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Calcium in PDB 4m3r: RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex, PDB code: 4m3r 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) 47.53 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.371, 119.391, 129.956, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex (pdb code 4m3r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex, PDB code: 4m3r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4m3r

Go back to Calcium Binding Sites List in 4m3r
Calcium binding site 1 out of 7 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 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 Dt/Dg at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:19.5
occ:1.00
OD1 A:ASP623 2.2 16.3 1.0
O1G A:ATP1001 2.2 19.7 1.0
OD2 A:ASP411 2.3 19.1 1.0
O A:LEU412 2.3 22.3 1.0
O2B A:ATP1001 2.3 19.6 1.0
O2A A:ATP1001 2.4 20.7 1.0
CG A:ASP623 3.4 19.3 1.0
PB A:ATP1001 3.4 19.8 1.0
CG A:ASP411 3.5 21.8 1.0
C A:LEU412 3.5 21.2 1.0
CA A:CA1003 3.5 62.7 1.0
PA A:ATP1001 3.6 20.1 1.0
PG A:ATP1001 3.6 20.2 1.0
O3A A:ATP1001 3.8 20.6 1.0
OD2 A:ASP623 3.8 18.2 1.0
O A:HOH1138 3.8 38.2 1.0
O3B A:ATP1001 3.9 20.8 1.0
N A:LEU412 3.9 22.2 1.0
CB A:ASP411 4.1 19.7 1.0
C5' A:ATP1001 4.1 19.8 1.0
CA A:LEU412 4.2 22.1 1.0
O2G A:ATP1001 4.3 19.6 1.0
O5' A:ATP1001 4.4 20.7 1.0
C A:ASP411 4.4 20.4 1.0
OD1 A:ASP411 4.5 25.6 1.0
N A:THR413 4.6 19.6 1.0
N A:SER414 4.6 18.6 1.0
O A:HOH1238 4.6 50.8 1.0
CB A:ASP623 4.6 19.2 1.0
N A:ALA415 4.6 17.2 1.0
CB A:ALA415 4.7 18.6 1.0
CB A:LEU412 4.7 20.8 1.0
O3G A:ATP1001 4.8 19.2 1.0
O1B A:ATP1001 4.8 19.9 1.0
O1A A:ATP1001 4.8 19.9 1.0
CA A:THR413 4.8 21.4 1.0
CA A:ASP411 4.9 19.0 1.0
C A:THR413 4.9 19.8 1.0

Calcium binding site 2 out of 7 in 4m3r

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Calcium binding site 2 out of 7 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 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 Dt/Dg at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:62.7
occ:1.00
OD2 A:ASP623 2.6 18.2 1.0
O2A A:ATP1001 2.6 20.7 1.0
O A:HOH1350 2.8 30.1 1.0
CG A:ASP623 3.4 19.3 1.0
OD2 A:ASP411 3.4 19.1 1.0
OD1 A:ASP623 3.5 16.3 1.0
CA A:CA1002 3.5 19.5 1.0
CG A:ASP411 3.7 21.8 1.0
CB A:ASP411 3.7 19.7 1.0
C3' P:DT115 3.8 23.7 1.0
PA A:ATP1001 3.8 20.1 1.0
C5' P:DT115 4.1 28.8 1.0
CB A:SER624 4.1 20.6 1.0
O P:HOH201 4.3 21.1 1.0
C4' P:DT115 4.3 25.4 1.0
O1A A:ATP1001 4.3 19.9 1.0
O5' A:ATP1001 4.3 20.7 1.0
OD1 A:ASP411 4.4 25.6 1.0
C5' A:ATP1001 4.4 19.8 1.0
OG A:SER624 4.6 21.7 1.0
O A:ASP621 4.6 19.6 1.0
O A:HOH1351 4.7 26.4 1.0
N A:SER624 4.7 18.8 1.0
C A:ASP623 4.8 20.0 1.0
O P:HOH207 4.8 27.8 1.0
CB A:ASP623 4.8 19.2 1.0
O1G A:ATP1001 4.8 19.7 1.0
CA A:SER624 4.9 20.5 1.0

Calcium binding site 3 out of 7 in 4m3r

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Calcium binding site 3 out of 7 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 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 Dt/Dg at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:42.0
occ:1.00
O A:HOH1199 2.1 34.2 1.0
O A:LYS531 2.2 36.3 1.0
OD1 A:ASN507 2.2 48.1 1.0
O A:ASN505 2.3 38.0 1.0
O A:HOH1149 2.5 37.5 1.0
O A:HOH1449 2.7 44.5 1.0
C A:LYS531 3.2 37.6 1.0
CG A:ASN507 3.4 46.3 1.0
C A:ASN505 3.6 41.1 1.0
CA A:LYS531 4.0 38.1 1.0
ND2 A:ASN507 4.1 43.8 1.0
N A:LYS532 4.1 41.1 1.0
N A:ASN507 4.1 50.3 1.0
C A:PRO506 4.2 47.6 1.0
CA A:PRO506 4.3 48.8 1.0
CA A:LYS532 4.3 42.6 1.0
CB A:ASN505 4.3 49.4 1.0
N A:PRO506 4.4 41.3 1.0
O A:LEU533 4.5 37.7 1.0
CB A:ASN507 4.6 47.1 1.0
CA A:ASN505 4.6 46.6 1.0
CB A:LYS531 4.6 41.5 1.0
O A:PRO506 4.7 54.4 1.0
O A:ALA502 4.7 37.4 1.0
C A:LYS532 4.7 45.3 1.0
CA A:ASN507 4.8 47.7 1.0
N A:LEU533 4.8 46.6 1.0
O A:ILE530 4.9 34.9 1.0

Calcium binding site 4 out of 7 in 4m3r

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Calcium binding site 4 out of 7 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 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 Dt/Dg at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:38.2
occ:1.00
OE1 A:GLU716 2.4 52.0 1.0
O A:HOH1138 2.4 38.2 1.0
O A:HOH1292 2.5 30.1 1.0
O A:HOH1261 2.5 30.2 1.0
O A:HOH1293 2.6 37.6 1.0
O A:HOH1294 3.0 37.8 1.0
CD A:GLU716 3.6 40.4 1.0
O A:HOH1238 3.8 50.8 1.0
NZ A:LYS486 4.2 34.2 1.0
CB A:ASP684 4.3 35.4 1.0
CG A:GLU716 4.3 34.6 1.0
OG1 A:THR413 4.4 21.1 1.0
OE2 A:GLU716 4.5 37.3 1.0
OD1 A:ASP411 4.6 25.6 1.0
O A:ASP411 4.7 20.5 1.0
O A:ASP684 4.7 19.7 1.0
O A:HOH1295 4.7 38.0 1.0
O A:HOH1414 4.7 42.3 1.0
OD2 A:ASP411 4.8 19.1 1.0
OD2 A:ASP684 4.9 50.5 1.0
CG A:ASP411 5.0 21.8 1.0
O A:ARG685 5.0 23.7 1.0

Calcium binding site 5 out of 7 in 4m3r

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Calcium binding site 5 out of 7 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 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 Dt/Dg at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:54.7
occ:1.00
O A:HOH1375 2.3 40.2 1.0
OE1 A:GLU116 2.5 29.7 1.0
OE2 A:GLU116 2.8 29.8 1.0
CD A:GLU116 3.0 27.9 1.0
CD1 A:ILE309 4.1 63.8 1.0
OD2 A:ASP114 4.3 57.5 1.0
CG A:GLU116 4.5 25.9 1.0
O A:ILE115 4.6 24.4 1.0

Calcium binding site 6 out of 7 in 4m3r

Go back to Calcium Binding Sites List in 4m3r
Calcium binding site 6 out of 7 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex


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 Dt/Dg at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:86.2
occ:1.00
OE1 A:GLU172 2.6 56.6 1.0
OE2 A:GLU177 2.8 46.6 1.0
OE2 A:GLU172 3.1 44.6 1.0
CD A:GLU172 3.2 44.7 1.0
OE1 A:GLU177 3.4 62.5 1.0
CD A:GLU177 3.4 51.8 1.0
CG A:GLU172 4.6 46.1 1.0
CB A:GLN171 4.9 42.9 1.0
CG A:GLU177 4.9 46.3 1.0

Calcium binding site 7 out of 7 in 4m3r

Go back to Calcium Binding Sites List in 4m3r
Calcium binding site 7 out of 7 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1008

b:90.4
occ:1.00
OD1 A:ASP861 2.4 62.5 1.0
O A:LEU857 2.9 52.3 1.0
OD2 A:ASP860 2.9 64.1 1.0
OD1 A:ASP860 3.0 70.2 1.0
CG A:ASP861 3.3 57.4 1.0
CG A:ASP860 3.3 63.4 1.0
OD2 A:ASP861 3.9 59.6 1.0
C A:LEU857 4.0 53.7 1.0
CB A:ASP861 4.3 51.9 1.0
CA A:ILE858 4.4 46.4 1.0
O A:HOH1429 4.5 52.2 1.0
N A:ASP861 4.6 44.4 1.0
N A:ILE858 4.7 50.5 1.0
CB A:ASP860 4.9 53.8 1.0
C A:ILE858 5.0 41.7 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: Sat Dec 12 04:57:46 2020

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