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

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dttp 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 Dttp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair, PDB code: 4dtx 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) 35.38 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.414, 120.208, 131.619, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.6

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dttp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair (pdb code 4dtx). 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 Dttp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair, PDB code: 4dtx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4dtx

Go back to Calcium Binding Sites List in 4dtx
Calcium binding site 1 out of 4 in the RB69 Dna Polymerase Ternary Complex with Dttp 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 Dttp 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:23.2
occ:1.00
 O2B A:TTP1001 2.2 32.0 1.0
OD1 A:ASP623 2.2 35.0 1.0
O1G A:TTP1001 2.3 35.0 1.0
O A:LEU412 2.3 20.4 1.0
OD2 A:ASP411 2.4 36.1 1.0
O2A A:TTP1001 2.5 38.2 1.0
OD1 A:ASP411 2.8 44.9 1.0
CG A:ASP411 2.9 35.4 1.0
PB A:TTP1001 3.3 34.8 1.0
CG A:ASP623 3.4 27.5 1.0
C A:LEU412 3.5 23.3 1.0
PG A:TTP1001 3.6 36.6 1.0
PA A:TTP1001 3.6 38.9 1.0
O3A A:TTP1001 3.7 39.5 1.0
O3B A:TTP1001 3.8 35.7 1.0
CA A:CA1003 3.8 49.6 1.0
OD2 A:ASP623 3.8 26.9 1.0
O A:HOH1646 3.9 41.6 1.0
N A:LEU412 4.1 21.0 1.0
O2G A:TTP1001 4.3 35.6 1.0
CA A:LEU412 4.3 21.1 1.0
O A:HOH1275 4.3 49.7 1.0
CB A:ASP411 4.4 32.1 1.0
N A:SER414 4.4 20.6 1.0
C5' A:TTP1001 4.4 32.2 1.0
N A:THR413 4.5 20.4 1.0
O5' A:TTP1001 4.5 34.9 1.0
CB A:ASP623 4.6 27.2 1.0
C A:ASP411 4.6 22.8 1.0
CA A:THR413 4.6 21.6 1.0
N A:LEU415 4.7 17.8 1.0
C A:THR413 4.7 21.7 1.0
O3G A:TTP1001 4.7 34.9 1.0
O1B A:TTP1001 4.7 37.9 1.0
O1A A:TTP1001 4.8 36.1 1.0
CB A:LEU412 4.9 20.3 1.0
CA A:ASP411 5.0 25.1 1.0

Calcium binding site 2 out of 4 in 4dtx

Go back to Calcium Binding Sites List in 4dtx
Calcium binding site 2 out of 4 in the RB69 Dna Polymerase Ternary Complex with Dttp 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 Dttp 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:49.6
occ:1.00
 O A:HOH1322 2.3 37.6 1.0
O2A A:TTP1001 2.6 38.2 1.0
OD2 A:ASP411 2.7 36.1 1.0
OD2 A:ASP623 2.7 26.9 1.0
CG A:ASP623 3.6 27.5 1.0
OD1 A:ASP623 3.7 35.0 1.0
CG A:ASP411 3.7 35.4 1.0
CA A:CA1002 3.8 23.2 1.0
PA A:TTP1001 3.8 38.9 1.0
CB A:SER624 3.9 28.2 1.0
C3' P:DOC115 4.0 25.1 1.0
O A:HOH1646 4.0 41.6 1.0
O1A A:TTP1001 4.2 36.1 1.0
C5' P:DOC115 4.3 29.3 1.0
O A:HOH1402 4.3 31.9 1.0
OG A:SER624 4.4 34.4 1.0
O A:HOH1743 4.4 46.5 1.0
CB A:ASP411 4.5 32.1 1.0
C4' P:DOC115 4.5 26.0 1.0
O5' A:TTP1001 4.5 34.9 1.0
OD1 A:ASP411 4.6 44.9 1.0
N A:SER624 4.7 24.9 1.0
O A:ASP621 4.7 22.6 1.0
C5' A:TTP1001 4.7 32.2 1.0
C A:ASP623 4.8 24.1 1.0
CA A:SER624 4.8 23.9 1.0
O P:HOH207 4.9 35.5 1.0
CB A:ASP623 5.0 27.2 1.0
O1G A:TTP1001 5.0 35.0 1.0
OE2 A:GLU686 5.0 53.0 1.0

Calcium binding site 3 out of 4 in 4dtx

Go back to Calcium Binding Sites List in 4dtx
Calcium binding site 3 out of 4 in the RB69 Dna Polymerase Ternary Complex with Dttp 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 Dttp 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:38.0
occ:1.00
 OD1 A:ASN507 2.2 45.3 1.0
O A:HOH1381 2.2 45.0 1.0
O A:LYS531 2.3 44.3 1.0
O A:ASN505 2.3 40.5 1.0
O A:HOH1464 2.5 37.0 1.0
O A:HOH1348 2.5 37.1 1.0
C A:LYS531 3.3 42.6 1.0
CG A:ASN507 3.4 45.6 1.0
C A:ASN505 3.6 42.8 1.0
ND2 A:ASN507 4.0 43.7 1.0
CA A:LYS531 4.1 40.3 1.0
CB A:ASN505 4.1 43.7 1.0
N A:LYS532 4.2 42.4 1.0
N A:ASN507 4.2 44.7 1.0
CA A:LYS532 4.4 43.5 1.0
C A:PRO506 4.4 42.6 1.0
CA A:PRO506 4.4 42.3 1.0
N A:PRO506 4.5 40.8 1.0
CA A:ASN505 4.5 43.4 1.0
O A:HOH1410 4.5 40.7 1.0
CB A:ASN507 4.5 45.5 1.0
O A:LEU533 4.6 35.3 1.0
O A:ALA502 4.7 35.4 1.0
CB A:LYS531 4.7 45.0 1.0
C A:LYS532 4.8 43.2 1.0
CA A:ASN507 4.8 45.8 1.0
N A:LEU533 4.9 37.9 1.0
O A:ILE530 4.9 33.4 1.0

Calcium binding site 4 out of 4 in 4dtx

Go back to Calcium Binding Sites List in 4dtx
Calcium binding site 4 out of 4 in the RB69 Dna Polymerase Ternary Complex with Dttp 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 Dttp 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:46.7
occ:1.00
 O A:HOH1473 2.3 38.7 1.0
O A:HOH1422 2.3 38.5 1.0
O A:HOH1113 2.5 28.6 1.0
OE2 A:GLU116 2.7 33.8 1.0
OE1 A:GLU116 2.7 35.4 1.0
CD A:GLU116 3.1 36.1 1.0
OD2 A:ASP114 4.3 43.6 1.0
O A:HOH1584 4.4 41.4 1.0
CG A:GLU116 4.6 25.5 1.0
O A:ILE115 4.7 23.7 1.0
CD1 A:ILE309 4.8 52.8 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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