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

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp 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 Datp Opposite An Abasic Site and Dda/Dt As the Penultimate Base-Pair, PDB code: 4dtn 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) 38.19 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.275, 118.129, 130.222, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.6

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 4dtn

Go back to Calcium Binding Sites List in 4dtn
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Datp 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:22.1
occ:1.00
 OD2 A:ASP623 2.2 25.3 1.0
O3G A:DTP1001 2.2 22.8 1.0
O2B A:DTP1001 2.3 20.1 1.0
O A:LEU412 2.3 21.3 1.0
OD2 A:ASP411 2.4 31.0 1.0
O2A A:DTP1001 2.4 21.9 1.0
OD1 A:ASP411 2.9 38.2 1.0
CG A:ASP411 2.9 29.2 1.0
CG A:ASP623 3.3 22.8 1.0
PB A:DTP1001 3.4 20.4 1.0
C A:LEU412 3.5 19.4 1.0
PG A:DTP1001 3.6 21.6 1.0
PA A:DTP1001 3.6 21.7 1.0
O3A A:DTP1001 3.7 21.0 1.0
O A:HOH1518 3.8 39.9 1.0
CA A:CA1003 3.8 50.0 1.0
OD1 A:ASP623 3.8 22.4 1.0
O3B A:DTP1001 3.9 22.2 1.0
N A:LEU412 4.0 19.1 1.0
C5' A:DTP1001 4.3 20.3 1.0
N A:SER414 4.3 16.9 1.0
CA A:LEU412 4.3 20.1 1.0
CB A:ASP411 4.3 25.3 1.0
O2G A:DTP1001 4.3 22.4 1.0
O5' A:DTP1001 4.4 20.9 1.0
N A:THR413 4.5 19.8 1.0
C A:ASP411 4.5 18.0 1.0
CB A:ASP623 4.5 21.6 1.0
C A:THR413 4.7 18.5 1.0
CA A:THR413 4.7 20.9 1.0
O A:HOH1650 4.7 42.6 1.0
O1G A:DTP1001 4.7 23.5 1.0
N A:LEU415 4.7 14.1 1.0
O1B A:DTP1001 4.8 20.3 1.0
O1A A:DTP1001 4.9 21.3 1.0
CB A:LEU412 4.9 18.6 1.0
CA A:ASP411 4.9 20.7 1.0

Calcium binding site 2 out of 5 in 4dtn

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Datp 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:50.0
occ:1.00
 O A:HOH1346 2.2 36.3 1.0
OD1 A:ASP411 2.4 38.2 1.0
O2A A:DTP1001 2.6 21.9 1.0
OD1 A:ASP623 2.6 22.4 1.0
O A:HOH1572 3.4 44.3 1.0
CG A:ASP411 3.5 29.2 1.0
CG A:ASP623 3.5 22.8 1.0
OD2 A:ASP623 3.6 25.3 1.0
PA A:DTP1001 3.7 21.7 1.0
C3' P:DA115 3.7 23.6 1.0
CA A:CA1002 3.8 22.1 1.0
CB A:SER624 4.0 26.1 1.0
OD2 A:ASP411 4.0 31.0 1.0
O A:HOH1518 4.1 39.9 1.0
O1A A:DTP1001 4.2 21.3 1.0
O P:HOH202 4.2 28.3 1.0
O5' A:DTP1001 4.3 20.9 1.0
OG A:SER624 4.4 29.7 1.0
CB A:ASP411 4.6 25.3 1.0
C5' A:DTP1001 4.6 20.3 1.0
O5' P:DA115 4.7 25.4 1.0
O A:ASP621 4.7 19.6 1.0
N A:SER624 4.8 19.2 1.0
C4' P:DA115 4.8 24.8 1.0
C2' P:DA115 4.8 22.1 1.0
C A:ASP623 4.9 20.5 1.0
C5' P:DA115 4.9 27.3 1.0
CB A:ASP623 4.9 21.6 1.0
CA A:SER624 4.9 22.9 1.0

Calcium binding site 3 out of 5 in 4dtn

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Datp 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:48.8
occ:1.00
 O A:HOH1326 2.2 40.9 1.0
O A:LYS531 2.2 46.1 1.0
O A:ASN505 2.3 41.9 1.0
OD1 A:ASN507 2.4 45.4 1.0
O A:HOH1104 2.5 35.5 1.0
O A:HOH1492 2.5 42.2 1.0
O A:HOH1377 2.7 42.5 1.0
C A:LYS531 3.2 43.0 1.0
CG A:ASN507 3.5 47.9 1.0
C A:ASN505 3.6 44.6 1.0
CA A:LYS531 3.9 43.2 1.0
ND2 A:ASN507 4.1 44.6 1.0
CB A:ASN505 4.1 50.0 1.0
N A:LYS532 4.2 42.1 1.0
N A:ASN507 4.3 52.9 1.0
CA A:LYS532 4.4 43.2 1.0
C A:PRO506 4.5 52.4 1.0
CA A:ASN505 4.5 49.0 1.0
CA A:PRO506 4.5 48.3 1.0
N A:PRO506 4.5 44.1 1.0
O A:ALA502 4.5 39.7 1.0
CB A:LYS531 4.6 46.0 1.0
CB A:ASN507 4.7 48.1 1.0
O A:LEU533 4.7 39.2 1.0
C A:LYS532 4.9 46.0 1.0
O A:ILE530 4.9 37.4 1.0
CA A:ASN507 4.9 48.9 1.0
N A:LEU533 5.0 41.8 1.0

Calcium binding site 4 out of 5 in 4dtn

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Datp 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:80.0
occ:1.00
 O A:HOH1650 2.4 42.6 1.0
O A:HOH1676 2.4 40.9 1.0
O A:HOH1470 2.5 32.7 1.0
OE1 A:GLU716 2.9 53.0 1.0
CD A:GLU716 3.8 45.0 1.0
CG A:GLU716 4.1 39.8 1.0
OD2 A:ASP411 4.2 31.0 1.0
O A:ASP411 4.3 18.8 1.0
CB A:ASP684 4.3 28.3 1.0
NZ A:LYS486 4.4 33.0 1.0
OE1 A:GLU686 4.5 43.3 1.0
CB A:ASP411 4.5 25.3 1.0
O A:HOH1291 4.5 38.3 1.0
O A:ASP684 4.5 21.2 1.0
O A:ARG685 4.8 21.0 1.0
CG A:ASP411 4.8 29.2 1.0
OE2 A:GLU716 4.8 50.6 1.0
OD2 A:ASP684 4.9 36.5 1.0
C A:ASP411 5.0 18.0 1.0
OG1 A:THR413 5.0 25.7 1.0

Calcium binding site 5 out of 5 in 4dtn

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Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Datp 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:40.7
occ:1.00
 O A:HOH1399 2.4 39.2 1.0
OE1 A:GLU116 2.5 25.7 1.0
O A:HOH1213 2.5 32.5 1.0
OE2 A:GLU116 2.7 25.9 1.0
CD A:GLU116 3.0 26.7 1.0
O A:HOH1477 4.1 31.4 1.0
OD2 A:ASP114 4.2 44.3 1.0
CG A:GLU116 4.5 23.3 1.0
O A:HOH1677 4.6 43.5 1.0
O A:ILE115 4.6 20.3 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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