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Calcium in PDB 4dtj: RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair, PDB code: 4dtj was solved by S.Xia, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.150, 119.871, 130.538, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.2

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair (pdb code 4dtj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair, PDB code: 4dtj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4dtj

Go back to Calcium Binding Sites List in 4dtj
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:15.6
occ:1.00
 OD2 A:ASP623 2.2 21.4 1.0
O1B A:TTP1001 2.2 13.5 1.0
O2G A:TTP1001 2.3 14.5 1.0
O A:LEU412 2.3 12.6 1.0
OD1 A:ASP411 2.4 30.1 1.0
O1A A:TTP1001 2.5 16.6 1.0
OD2 A:ASP411 2.6 30.0 1.0
CG A:ASP411 2.8 23.4 1.0
CG A:ASP623 3.3 17.0 1.0
PB A:TTP1001 3.3 13.6 1.0
C A:LEU412 3.5 13.6 1.0
PG A:TTP1001 3.6 15.2 1.0
PA A:TTP1001 3.6 17.7 1.0
O3A A:TTP1001 3.7 15.9 1.0
CA A:CA1003 3.7 38.4 1.0
OD1 A:ASP623 3.7 17.8 1.0
O A:HOH1688 3.8 33.7 1.0
O3B A:TTP1001 3.8 14.7 1.0
N A:LEU412 4.0 13.4 1.0
C5' A:TTP1001 4.3 12.5 1.0
CB A:ASP411 4.3 21.2 1.0
CA A:LEU412 4.3 12.7 1.0
O1G A:TTP1001 4.3 15.0 1.0
N A:SER414 4.4 12.6 1.0
O5' A:TTP1001 4.5 13.9 1.0
N A:THR413 4.5 13.5 1.0
C A:ASP411 4.5 14.5 1.0
CB A:ASP623 4.5 15.6 1.0
N A:LEU415 4.7 10.7 1.0
CA A:THR413 4.7 14.7 1.0
C A:THR413 4.7 13.4 1.0
O2B A:TTP1001 4.7 15.5 1.0
O3G A:TTP1001 4.7 15.6 1.0
O A:HOH1910 4.8 49.5 1.0
CB A:LEU412 4.8 11.7 1.0
O2A A:TTP1001 4.8 16.5 1.0
CA A:ASP411 4.9 16.6 1.0

Calcium binding site 2 out of 5 in 4dtj

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:38.4
occ:1.00
 O A:HOH1679 2.2 24.8 1.0
OD1 A:ASP411 2.5 30.1 1.0
O1A A:TTP1001 2.6 16.6 1.0
OD1 A:ASP623 2.6 17.8 1.0
CG A:ASP623 3.5 17.0 1.0
CG A:ASP411 3.6 23.4 1.0
OD2 A:ASP623 3.7 21.4 1.0
CA A:CA1002 3.7 15.6 1.0
C3' P:DT115 3.8 17.1 1.0
PA A:TTP1001 3.8 17.7 1.0
CB A:SER624 3.9 18.7 1.0
O A:HOH1688 3.9 33.7 1.0
O A:HOH1278 4.2 23.3 1.0
O2A A:TTP1001 4.3 16.5 1.0
CB A:ASP411 4.4 21.2 1.0
OD2 A:ASP411 4.4 30.0 1.0
OG A:SER624 4.4 22.2 1.0
O5' A:TTP1001 4.5 13.9 1.0
C5' A:TTP1001 4.7 12.5 1.0
N A:SER624 4.7 14.3 1.0
O A:ASP621 4.7 11.5 1.0
C A:ASP623 4.8 14.7 1.0
O5' P:DT115 4.8 17.5 1.0
OE2 A:GLU686 4.8 37.6 1.0
CA A:SER624 4.8 15.5 1.0
C4' P:DT115 4.8 16.6 1.0
C5' P:DT115 4.9 17.7 1.0
O P:HOH210 4.9 24.9 1.0
C2' P:DT115 4.9 16.5 1.0
CB A:ASP623 4.9 15.6 1.0
O2G A:TTP1001 5.0 14.5 1.0
O A:ASP623 5.0 12.5 1.0

Calcium binding site 3 out of 5 in 4dtj

Go back to Calcium Binding Sites List in 4dtj
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:28.4
occ:1.00
 OD1 A:ASN507 2.2 36.5 1.0
O A:LYS531 2.3 31.7 1.0
O A:ASN505 2.3 26.7 1.0
O A:HOH1340 2.3 37.8 1.0
O A:HOH1281 2.5 25.3 1.0
O A:HOH1260 2.5 28.5 1.0
O A:HOH1738 2.6 34.8 1.0
C A:LYS531 3.3 32.7 1.0
CG A:ASN507 3.4 35.1 1.0
C A:ASN505 3.5 28.4 1.0
ND2 A:ASN507 4.0 31.4 1.0
CA A:LYS531 4.0 30.6 1.0
N A:ASN507 4.1 32.3 1.0
CB A:ASN505 4.2 32.9 1.0
N A:LYS532 4.2 31.8 1.0
C A:PRO506 4.3 29.7 1.0
CA A:PRO506 4.4 27.7 1.0
CA A:LYS532 4.4 32.1 1.0
N A:PRO506 4.4 27.0 1.0
CA A:ASN505 4.5 31.1 1.0
CB A:ASN507 4.5 34.5 1.0
O A:LEU533 4.6 28.5 1.0
O A:ALA502 4.7 27.8 1.0
O A:HOH1317 4.7 32.0 1.0
CB A:LYS531 4.7 33.0 1.0
CA A:ASN507 4.7 32.8 1.0
C A:LYS532 4.8 31.4 1.0
O A:PRO506 4.9 29.6 1.0
O A:ILE530 4.9 23.2 1.0
N A:LEU533 4.9 28.9 1.0

Calcium binding site 4 out of 5 in 4dtj

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:47.1
occ:1.00
 O A:HOH1793 2.4 35.1 1.0
O A:HOH1682 2.4 57.8 1.0
O A:HOH1910 2.5 49.5 1.0
O A:HOH1279 2.5 28.9 1.0
OE1 A:GLU716 3.6 35.1 1.0
OD2 A:ASP411 3.8 30.0 1.0
O A:HOH1501 4.0 22.9 1.0
NZ A:LYS486 4.2 21.6 1.0
O A:ASP411 4.5 16.4 1.0
OG1 A:THR413 4.5 18.5 1.0
CD A:GLU716 4.5 32.7 1.0
CB A:ASP684 4.6 23.4 1.0
OE1 A:GLU686 4.6 39.6 1.0
CG A:GLU716 4.8 28.5 1.0
CG A:ASP411 4.8 23.4 1.0
OD2 A:ASP684 4.8 29.7 1.0
CB A:ASP411 4.9 21.2 1.0
O A:ASP684 5.0 16.8 1.0

Calcium binding site 5 out of 5 in 4dtj

Go back to Calcium Binding Sites List in 4dtj
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddt/Da As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:35.1
occ:1.00
 O A:HOH1312 2.3 25.4 1.0
O A:HOH1825 2.5 34.6 1.0
O A:HOH1134 2.5 16.6 1.0
OE1 A:GLU116 2.6 20.5 1.0
OE2 A:GLU116 2.7 21.1 1.0
CD A:GLU116 3.0 20.1 1.0
O A:HOH1769 4.1 25.1 1.0
OD2 A:ASP114 4.2 29.0 1.0
O A:HOH1654 4.3 32.9 1.0
CG A:GLU116 4.5 15.2 1.0
O A:ILE115 4.6 13.9 1.0
CD1 A:ILE309 4.7 39.5 1.0

Reference:

S.Xia, A.Vashishtha, D.Bulkley, S.H.Eom, J.Wang, W.H.Konigsberg. Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and Beyond Abasic Sites in Dna. Biochemistry V. 51 4922 2012.
ISSN: ISSN 0006-2960
PubMed: 22630605
DOI: 10.1021/BI300296Q
Page generated: Sat Jul 13 23:36:19 2024

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