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Calcium in PDB 4m45: RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex, PDB code: 4m45 was solved by S.Xia, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.30 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.952, 120.530, 130.685, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex (pdb code 4m45). 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 Dg/Dt at Position N-5 of Primer/Template Duplex, PDB code: 4m45:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4m45

Go back to Calcium Binding Sites List in 4m45
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex


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 Dg/Dt at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:21.3
occ:1.00
 O2B A:ATP1001 2.2 21.0 1.0
OD2 A:ASP411 2.3 20.7 1.0
O A:LEU412 2.3 19.4 1.0
OD1 A:ASP623 2.3 19.2 1.0
O1G A:ATP1001 2.3 20.1 1.0
O2A A:ATP1001 2.4 21.7 1.0
PB A:ATP1001 3.4 20.7 1.0
CG A:ASP623 3.4 22.6 1.0
CG A:ASP411 3.4 22.9 1.0
C A:LEU412 3.5 19.5 1.0
CA A:CA1003 3.5 49.0 1.0
PA A:ATP1001 3.6 22.5 1.0
PG A:ATP1001 3.6 20.8 1.0
OD2 A:ASP623 3.8 19.7 1.0
O3A A:ATP1001 3.8 21.9 1.0
O3B A:ATP1001 3.9 22.0 1.0
O A:HOH1698 3.9 38.6 1.0
N A:LEU412 3.9 19.0 1.0
CB A:ASP411 4.0 20.5 1.0
O A:HOH1124 4.0 30.9 1.0
CA A:LEU412 4.2 19.6 1.0
C5' A:ATP1001 4.2 18.9 1.0
O2G A:ATP1001 4.3 21.5 1.0
C A:ASP411 4.4 20.2 1.0
O5' A:ATP1001 4.4 20.4 1.0
OD1 A:ASP411 4.5 24.5 1.0
N A:THR413 4.5 20.0 1.0
N A:SER414 4.6 19.3 1.0
N A:ALA415 4.7 18.5 1.0
CB A:LEU412 4.7 17.7 1.0
CB A:ALA415 4.7 17.2 1.0
CB A:ASP623 4.7 20.8 1.0
O1B A:ATP1001 4.7 21.6 1.0
O3G A:ATP1001 4.8 22.2 1.0
CA A:THR413 4.8 21.5 1.0
O1A A:ATP1001 4.8 20.3 1.0
CA A:ASP411 4.8 20.8 1.0
C A:THR413 4.9 19.8 1.0
O A:ASP411 4.9 20.8 1.0

Calcium binding site 2 out of 5 in 4m45

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex


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 Dg/Dt at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:49.0
occ:1.00
 O A:HOH1256 2.4 29.2 1.0
O2A A:ATP1001 2.7 21.7 1.0
OD2 A:ASP623 2.7 19.7 1.0
OD2 A:ASP411 3.4 20.7 1.0
CA A:CA1002 3.5 21.3 1.0
CG A:ASP411 3.6 22.9 1.0
CG A:ASP623 3.6 22.6 1.0
CB A:ASP411 3.6 20.5 1.0
OD1 A:ASP623 3.7 19.2 1.0
C3' P:DC115 3.8 22.3 1.0
O A:HOH1698 3.9 38.6 1.0
PA A:ATP1001 3.9 22.5 1.0
CB A:SER624 4.0 20.2 1.0
C5' P:DC115 4.2 25.0 1.0
OD1 A:ASP411 4.3 24.5 1.0
O P:HOH207 4.4 23.2 1.0
O1A A:ATP1001 4.4 20.3 1.0
C4' P:DC115 4.4 22.7 1.0
O A:HOH1247 4.5 29.4 1.0
O5' A:ATP1001 4.5 20.4 1.0
OG A:SER624 4.6 23.0 1.0
C5' A:ATP1001 4.6 18.9 1.0
O P:HOH206 4.6 22.2 1.0
O A:ASP621 4.7 19.5 1.0
N A:SER624 4.8 20.8 1.0
O1G A:ATP1001 4.8 20.1 1.0
C A:ASP623 4.9 22.3 1.0
CA A:SER624 4.9 20.8 1.0
CB A:ASP623 5.0 20.8 1.0

Calcium binding site 3 out of 5 in 4m45

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex


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 Dg/Dt at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:40.1
occ:1.00
 O A:HOH1283 2.1 40.3 1.0
OD1 A:ASN507 2.3 49.0 1.0
O A:ASN505 2.3 39.1 1.0
O A:LYS531 2.3 41.7 1.0
O A:HOH1294 2.5 39.7 1.0
O A:HOH1208 2.6 32.3 1.0
C A:LYS531 3.3 40.9 1.0
CG A:ASN507 3.4 45.1 1.0
C A:ASN505 3.5 40.8 1.0
ND2 A:ASN507 4.0 42.0 1.0
CA A:LYS531 4.1 40.4 1.0
CB A:ASN505 4.1 42.2 1.0
N A:LYS532 4.2 37.8 1.0
N A:ASN507 4.2 42.6 1.0
C A:PRO506 4.3 42.6 1.0
CA A:PRO506 4.4 41.0 1.0
N A:PRO506 4.4 38.9 1.0
CA A:LYS532 4.4 39.9 1.0
CA A:ASN505 4.4 42.9 1.0
O A:LEU533 4.5 37.0 1.0
CB A:ASN507 4.6 44.8 1.0
O A:ALA502 4.7 36.2 1.0
CB A:LYS531 4.7 46.0 1.0
C A:LYS532 4.8 41.8 1.0
CA A:ASN507 4.8 45.4 1.0
O A:PRO506 4.8 44.0 1.0
N A:LEU533 4.9 37.6 1.0
O A:ILE530 4.9 33.4 1.0

Calcium binding site 4 out of 5 in 4m45

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex


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 Dg/Dt at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:37.9
occ:1.00
 O A:HOH1222 2.4 28.5 1.0
O A:HOH1182 2.4 24.0 1.0
O A:HOH1651 2.5 38.4 1.0
O A:HOH1278 2.6 31.2 1.0
O A:HOH1124 3.1 30.9 1.0
O A:HOH1652 3.3 35.8 1.0
OE1 A:GLU716 3.4 40.3 1.0
NZ A:LYS486 4.3 31.9 1.0
CB A:ASP684 4.4 30.9 1.0
CD A:GLU716 4.4 38.7 1.0
OG1 A:THR413 4.4 23.2 1.0
OD1 A:ASP411 4.5 24.5 1.0
CG A:GLU716 4.5 35.1 1.0
O A:ASP411 4.5 20.8 1.0
O A:ASP684 4.6 22.2 1.0
O A:HOH1550 4.8 33.9 1.0
OD2 A:ASP411 4.8 20.7 1.0
CG A:ASP411 4.9 22.9 1.0
OD2 A:ASP684 4.9 43.2 1.0
O A:ARG685 5.0 23.6 1.0

Calcium binding site 5 out of 5 in 4m45

Go back to Calcium Binding Sites List in 4m45
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-5 of Primer/Template Duplex


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 Dg/Dt at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:46.0
occ:1.00
 O A:HOH1573 2.2 36.2 1.0
O A:HOH1574 2.4 37.2 1.0
O A:HOH1103 2.5 25.7 1.0
O A:HOH1575 2.6 52.1 1.0
OE1 A:GLU116 2.6 31.2 1.0
OE2 A:GLU116 2.7 34.0 1.0
CD A:GLU116 3.0 29.3 1.0
CD1 A:ILE309 3.9 54.8 1.0
O A:HOH1576 4.2 33.0 1.0
OD2 A:ASP114 4.3 42.9 1.0
O A:HOH1491 4.4 33.5 1.0
CG A:GLU116 4.6 23.7 1.0
O A:ILE115 4.7 22.6 1.0

Reference:

S.Xia, W.H.Konigsberg. Mispairs with Watson-Crick Base-Pair Geometry Observed in Ternary Complexes of An RB69 Dna Polymerase Variant. Protein Sci. V. 23 508 2014.
ISSN: ISSN 0961-8368
PubMed: 24458997
DOI: 10.1002/PRO.2434
Page generated: Wed Jul 9 00:11:55 2025

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