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

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp Opposite An Abasic Site and Dda/Dt As the Penultimate Base-Pair, PDB code: 4dtp 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) 37.77 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.519, 118.344, 130.730, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.9

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 4dtp

Go back to Calcium Binding Sites List in 4dtp
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:20.7
occ:1.00
 OD2 A:ASP411 2.2 30.4 1.0
OD2 A:ASP623 2.2 25.9 1.0
O1G A:DGT1001 2.2 23.9 1.0
O1B A:DGT1001 2.3 20.1 1.0
O1A A:DGT1001 2.3 20.1 1.0
O A:LEU412 2.3 20.9 1.0
CG A:ASP623 3.4 24.4 1.0
CG A:ASP411 3.4 28.8 1.0
PB A:DGT1001 3.4 20.3 1.0
C A:LEU412 3.5 20.0 1.0
PA A:DGT1001 3.5 20.2 1.0
PG A:DGT1001 3.5 22.9 1.0
CA A:CA1003 3.7 56.2 1.0
O3A A:DGT1001 3.7 20.7 1.0
O A:HOH1460 3.8 29.9 1.0
OD1 A:ASP623 3.9 22.0 1.0
O3B A:DGT1001 3.9 22.1 1.0
N A:LEU412 4.0 19.9 1.0
CB A:ASP411 4.1 27.6 1.0
C5' A:DGT1001 4.2 21.0 1.0
O A:HOH1302 4.2 45.1 1.0
O2G A:DGT1001 4.3 23.7 1.0
OD1 A:ASP411 4.3 46.5 1.0
CA A:LEU412 4.3 20.1 1.0
N A:SER414 4.3 17.1 1.0
O5' A:DGT1001 4.4 20.9 1.0
N A:THR413 4.5 19.4 1.0
C A:ASP411 4.5 20.5 1.0
CB A:ASP623 4.6 22.4 1.0
O3G A:DGT1001 4.7 22.4 1.0
CA A:THR413 4.7 19.7 1.0
C A:THR413 4.7 18.0 1.0
O2B A:DGT1001 4.8 20.3 1.0
N A:LEU415 4.8 15.3 1.0
O2A A:DGT1001 4.8 20.2 1.0
CB A:LEU412 4.9 18.7 1.0
CA A:ASP411 5.0 21.7 1.0

Calcium binding site 2 out of 5 in 4dtp

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:56.2
occ:1.00
 OD1 A:ASP623 2.7 22.0 1.0
O1A A:DGT1001 2.7 20.1 1.0
O A:HOH1500 2.7 30.5 1.0
O A:HOH1465 3.1 38.2 1.0
OD2 A:ASP411 3.3 30.4 1.0
CG A:ASP623 3.5 24.4 1.0
OD2 A:ASP623 3.6 25.9 1.0
CA A:CA1002 3.7 20.7 1.0
CG A:ASP411 3.8 28.8 1.0
C3' P:DA115 3.8 21.8 1.0
PA A:DGT1001 3.8 20.2 1.0
CB A:ASP411 3.9 27.6 1.0
CB A:SER624 4.0 25.0 1.0
O A:HOH1460 4.1 29.9 1.0
O P:HOH201 4.3 25.9 1.0
O2A A:DGT1001 4.3 20.2 1.0
O5' A:DGT1001 4.4 20.9 1.0
OG A:SER624 4.5 28.2 1.0
C5' A:DGT1001 4.6 21.0 1.0
OD1 A:ASP411 4.7 46.5 1.0
O A:ASP621 4.8 16.4 1.0
O5' P:DA115 4.8 23.4 1.0
N A:SER624 4.8 21.2 1.0
C4' P:DA115 4.8 21.6 1.0
C5' P:DA115 4.8 23.5 1.0
OE2 A:GLU686 4.9 58.5 1.0
C A:ASP623 4.9 21.5 1.0
CA A:SER624 4.9 24.1 1.0
CB A:ASP623 4.9 22.4 1.0
C2' P:DA115 4.9 20.4 1.0

Calcium binding site 3 out of 5 in 4dtp

Go back to Calcium Binding Sites List in 4dtp
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:50.8
occ:1.00
 O A:ASN505 2.2 43.6 1.0
O A:LYS531 2.3 53.6 1.0
O A:HOH1224 2.3 44.3 1.0
OD1 A:ASN507 2.4 46.9 1.0
O A:HOH1598 2.5 36.8 1.0
O A:HOH1239 2.6 47.2 1.0
O A:HOH1427 2.7 49.1 1.0
C A:LYS531 3.3 48.0 1.0
C A:ASN505 3.5 44.6 1.0
CG A:ASN507 3.5 48.8 1.0
CB A:ASN505 3.9 49.7 1.0
CA A:LYS531 4.1 46.0 1.0
ND2 A:ASN507 4.2 47.9 1.0
N A:LYS532 4.2 45.6 1.0
N A:ASN507 4.2 56.0 1.0
CA A:ASN505 4.3 47.2 1.0
CA A:LYS532 4.4 47.5 1.0
CA A:PRO506 4.4 47.1 1.0
C A:PRO506 4.4 53.7 1.0
N A:PRO506 4.4 44.0 1.0
O A:LEU533 4.5 43.6 1.0
O A:ALA502 4.6 49.5 1.0
CB A:ASN507 4.7 46.5 1.0
CB A:LYS531 4.7 47.6 1.0
C A:LYS532 4.8 52.4 1.0
CA A:ASN507 4.8 52.6 1.0
N A:LEU533 4.9 47.5 1.0
O A:ILE530 4.9 40.2 1.0

Calcium binding site 4 out of 5 in 4dtp

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:67.3
occ:1.00
 O A:HOH1302 2.2 45.1 1.0
O A:HOH1290 2.4 36.9 1.0
O A:HOH1433 2.5 40.3 1.0
OE1 A:GLU716 2.6 50.1 1.0
CD A:GLU716 3.7 47.9 1.0
OD1 A:ASP411 4.0 46.5 1.0
CG A:GLU716 4.1 42.8 1.0
O A:HOH1158 4.2 27.9 1.0
NZ A:LYS486 4.2 29.3 1.0
CB A:ASP684 4.3 26.1 1.0
O A:ASP411 4.5 19.9 1.0
OG1 A:THR413 4.5 26.6 1.0
OD2 A:ASP684 4.5 39.6 1.0
OE2 A:GLU716 4.8 47.1 1.0
CG A:ASP411 4.9 28.8 1.0
O A:ASP684 4.9 23.8 1.0
OE1 A:GLU686 4.9 51.5 1.0
CG A:ASP684 4.9 33.3 1.0

Calcium binding site 5 out of 5 in 4dtp

Go back to Calcium Binding Sites List in 4dtp
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp 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 Dgtp 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:42.9
occ:1.00
 O A:HOH1548 2.3 41.3 1.0
O A:HOH1586 2.5 39.4 1.0
O A:HOH1172 2.5 30.6 1.0
OE1 A:GLU116 2.6 28.2 1.0
OE2 A:GLU116 2.7 32.6 1.0
CD A:GLU116 3.0 29.7 1.0
O A:HOH1430 4.1 30.4 1.0
O A:ILE115 4.5 22.8 1.0
CG A:GLU116 4.5 27.6 1.0
OD2 A:ASP114 4.6 39.4 1.0
O A:HOH1347 4.6 34.8 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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