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

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair, PDB code: 4dtu 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) 38.25 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.925, 120.012, 130.569, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.1

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dgtp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair (pdb code 4dtu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Dgtp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair, PDB code: 4dtu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4dtu

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Calcium binding site 1 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:20.4
occ:1.00
 OD1 A:ASP623 2.2 29.4 1.0
O2B A:DGT1001 2.2 17.7 1.0
O1G A:DGT1001 2.2 20.4 1.0
O A:LEU412 2.3 18.2 1.0
O2A A:DGT1001 2.4 23.1 1.0
OD2 A:ASP411 2.5 37.8 1.0
OD1 A:ASP411 2.6 45.1 1.0
CG A:ASP411 2.9 28.6 1.0
PB A:DGT1001 3.3 19.6 1.0
CG A:ASP623 3.3 23.4 1.0
C A:LEU412 3.5 20.0 1.0
PG A:DGT1001 3.5 21.4 1.0
PA A:DGT1001 3.6 23.5 1.0
O3A A:DGT1001 3.7 22.8 1.0
CA A:CA1003 3.7 49.3 1.0
OD2 A:ASP623 3.8 26.0 1.0
O3B A:DGT1001 3.8 22.5 1.0
O A:HOH1464 3.9 35.2 1.0
N A:LEU412 4.0 17.6 1.0
O2G A:DGT1001 4.2 21.4 1.0
CA A:LEU412 4.3 19.2 1.0
CB A:ASP411 4.3 27.7 1.0
C5' A:DGT1001 4.4 18.3 1.0
N A:SER414 4.4 17.8 1.0
O A:HOH1407 4.4 47.0 1.0
N A:THR413 4.5 21.2 1.0
O5' A:DGT1001 4.5 20.2 1.0
C A:ASP411 4.5 20.6 1.0
CB A:ASP623 4.6 23.8 1.0
CA A:THR413 4.6 21.2 1.0
N A:LEU415 4.7 17.0 1.0
C A:THR413 4.7 19.9 1.0
O3G A:DGT1001 4.7 21.2 1.0
O1B A:DGT1001 4.7 21.5 1.0
O1A A:DGT1001 4.8 23.4 1.0
CB A:LEU412 4.9 18.3 1.0
CA A:ASP411 4.9 22.9 1.0

Calcium binding site 2 out of 6 in 4dtu

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Calcium binding site 2 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:49.3
occ:1.00
 O A:HOH1486 2.2 41.5 1.0
OD2 A:ASP411 2.5 37.8 1.0
O2A A:DGT1001 2.7 23.1 1.0
OD2 A:ASP623 2.7 26.0 1.0
O A:HOH1684 3.0 36.0 1.0
O A:HOH1685 3.0 44.9 1.0
CG A:ASP623 3.6 23.4 1.0
CG A:ASP411 3.6 28.6 1.0
OD1 A:ASP623 3.7 29.4 1.0
CA A:CA1002 3.7 20.4 1.0
PA A:DGT1001 3.8 23.5 1.0
C3' P:DOC115 3.9 22.9 1.0
CB A:SER624 3.9 22.9 1.0
O A:HOH1464 4.0 35.2 1.0
C5' P:DOC115 4.1 28.6 1.0
O1A A:DGT1001 4.2 23.4 1.0
O A:HOH1322 4.3 30.2 1.0
C4' P:DOC115 4.4 23.8 1.0
OG A:SER624 4.4 31.0 1.0
CB A:ASP411 4.4 27.7 1.0
OD1 A:ASP411 4.4 45.1 1.0
O5' A:DGT1001 4.6 20.2 1.0
O A:ASP621 4.7 20.6 1.0
C5' A:DGT1001 4.8 18.3 1.0
N A:SER624 4.8 20.1 1.0
C A:ASP623 4.8 22.8 1.0
O P:HOH314 4.9 39.9 1.0
CA A:SER624 4.9 22.3 1.0
O1G A:DGT1001 4.9 20.4 1.0
OE2 A:GLU686 4.9 59.0 1.0
CB A:ASP623 5.0 23.8 1.0

Calcium binding site 3 out of 6 in 4dtu

Go back to Calcium Binding Sites List in 4dtu
Calcium binding site 3 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:37.3
occ:1.00
 OD1 A:ASN507 2.2 43.7 1.0
O A:LYS531 2.3 40.6 1.0
O A:ASN505 2.3 38.2 1.0
O A:HOH1313 2.4 38.0 1.0
O A:HOH1317 2.5 30.5 1.0
O A:HOH1315 2.5 31.4 1.0
C A:LYS531 3.3 39.9 1.0
CG A:ASN507 3.4 43.9 1.0
C A:ASN505 3.6 41.3 1.0
CA A:LYS531 4.1 37.9 1.0
ND2 A:ASN507 4.1 43.5 1.0
CB A:ASN505 4.1 40.6 1.0
N A:ASN507 4.1 42.2 1.0
N A:LYS532 4.2 37.8 1.0
C A:PRO506 4.3 40.2 1.0
CA A:LYS532 4.4 37.8 1.0
CA A:PRO506 4.4 39.6 1.0
N A:PRO506 4.5 39.1 1.0
CA A:ASN505 4.5 42.0 1.0
O A:LEU533 4.5 31.9 1.0
CB A:ASN507 4.5 42.4 1.0
O A:HOH1613 4.6 39.6 1.0
O A:ALA502 4.7 33.8 1.0
C A:LYS532 4.7 36.2 1.0
CA A:ASN507 4.7 42.4 1.0
CB A:LYS531 4.8 41.1 1.0
N A:LEU533 4.8 34.5 1.0
O A:ILE530 4.9 30.6 1.0
O A:PRO506 4.9 41.9 1.0

Calcium binding site 4 out of 6 in 4dtu

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Calcium binding site 4 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:46.0
occ:1.00
 O A:HOH1316 2.3 33.3 1.0
O A:HOH1565 2.4 46.0 1.0
O A:HOH1129 2.4 25.7 1.0
OE1 A:GLU116 2.6 31.9 1.0
OE2 A:GLU116 2.7 30.3 1.0
CD A:GLU116 3.0 31.3 1.0
OD2 A:ASP114 4.1 47.6 1.0
O A:HOH1566 4.2 33.7 1.0
O A:HOH1774 4.3 44.1 1.0
O A:HOH1567 4.4 38.4 1.0
CG A:GLU116 4.5 21.5 1.0
O A:ILE115 4.6 21.6 1.0
CD1 A:ILE309 4.9 50.3 1.0

Calcium binding site 5 out of 6 in 4dtu

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Calcium binding site 5 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 5 of RB69 Dna Polymerase Ternary Complex with Dgtp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:63.6
occ:1.00
 O A:HOH1277 2.4 31.4 0.5
O A:HOH1672 2.5 37.9 1.0
O A:HOH1407 2.5 47.0 1.0
OE1 A:GLU716 2.6 63.3 1.0
O A:HOH1152 2.7 38.8 1.0
CD A:GLU716 3.4 54.6 1.0
OD1 A:ASP411 3.8 45.1 1.0
O A:HOH1277 4.0 13.1 0.5
CG A:GLU716 4.1 49.1 1.0
OE2 A:GLU716 4.2 49.3 1.0
NZ A:LYS486 4.3 33.0 1.0
OG1 A:THR413 4.4 26.1 1.0
O A:ASP411 4.4 20.9 1.0
OE1 A:GLU686 4.4 55.7 1.0
CB A:ASP684 4.5 32.7 1.0
CG A:ASP411 4.8 28.6 1.0
OD2 A:ASP684 4.8 49.1 1.0
CB A:ASP411 4.8 27.7 1.0
O A:ASP684 4.9 21.7 1.0

Calcium binding site 6 out of 6 in 4dtu

Go back to Calcium Binding Sites List in 4dtu
Calcium binding site 6 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 6 of RB69 Dna Polymerase Ternary Complex with Dgtp Opposite An Abasic Site and Ddc/Dg As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca201

b:61.0
occ:1.00
 O T:HOH127 2.5 44.6 1.0
O T:HOH129 2.6 36.4 1.0
O T:HOH128 2.7 51.0 1.0
N7 P:DG105 4.6 49.8 1.0
O4 T:DT13 4.6 32.3 1.0
O6 T:DG12 4.7 28.9 1.0
N7 T:DG12 4.7 29.9 1.0
O6 P:DG106 4.8 32.2 1.0
C8 P:DG105 4.8 48.0 1.0
N7 P:DG106 4.9 39.0 1.0
N6 P:DA107 5.0 30.2 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: Tue Jul 8 19:35:16 2025

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