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

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dctp 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 Dctp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair, PDB code: 4dts 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) 35.32 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.047, 120.102, 130.688, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.6

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 4dts

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Calcium binding site 1 out of 4 in the RB69 Dna Polymerase Ternary Complex with Dctp 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 Dctp 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:22.2
occ:1.00
 OD1 A:ASP623 2.1 37.1 1.0
O1G A:DCP1001 2.2 21.9 1.0
O2B A:DCP1001 2.3 19.1 1.0
O A:LEU412 2.3 16.9 1.0
OD2 A:ASP411 2.4 33.7 1.0
OD1 A:ASP411 2.6 32.0 1.0
CG A:ASP411 2.8 31.6 1.0
O2A A:DCP1001 2.9 34.6 1.0
O A:HOH1373 3.0 49.7 1.0
CG A:ASP623 3.3 28.6 1.0
PB A:DCP1001 3.4 20.9 1.0
C A:LEU412 3.5 19.1 1.0
PG A:DCP1001 3.5 22.3 1.0
O3A A:DCP1001 3.7 26.5 1.0
O3B A:DCP1001 3.8 21.1 1.0
CA A:CA1003 3.9 41.1 1.0
PA A:DCP1001 3.9 30.6 1.0
OD2 A:ASP623 4.0 28.1 1.0
N A:LEU412 4.2 17.9 1.0
O A:HOH1713 4.2 47.5 1.0
CB A:ASP411 4.3 26.3 1.0
N A:SER414 4.3 17.0 1.0
O2G A:DCP1001 4.3 20.9 1.0
CA A:LEU412 4.4 17.9 1.0
CB A:ASP623 4.4 23.6 1.0
N A:THR413 4.4 17.7 1.0
CA A:THR413 4.5 19.9 1.0
C A:ASP411 4.6 18.9 1.0
C5' A:DCP1001 4.6 21.5 1.0
C A:THR413 4.6 19.6 1.0
O3G A:DCP1001 4.6 23.2 1.0
O1B A:DCP1001 4.8 22.6 1.0
N A:LEU415 4.8 16.2 1.0
O5' A:DCP1001 4.8 24.2 1.0
CA A:ASP411 4.9 22.3 1.0
CB A:LEU412 4.9 16.2 1.0
O A:ASP623 5.0 19.3 1.0

Calcium binding site 2 out of 4 in 4dts

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Calcium binding site 2 out of 4 in the RB69 Dna Polymerase Ternary Complex with Dctp 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 Dctp 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:41.1
occ:1.00
 O A:HOH1688 2.4 32.4 1.0
O2A A:DCP1001 2.5 34.6 1.0
OD2 A:ASP623 2.6 28.1 1.0
OD2 A:ASP411 2.9 33.7 1.0
O A:HOH1373 3.1 49.7 1.0
CG A:ASP623 3.3 28.6 1.0
OD1 A:ASP623 3.4 37.1 1.0
PA A:DCP1001 3.8 30.6 1.0
C3' P:DOC115 3.9 23.6 1.0
CA A:CA1002 3.9 22.2 1.0
CB A:SER624 3.9 28.8 1.0
CG A:ASP411 4.0 31.6 1.0
C5' P:DOC115 4.2 30.7 1.0
O A:HOH1409 4.3 29.9 1.0
OG A:SER624 4.3 35.4 1.0
O1A A:DCP1001 4.3 29.7 1.0
C4' P:DOC115 4.4 26.1 1.0
O5' A:DCP1001 4.7 24.2 1.0
C5' A:DCP1001 4.7 21.5 1.0
O A:HOH1886 4.7 31.3 1.0
N A:SER624 4.7 21.6 1.0
OD1 A:ASP411 4.8 32.0 1.0
O A:ASP621 4.8 19.7 1.0
CB A:ASP623 4.8 23.6 1.0
O5' P:DOC115 4.8 28.3 1.0
CB A:ASP411 4.8 26.3 1.0
C A:ASP623 4.9 21.1 1.0
O3A A:DCP1001 4.9 26.5 1.0
CA A:SER624 4.9 23.1 1.0
OE2 A:GLU686 4.9 49.6 1.0

Calcium binding site 3 out of 4 in 4dts

Go back to Calcium Binding Sites List in 4dts
Calcium binding site 3 out of 4 in the RB69 Dna Polymerase Ternary Complex with Dctp 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 Dctp 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:34.7
occ:1.00
 OD1 A:ASN507 2.2 40.3 1.0
O A:LYS531 2.2 38.5 1.0
O A:HOH1411 2.3 42.2 1.0
O A:ASN505 2.3 37.5 1.0
O A:HOH1269 2.4 32.2 1.0
O A:HOH1327 2.6 33.9 1.0
O A:HOH1698 2.6 45.0 1.0
C A:LYS531 3.2 37.5 1.0
CG A:ASN507 3.3 44.5 1.0
C A:ASN505 3.6 37.1 1.0
ND2 A:ASN507 4.0 38.6 1.0
CA A:LYS531 4.0 36.0 1.0
N A:LYS532 4.1 36.7 1.0
N A:ASN507 4.1 42.8 1.0
CB A:ASN505 4.2 37.9 1.0
CA A:LYS532 4.3 36.7 1.0
C A:PRO506 4.4 37.8 1.0
CA A:PRO506 4.4 37.6 1.0
N A:PRO506 4.5 35.6 1.0
CA A:ASN505 4.5 39.1 1.0
O A:LEU533 4.5 33.3 1.0
CB A:ASN507 4.5 43.8 1.0
O A:HOH1370 4.6 37.7 1.0
O A:ALA502 4.7 34.6 1.0
CB A:LYS531 4.7 37.6 1.0
C A:LYS532 4.7 36.1 1.0
CA A:ASN507 4.7 42.5 1.0
N A:LEU533 4.8 32.2 1.0
O A:ILE530 4.9 28.0 1.0

Calcium binding site 4 out of 4 in 4dts

Go back to Calcium Binding Sites List in 4dts
Calcium binding site 4 out of 4 in the RB69 Dna Polymerase Ternary Complex with Dctp 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 Dctp 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:47.4
occ:1.00
 O A:HOH1534 2.3 36.3 1.0
O A:HOH1544 2.5 39.5 1.0
O A:HOH1114 2.5 20.9 1.0
OE1 A:GLU116 2.6 32.4 1.0
OE2 A:GLU116 2.7 31.2 1.0
CD A:GLU116 3.0 30.6 1.0
OD2 A:ASP114 4.2 40.7 1.0
O A:HOH1620 4.2 30.4 1.0
CG A:GLU116 4.5 21.8 1.0
O A:HOH1546 4.6 37.8 1.0
O A:ILE115 4.6 20.7 1.0
CD1 A:ILE309 4.8 45.0 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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