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Calcium in PDB 4dtr: RB69 Dna Polymerase Ternary Complex with Datp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair

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

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Datp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair, PDB code: 4dtr 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) 44.20 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.016, 120.145, 130.524, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.8

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 4dtr

Go back to Calcium Binding Sites List in 4dtr
Calcium binding site 1 out of 4 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite An Abasic Site and Ddc/Dg 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 Datp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:28.6
occ:1.00
 OD1 A:ASP623 2.1 32.9 1.0
O2B A:DTP1001 2.2 28.1 1.0
O1G A:DTP1001 2.2 25.4 1.0
O A:LEU412 2.3 29.3 1.0
OD2 A:ASP411 2.4 47.9 1.0
O2A A:DTP1001 2.5 27.8 1.0
OD1 A:ASP411 2.8 45.5 1.0
CG A:ASP411 2.9 35.8 1.0
CG A:ASP623 3.3 27.9 1.0
PB A:DTP1001 3.3 26.8 1.0
C A:LEU412 3.5 30.4 1.0
PG A:DTP1001 3.5 27.9 1.0
PA A:DTP1001 3.6 28.9 1.0
CA A:CA1003 3.6 51.7 1.0
O3A A:DTP1001 3.7 29.3 1.0
OD2 A:ASP623 3.7 27.4 1.0
O A:HOH1243 3.8 44.6 1.0
O3B A:DTP1001 3.8 27.0 1.0
N A:LEU412 4.1 27.3 1.0
C5' A:DTP1001 4.3 24.3 1.0
O2G A:DTP1001 4.3 25.7 1.0
CA A:LEU412 4.3 27.7 1.0
O A:HOH1433 4.4 49.3 1.0
CB A:ASP411 4.4 31.8 1.0
O5' A:DTP1001 4.4 26.6 1.0
N A:SER414 4.4 24.2 1.0
CB A:ASP623 4.5 25.1 1.0
N A:THR413 4.5 30.0 1.0
C A:ASP411 4.5 30.1 1.0
CA A:THR413 4.7 25.8 1.0
O3G A:DTP1001 4.7 31.3 1.0
O1B A:DTP1001 4.7 30.6 1.0
N A:LEU415 4.7 19.2 1.0
C A:THR413 4.7 27.5 1.0
CB A:LEU412 4.8 24.2 1.0
O1A A:DTP1001 4.9 33.8 1.0
CA A:ASP411 4.9 29.2 1.0

Calcium binding site 2 out of 4 in 4dtr

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Calcium binding site 2 out of 4 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite An Abasic Site and Ddc/Dg 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 Datp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:51.7
occ:1.00
 O A:HOH1428 2.4 45.9 1.0
OD2 A:ASP411 2.5 47.9 1.0
O2A A:DTP1001 2.6 27.8 1.0
OD2 A:ASP623 2.6 27.4 1.0
CG A:ASP623 3.5 27.9 1.0
OD1 A:ASP623 3.6 32.9 1.0
CA A:CA1002 3.6 28.6 1.0
CG A:ASP411 3.6 35.8 1.0
PA A:DTP1001 3.8 28.9 1.0
O A:HOH1243 3.9 44.6 1.0
CB A:SER624 4.0 28.6 1.0
C3' P:DOC115 4.0 26.1 1.0
C5' P:DOC115 4.2 30.9 1.0
O1A A:DTP1001 4.3 33.8 1.0
CB A:ASP411 4.4 31.8 1.0
O A:HOH1216 4.4 29.3 1.0
O5' A:DTP1001 4.5 26.6 1.0
C4' P:DOC115 4.5 26.9 1.0
OD1 A:ASP411 4.5 45.5 1.0
OG A:SER624 4.6 33.6 1.0
N A:SER624 4.7 27.4 1.0
C5' A:DTP1001 4.7 24.3 1.0
O A:ASP621 4.7 26.2 1.0
C A:ASP623 4.7 28.2 1.0
CA A:SER624 4.8 29.8 1.0
CB A:ASP623 4.9 25.1 1.0
OE2 A:GLU686 4.9 63.8 1.0
O1G A:DTP1001 4.9 25.4 1.0
O A:ASP623 5.0 27.9 1.0

Calcium binding site 3 out of 4 in 4dtr

Go back to Calcium Binding Sites List in 4dtr
Calcium binding site 3 out of 4 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite An Abasic Site and Ddc/Dg 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 Datp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:45.5
occ:1.00
 OD1 A:ASN507 2.1 47.7 1.0
O A:HOH1484 2.3 45.5 1.0
O A:LYS531 2.3 52.7 1.0
O A:ASN505 2.3 51.5 1.0
O A:HOH1376 2.5 40.1 1.0
O A:HOH1275 2.6 40.5 1.0
CG A:ASN507 3.2 56.0 1.0
C A:LYS531 3.3 59.4 1.0
C A:ASN505 3.6 48.9 1.0
ND2 A:ASN507 3.8 55.1 1.0
N A:ASN507 4.1 47.0 1.0
CB A:ASN505 4.1 51.0 1.0
CA A:LYS531 4.1 56.0 1.0
N A:LYS532 4.2 50.8 1.0
CA A:LYS532 4.3 51.3 1.0
C A:PRO506 4.3 47.3 1.0
O A:HOH1606 4.4 47.6 1.0
CA A:PRO506 4.4 45.2 1.0
O A:LEU533 4.5 39.1 1.0
CB A:ASN507 4.5 54.5 1.0
CA A:ASN505 4.5 50.4 1.0
N A:PRO506 4.5 47.3 1.0
O A:ALA502 4.6 47.4 1.0
C A:LYS532 4.7 49.5 1.0
CA A:ASN507 4.7 51.5 1.0
N A:LEU533 4.8 47.9 1.0
CB A:LYS531 4.8 51.6 1.0
O A:ILE530 4.9 39.1 1.0
O A:PRO506 4.9 52.0 1.0

Calcium binding site 4 out of 4 in 4dtr

Go back to Calcium Binding Sites List in 4dtr
Calcium binding site 4 out of 4 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite An Abasic Site and Ddc/Dg 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 Datp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:65.5
occ:1.00
 O A:HOH1259 2.4 39.0 1.0
O A:HOH1115 2.5 33.4 1.0
OE1 A:GLU116 2.7 38.8 1.0
OE2 A:GLU116 2.7 39.5 1.0
CD A:GLU116 3.1 40.8 1.0
O A:HOH1585 4.1 45.2 1.0
OD2 A:ASP114 4.2 53.3 1.0
O A:HOH1548 4.3 46.0 1.0
O A:ILE115 4.6 28.3 1.0
CG A:GLU116 4.6 33.4 1.0
CD1 A:ILE309 4.9 42.9 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 23:38:24 2024

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