1.0
C4 D:DG805 4.9 17.9 1.0
O4' D:DG806 5.0 5.2 1.0
C4' E:DA917 5.0 2.0 1.0

Calcium binding site 2 out of 8 in 2atl

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Calcium binding site 2 out of 8 in the Unmodified 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 Unmodified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1418

b:99.5
occ:1.00
 O H:HOH1513 2.4 2.0 1.0
O H:HOH1509 2.7 39.9 1.0
O H:HOH1511 3.5 2.0 1.0
O H:HOH1510 3.8 2.8 1.0
O H:HOH1512 4.0 2.0 1.0
N3 H:DG1805 4.2 38.4 1.0
O4' H:DG1805 4.5 39.0 1.0
C1' H:DG1805 4.6 38.5 1.0
O3' H:DG1805 4.7 38.1 1.0
N2 H:DG1805 4.9 38.2 1.0
C2 H:DG1805 4.9 38.5 1.0

Calcium binding site 3 out of 8 in 2atl

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Calcium binding site 3 out of 8 in the Unmodified 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 Unmodified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:2.0
occ:1.00
 O1G A:DCP414 2.1 17.5 1.0
O2A A:DCP414 2.1 2.0 1.0
O A:PHE8 2.3 2.0 1.0
OD1 A:ASP7 2.4 2.0 1.0
OD2 A:ASP105 2.4 2.0 1.0
O1B A:DCP414 2.5 4.3 1.0
O A:HOH503 3.1 2.0 1.0
NZ A:LYS159 3.3 5.8 1.0
CG A:ASP105 3.4 2.0 1.0
O A:HOH501 3.4 2.0 1.0
CG A:ASP7 3.4 2.0 1.0
PA A:DCP414 3.5 2.0 1.0
C A:PHE8 3.5 2.0 1.0
PG A:DCP414 3.5 18.7 1.0
PB A:DCP414 3.6 3.4 1.0
O3A A:DCP414 3.9 2.0 1.0
OD1 A:ASP105 3.9 2.0 1.0
OD2 A:ASP7 3.9 2.0 1.0
C5' A:DCP414 3.9 2.0 1.0
O3B A:DCP414 4.0 10.5 1.0
N A:PHE8 4.0 2.0 1.0
O5' A:DCP414 4.2 2.0 1.0
CA A:PHE8 4.3 2.0 1.0
O3G A:DCP414 4.4 17.2 1.0
O2G A:DCP414 4.4 18.0 1.0
N A:ASP9 4.5 2.0 1.0
N A:TYR10 4.5 2.0 1.0
O1A A:DCP414 4.5 2.0 1.0
C A:ASP7 4.6 2.0 1.0
CA A:ASP9 4.6 2.0 1.0
CB A:ASP105 4.6 2.0 1.0
CB A:ASP7 4.7 2.0 1.0
C A:ASP9 4.7 2.0 1.0
CE A:LYS159 4.7 5.5 1.0
CA A:CA416 4.8 2.0 1.0
N A:PHE11 4.8 2.0 1.0
O2B A:DCP414 4.9 2.0 1.0
CB A:PHE11 4.9 2.0 1.0
CB A:PHE8 4.9 2.0 1.0
O A:ASP105 5.0 2.0 1.0

Calcium binding site 4 out of 8 in 2atl

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Calcium binding site 4 out of 8 in the Unmodified 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 Unmodified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:2.0
occ:1.00
 OE2 A:GLU106 2.3 4.2 1.0
OD2 A:ASP7 2.3 2.0 1.0
O A:HOH503 2.5 2.0 1.0
OP1 D:DDG813 2.5 2.0 1.0
O A:HOH502 2.9 2.0 1.0
CD A:GLU106 3.4 3.2 1.0
CG A:ASP7 3.5 2.0 1.0
P D:DDG813 3.5 2.0 1.0
O5' D:DDG813 3.6 2.0 1.0
C5' D:DDG813 3.7 2.0 1.0
NZ A:LYS159 3.9 5.8 1.0
CG A:GLU106 4.0 2.0 1.0
OD1 A:ASP7 4.0 2.0 1.0
O2A A:DCP414 4.1 2.0 1.0
CE A:LYS152 4.2 7.7 1.0
OP2 D:DDG813 4.3 2.0 1.0
OE1 A:GLU106 4.4 3.2 1.0
O D:HOH502 4.5 2.1 1.0
CE A:LYS159 4.5 5.5 1.0
NZ A:LYS152 4.6 8.7 1.0
O A:HOH547 4.6 2.0 1.0
CB A:ASP7 4.7 2.0 1.0
CA A:CA415 4.8 2.0 1.0
O1A A:DCP414 4.8 2.0 1.0
CZ A:PHE5 4.8 2.0 1.0
O3' D:DA812 4.8 2.0 1.0
OD1 A:ASP105 4.9 2.0 1.0
C4' D:DDG813 4.9 2.0 1.0
C3' D:DDG813 5.0 2.0 1.0

Calcium binding site 5 out of 8 in 2atl

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Calcium binding site 5 out of 8 in the Unmodified 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 Unmodified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:7.3
occ:1.00
 O A:ALA181 2.1 10.3 1.0
O A:HOH504 2.3 2.0 1.0
O A:HOH506 2.5 7.8 1.0
O A:HOH543 2.6 2.0 1.0
O A:ILE186 2.7 9.9 1.0
O D:HOH505 3.1 2.0 1.0
O A:HOH505 3.2 2.0 1.0
C A:ALA181 3.3 10.6 1.0
C A:ILE186 4.0 10.1 1.0
N A:ASP182 4.2 10.3 1.0
CA A:ASP182 4.2 9.8 1.0
CA A:ALA181 4.3 11.1 1.0
OD1 A:ASP182 4.5 8.9 1.0
OP2 D:DA812 4.6 2.0 1.0
CA A:GLY187 4.7 11.5 1.0
CB A:ALA181 4.7 11.1 1.0
OP1 D:DA812 4.8 2.0 1.0
N A:GLY187 4.8 10.7 1.0
C A:ASP182 4.8 9.5 1.0
N A:VAL183 5.0 9.4 1.0
CA A:ILE186 5.0 9.9 1.0

Calcium binding site 6 out of 8 in 2atl

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Calcium binding site 6 out of 8 in the Unmodified 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 Unmodified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:2.2
occ:1.00
 O B:HOH1501 2.2 2.0 1.0
O2A B:DCP1414 2.3 4.2 1.0
OD2 B:ASP1105 2.3 2.0 1.0
O B:PHE1008 2.3 3.2 1.0
O1B B:DCP1414 2.4 9.8 1.0
OD1 B:ASP1007 2.4 3.5 1.0
O1G B:DCP1414 2.9 16.1 1.0
NZ B:LYS1159 3.1 15.8 1.0
PB B:DCP1414 3.5 9.8 1.0
C B:PHE1008 3.5 3.0 1.0
O2G B:DCP1414 3.5 16.0 1.0
CG B:ASP1105 3.5 2.0 1.0
CG B:ASP1007 3.5 2.0 1.0
PA B:DCP1414 3.5 5.3 1.0
PG B:DCP1414 3.6 17.0 1.0
CA B:CA1416 3.7 4.0 1.0
O3A B:DCP1414 3.8 7.5 1.0
O3B B:DCP1414 3.9 13.1 1.0
OD2 B:ASP1007 4.0 3.1 1.0
N B:PHE1008 4.0 2.0 1.0
C5' B:DCP1414 4.1 2.0 1.0
CA B:PHE1008 4.3 2.5 1.0
O5' B:DCP1414 4.3 2.4 1.0
C B:ASP1007 4.3 2.0 1.0
OD1 B:ASP1105 4.4 2.0 1.0
CB B:ASP1105 4.4 2.0 1.0
N B:ASP1009 4.4 3.2 1.0
O B:HOH1503 4.5 10.9 1.0
N B:TYR1010 4.5 3.5 1.0
CE B:LYS1159 4.5 16.1 1.0
CA B:ASP1009 4.6 3.4 1.0
O1A B:DCP1414 4.6 4.7 1.0
O B:ASP1007 4.6 2.0 1.0
O2B B:DCP1414 4.7 9.3 1.0
C B:ASP1009 4.8 3.5 1.0
CB B:ASP1007 4.8 2.0 1.0
CB B:PHE1008 5.0 2.4 1.0
O3G B:DCP1414 5.0 16.6 1.0
CA B:ASP1007 5.0 2.0 1.0

Calcium binding site 7 out of 8 in 2atl

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Calcium binding site 7 out of 8 in the Unmodified 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 Unmodified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:4.0
occ:1.00
 O B:HOH1502 2.3 2.0 1.0
OE2 B:GLU1106 2.3 3.3 1.0
OD2 B:ASP1007 2.3 3.1 1.0
O B:HOH1503 2.8 10.9 1.0
O2A B:DCP1414 2.9 4.2 1.0
OP1 H:DDG1813 2.9 2.0 1.0
CG B:ASP1007 3.2 2.0 1.0
NZ B:LYS1159 3.3 15.8 1.0
O H:HOH1504 3.3 14.8 1.0
OD1 B:ASP1007 3.4 3.5 1.0
CD B:GLU1106 3.4 2.0 1.0
CA B:CA1415 3.7 2.2 1.0
OD2 B:ASP1105 3.8 2.0 1.0
CG B:GLU1106 3.9 2.0 1.0
P H:DDG1813 4.0 2.0 1.0
OD1 B:ASP1105 4.0 2.0 1.0
O5' H:DDG1813 4.1 2.0 1.0
O1A B:DCP1414 4.1 4.7 1.0
PA B:DCP1414 4.1 5.3 1.0
C3' H:DDG1813 4.3 2.0 1.0
CG B:ASP1105 4.3 2.0 1.0
CE B:LYS1159 4.4 16.1 1.0
OE1 B:GLU1106 4.4 2.0 1.0
OP2 H:DDG1813 4.5 2.3 1.0
C5' H:DDG1813 4.6 2.0 1.0
CB B:ASP1007 4.6 2.0 1.0
O2G B:DCP1414 4.8 16.0 1.0
O5' B:DCP1414 4.8 2.4 1.0
C4' H:DDG1813 4.9 2.0 1.0

Calcium binding site 8 out of 8 in 2atl

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Calcium binding site 8 out of 8 in the Unmodified Insertion Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Unmodified Insertion Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:18.0
occ:1.00
 O B:HOH1505 2.1 6.1 1.0
O B:ALA1181 2.3 17.9 1.0
O B:HOH1508 2.3 75.2 1.0
O B:ILE1186 2.4 14.7 1.0
O B:HOH1506 3.4 2.0 1.0
C B:ALA1181 3.5 17.8 1.0
C B:ILE1186 3.6 15.0 1.0
CA B:GLY1187 4.0 15.2 1.0
N B:GLY1187 4.2 15.0 1.0
CA B:ALA1181 4.2 17.9 1.0
O B:VAL1183 4.3 16.3 1.0
OP1 H:DA1812 4.3 7.8 1.0
C B:GLY1187 4.4 15.5 1.0
O B:GLY1187 4.4 15.4 1.0
N B:ASP1182 4.5 17.4 1.0
CB B:ALA1181 4.5 18.0 1.0
OP2 H:DA1812 4.5 8.6 1.0
CA B:ASP1182 4.6 17.1 1.0
CA B:ILE1186 4.7 15.2 1.0
C B:ASP1182 4.9 16.8 1.0
N B:VAL1183 5.0 16.5 1.0
P H:DA1812 5.0 8.4 1.0
CB B:ILE1186 5.0 15.3 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 04:23:08 2025

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