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

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dctp Opposite An Abasic Site and Ddg/Dc 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 Ddg/Dc As the Penultimate Base-Pair, PDB code: 4dtm 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) 45.65 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.178, 120.499, 130.752, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 4dtm

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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 Ddg/Dc 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 Ddg/Dc As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:29.6
occ:1.00
 O1G A:DCP1001 2.2 36.5 1.0
OD2 A:ASP623 2.2 32.9 1.0
O1B A:DCP1001 2.3 24.0 1.0
O A:LEU412 2.4 20.8 1.0
O A:HOH1196 2.5 44.0 1.0
OD1 A:ASP411 2.5 36.1 1.0
OD2 A:ASP411 2.6 36.4 1.0
CG A:ASP411 2.9 36.2 1.0
PB A:DCP1001 3.3 27.7 1.0
O3A A:DCP1001 3.3 33.1 1.0
CG A:ASP623 3.4 30.6 1.0
PG A:DCP1001 3.5 32.1 1.0
C A:LEU412 3.6 23.1 1.0
O3B A:DCP1001 3.8 31.4 1.0
CA A:CA1003 4.0 57.6 1.0
OD1 A:ASP623 4.1 28.4 1.0
N A:SER414 4.2 20.2 1.0
N A:LEU412 4.3 23.0 1.0
CB A:ASP411 4.3 30.4 1.0
O2G A:DCP1001 4.4 28.7 1.0
CB A:ASP623 4.4 24.9 1.0
CA A:LEU412 4.5 22.5 1.0
N A:THR413 4.5 23.6 1.0
CA A:THR413 4.5 24.3 1.0
O1A A:DCP1001 4.5 35.5 1.0
PA A:DCP1001 4.5 35.0 1.0
O3G A:DCP1001 4.6 35.0 1.0
C A:THR413 4.6 22.5 1.0
C A:ASP411 4.6 24.0 1.0
O2B A:DCP1001 4.7 27.0 1.0
C5' A:DCP1001 4.7 26.0 1.0
N A:LEU415 4.8 19.4 1.0
CA A:ASP411 4.9 27.4 1.0
CA A:SER414 5.0 20.9 1.0

Calcium binding site 2 out of 5 in 4dtm

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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 Ddg/Dc 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 Ddg/Dc As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:57.6
occ:1.00
 O A:HOH1196 2.4 44.0 1.0
OD1 A:ASP623 2.7 28.4 1.0
O1A A:DCP1001 3.1 35.5 1.0
OD1 A:ASP411 3.1 36.1 1.0
OD2 A:ASP623 3.4 32.9 1.0
CG A:ASP623 3.5 30.6 1.0
C3' P:DG115 3.7 24.7 1.0
O P:HOH215 4.0 36.1 1.0
CA A:CA1002 4.0 29.6 1.0
CG A:ASP411 4.1 36.2 1.0
CB A:SER624 4.1 28.7 1.0
O A:HOH1278 4.1 31.2 1.0
OG A:SER624 4.2 34.0 1.0
PA A:DCP1001 4.3 35.0 1.0
O3A A:DCP1001 4.5 33.1 1.0
O5' P:DG115 4.5 25.7 1.0
C5' A:DCP1001 4.7 26.0 1.0
OD2 A:ASP411 4.7 36.4 1.0
O P:HOH211 4.7 33.6 1.0
C5' P:DG115 4.7 25.7 1.0
C4' P:DG115 4.8 25.2 1.0
OE2 A:GLU686 4.8 46.2 1.0
C2' P:DG115 4.9 27.5 1.0
CB A:ASP623 4.9 24.9 1.0
N A:SER624 5.0 24.7 1.0
O5' A:DCP1001 5.0 32.6 1.0
CB A:ASP411 5.0 30.4 1.0

Calcium binding site 3 out of 5 in 4dtm

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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 Ddg/Dc 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 Ddg/Dc As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:43.5
occ:1.00
 OD1 A:ASN507 2.1 48.8 1.0
O A:HOH1333 2.2 45.5 1.0
O A:LYS531 2.3 45.9 1.0
O A:ASN505 2.3 41.0 1.0
O A:HOH1104 2.4 33.9 1.0
O A:HOH1505 2.6 41.0 1.0
C A:LYS531 3.3 44.1 1.0
CG A:ASN507 3.3 49.8 1.0
C A:ASN505 3.6 42.2 1.0
ND2 A:ASN507 3.9 42.1 1.0
CA A:LYS531 4.0 44.8 1.0
N A:ASN507 4.1 45.5 1.0
N A:LYS532 4.2 44.6 1.0
CB A:ASN505 4.2 48.5 1.0
C A:PRO506 4.3 42.8 1.0
CA A:PRO506 4.3 40.0 1.0
CA A:LYS532 4.4 45.0 1.0
N A:PRO506 4.4 38.5 1.0
CB A:ASN507 4.5 47.3 1.0
O A:LEU533 4.5 39.0 1.0
CA A:ASN505 4.5 48.1 1.0
O A:HOH1539 4.6 39.3 1.0
O A:ALA502 4.7 39.3 1.0
CA A:ASN507 4.7 48.5 1.0
CB A:LYS531 4.8 45.7 1.0
C A:LYS532 4.8 45.6 1.0
N A:LEU533 4.8 43.3 1.0
O A:ILE530 4.9 38.8 1.0
O A:PRO506 4.9 44.8 1.0

Calcium binding site 4 out of 5 in 4dtm

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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 Ddg/Dc 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 Ddg/Dc As the Penultimate Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:74.5
occ:1.00
 O A:HOH1657 2.2 37.5 1.0
O A:HOH1195 2.3 38.0 1.0
OE1 A:GLU716 3.3 59.3 1.0
OD2 A:ASP411 3.5 36.4 1.0
CD A:GLU716 4.1 52.5 1.0
CG A:GLU716 4.3 49.9 1.0
O A:ASP411 4.3 25.0 1.0
NZ A:LYS486 4.4 31.6 1.0
CG A:ASP411 4.4 36.2 1.0
CB A:ASP411 4.5 30.4 1.0
OG1 A:THR413 4.6 31.0 1.0
CB A:ASP684 4.6 31.5 1.0
OE1 A:GLU686 4.8 43.1 1.0
OD2 A:ASP684 4.8 42.7 1.0
O1G A:DCP1001 4.9 36.5 1.0

Calcium binding site 5 out of 5 in 4dtm

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

b:54.0
occ:1.00
 O A:HOH1366 2.3 36.3 1.0
O A:HOH1127 2.5 25.5 1.0
OE1 A:GLU116 2.7 29.9 1.0
OE2 A:GLU116 2.8 31.6 1.0
CD A:GLU116 3.1 30.4 1.0
O A:HOH1568 4.2 35.7 1.0
OD2 A:ASP114 4.4 37.2 1.0
CG A:GLU116 4.6 23.9 1.0
O A:ILE115 4.7 26.7 1.0
CD1 A:ILE309 4.7 47.6 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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