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

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dctp Opposite An Abasic Site and Dda/Dt 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 Dda/Dt As the Penultimate Base-Pair, PDB code: 4dto 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 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.238, 119.256, 130.920, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.5

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite An Abasic Site and Dda/Dt As the Penultimate Base-Pair (pdb code 4dto). 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 Dctp Opposite An Abasic Site and Dda/Dt As the Penultimate Base-Pair, PDB code: 4dto:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4dto

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Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite An Abasic Site and Dda/Dt 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 Dda/Dt As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:28.0
occ:1.00
 OD2 A:ASP623 2.2 33.0 1.0
O3G A:DCP1001 2.3 27.7 1.0
O A:LEU412 2.3 23.3 1.0
O2B A:DCP1001 2.3 24.9 1.0
OD2 A:ASP411 2.4 36.1 1.0
OD1 A:ASP411 2.8 36.2 1.0
CG A:ASP411 2.9 31.8 1.0
O2A A:DCP1001 3.0 39.7 1.0
CG A:ASP623 3.3 30.0 1.0
PB A:DCP1001 3.4 25.4 1.0
C A:LEU412 3.5 23.7 1.0
PG A:DCP1001 3.6 27.1 1.0
O3A A:DCP1001 3.7 29.4 1.0
O3B A:DCP1001 3.9 27.6 1.0
PA A:DCP1001 4.0 31.6 1.0
OD1 A:ASP623 4.0 30.7 1.0
CA A:CA1003 4.0 59.5 1.0
N A:LEU412 4.0 22.5 1.0
O A:HOH1188 4.1 40.0 1.0
N A:SER414 4.3 20.2 1.0
CA A:LEU412 4.3 23.1 1.0
CB A:ASP411 4.3 28.7 1.0
CB A:ASP623 4.4 25.1 1.0
N A:THR413 4.4 22.5 1.0
O2G A:DCP1001 4.4 25.7 1.0
CA A:THR413 4.5 25.2 1.0
C A:ASP411 4.5 21.3 1.0
C5' A:DCP1001 4.5 26.2 1.0
C A:THR413 4.6 21.5 1.0
O1G A:DCP1001 4.7 26.2 1.0
O1B A:DCP1001 4.8 25.4 1.0
O5' A:DCP1001 4.8 31.2 1.0
N A:LEU415 4.8 18.3 1.0
CA A:ASP411 4.9 22.1 1.0
CB A:LEU412 4.9 19.9 1.0
O A:ASP623 5.0 22.7 1.0

Calcium binding site 2 out of 5 in 4dto

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite An Abasic Site and Dda/Dt 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 Dda/Dt As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:59.5
occ:1.00
 O2A A:DCP1001 2.6 39.7 1.0
OD1 A:ASP623 2.7 30.7 1.0
OD1 A:ASP411 2.8 36.2 1.0
CG A:ASP623 3.5 30.0 1.0
OD2 A:ASP623 3.5 33.0 1.0
C3' P:DA115 3.7 24.2 1.0
CG A:ASP411 3.8 31.8 1.0
PA A:DCP1001 3.9 31.6 1.0
O A:HOH1277 4.0 32.0 1.0
CB A:SER624 4.0 27.1 1.0
CA A:CA1002 4.0 28.0 1.0
O A:HOH1524 4.4 35.0 1.0
O1A A:DCP1001 4.4 31.9 1.0
OG A:SER624 4.4 31.6 1.0
OD2 A:ASP411 4.4 36.1 1.0
O5' P:DA115 4.5 25.4 1.0
C5' A:DCP1001 4.7 26.2 1.0
C5' P:DA115 4.7 25.9 1.0
C4' P:DA115 4.7 24.2 1.0
O A:ASP621 4.8 20.9 1.0
O5' A:DCP1001 4.8 31.2 1.0
N A:SER624 4.8 24.6 1.0
C2' P:DA115 4.8 23.7 1.0
CB A:ASP411 4.9 28.7 1.0
CB A:ASP623 4.9 25.1 1.0
C A:ASP623 4.9 25.3 1.0
CA A:SER624 4.9 26.6 1.0

Calcium binding site 3 out of 5 in 4dto

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite An Abasic Site and Dda/Dt 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 Dda/Dt As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:55.0
occ:1.00
 O A:LYS531 2.2 45.1 1.0
O A:ASN505 2.3 43.7 1.0
O A:HOH1235 2.3 45.3 1.0
OD1 A:ASN507 2.4 50.9 1.0
O A:HOH1115 2.5 44.9 1.0
O A:HOH1298 2.6 46.4 1.0
O A:HOH1503 2.8 55.8 1.0
C A:LYS531 3.2 46.8 1.0
CG A:ASN507 3.5 52.4 1.0
C A:ASN505 3.5 48.7 1.0
CA A:LYS531 4.0 43.3 1.0
N A:LYS532 4.1 47.1 1.0
N A:ASN507 4.2 57.5 1.0
ND2 A:ASN507 4.2 53.3 1.0
CA A:PRO506 4.3 51.6 1.0
CB A:ASN505 4.3 54.7 1.0
C A:PRO506 4.3 57.2 1.0
CA A:LYS532 4.3 50.2 1.0
N A:PRO506 4.4 46.3 1.0
O A:LEU533 4.5 42.2 1.0
CA A:ASN505 4.5 54.6 1.0
O A:ALA502 4.6 45.3 1.0
CB A:ASN507 4.7 53.4 1.0
CB A:LYS531 4.7 45.3 1.0
C A:LYS532 4.8 51.0 1.0
O A:ILE530 4.8 39.5 1.0
CA A:ASN507 4.8 54.8 1.0
O A:PRO506 4.9 61.9 1.0
N A:LEU533 4.9 47.8 1.0

Calcium binding site 4 out of 5 in 4dto

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite An Abasic Site and Dda/Dt 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 Dda/Dt As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:69.5
occ:1.00
 O A:HOH1329 2.2 49.3 1.0
O A:HOH1188 2.3 40.0 1.0
OE1 A:GLU716 3.1 57.7 1.0
CD A:GLU716 3.7 51.3 1.0
OD2 A:ASP411 3.7 36.1 1.0
CG A:GLU716 3.9 46.2 1.0
OE1 A:GLU686 4.1 43.5 1.0
CB A:ASP411 4.3 28.7 1.0
NZ A:LYS486 4.4 38.4 1.0
O A:ASP411 4.4 20.9 1.0
CG A:ASP411 4.5 31.8 1.0
O A:HOH1241 4.5 40.2 1.0
OE2 A:GLU716 4.6 55.0 1.0
CB A:ASP684 4.7 31.4 1.0
CG A:GLU686 4.7 38.3 1.0
CD A:GLU686 4.8 40.8 1.0
O3G A:DCP1001 4.8 27.7 1.0
OG1 A:THR413 4.9 30.4 1.0
O A:ASP684 4.9 24.2 1.0
C A:ASP411 5.0 21.3 1.0

Calcium binding site 5 out of 5 in 4dto

Go back to Calcium Binding Sites List in 4dto
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite An Abasic Site and Dda/Dt 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 Dctp Opposite An Abasic Site and Dda/Dt As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:43.6
occ:1.00
 O A:HOH1149 2.3 39.8 1.0
O A:HOH1505 2.4 42.9 1.0
OE2 A:GLU116 2.6 31.1 1.0
O A:HOH1470 2.6 43.7 1.0
OE1 A:GLU116 2.6 34.6 1.0
CD A:GLU116 3.0 31.3 1.0
CG A:GLU116 4.5 27.9 1.0
OD2 A:ASP114 4.5 44.7 1.0
O A:ILE115 4.6 29.1 1.0
O A:HOH1451 4.7 44.3 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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