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Calcium in PDB 4m3x: RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-5 of Primer/Template Duplex

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-5 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-5 of Primer/Template Duplex, PDB code: 4m3x 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) 49.26 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.118, 119.820, 130.266, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-5 of Primer/Template Duplex (pdb code 4m3x). 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 Dt/Dg at Position N-5 of Primer/Template Duplex, PDB code: 4m3x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4m3x

Go back to Calcium Binding Sites List in 4m3x
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:24.8
occ:1.00
 O2B A:ATP1001 2.2 20.1 1.0
OD2 A:ASP411 2.3 28.4 1.0
O1G A:ATP1001 2.3 24.3 1.0
O A:LEU412 2.3 23.0 1.0
OD2 A:ASP623 2.4 17.7 1.0
O2A A:ATP1001 2.4 19.7 1.0
PB A:ATP1001 3.4 22.3 1.0
CG A:ASP411 3.5 31.7 1.0
CG A:ASP623 3.5 18.8 1.0
CA A:CA1003 3.5 52.7 1.0
C A:LEU412 3.5 22.4 1.0
PG A:ATP1001 3.6 22.9 1.0
PA A:ATP1001 3.7 19.0 1.0
O3A A:ATP1001 3.8 20.1 1.0
O3B A:ATP1001 3.9 21.2 1.0
O A:HOH1102 3.9 32.5 1.0
O A:HOH1214 3.9 38.9 1.0
OD1 A:ASP623 4.0 16.1 1.0
CB A:ASP411 4.0 30.8 1.0
O2G A:ATP1001 4.1 23.5 1.0
N A:LEU412 4.1 22.5 1.0
C5' A:ATP1001 4.2 20.1 1.0
CA A:LEU412 4.3 21.6 1.0
C A:ASP411 4.3 26.1 1.0
OD1 A:ASP411 4.5 31.3 1.0
O5' A:ATP1001 4.5 21.5 1.0
N A:SER414 4.5 24.0 1.0
N A:THR413 4.5 23.1 1.0
N A:ALA415 4.7 21.2 1.0
CA A:THR413 4.7 24.4 1.0
CB A:LEU412 4.7 22.3 1.0
O A:ASP411 4.7 29.1 1.0
O1B A:ATP1001 4.8 21.5 1.0
CB A:ASP623 4.8 21.4 1.0
O3G A:ATP1001 4.8 29.0 1.0
CB A:ALA415 4.8 21.5 1.0
CA A:ASP411 4.8 26.5 1.0
C A:THR413 4.9 23.9 1.0
O1A A:ATP1001 5.0 21.1 1.0

Calcium binding site 2 out of 5 in 4m3x

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:52.7
occ:1.00
 O2A A:ATP1001 2.7 19.7 1.0
OD1 A:ASP623 2.8 16.1 1.0
OD2 A:ASP411 3.3 28.4 1.0
CA A:CA1002 3.5 24.8 1.0
CG A:ASP623 3.5 18.8 1.0
CG A:ASP411 3.5 31.7 1.0
OD2 A:ASP623 3.6 17.7 1.0
CB A:ASP411 3.6 30.8 1.0
C3' P:DC115 3.8 24.3 1.0
PA A:ATP1001 4.0 19.0 1.0
O A:HOH1214 4.0 38.9 1.0
CB A:SER624 4.0 24.5 1.0
C5' P:DC115 4.1 34.8 1.0
OD1 A:ASP411 4.3 31.3 1.0
C4' P:DC115 4.5 27.5 1.0
C5' A:ATP1001 4.5 20.1 1.0
O5' A:ATP1001 4.5 21.5 1.0
OG A:SER624 4.5 24.5 1.0
O A:HOH1237 4.6 38.8 1.0
O1A A:ATP1001 4.6 21.1 1.0
O P:HOH202 4.7 23.1 1.0
O1G A:ATP1001 4.7 24.3 1.0
O A:ASP621 4.8 19.0 1.0
N A:SER624 4.8 23.1 1.0
C A:ASP623 4.8 23.0 1.0
O A:HOH1111 4.8 22.0 1.0
CA A:SER624 4.9 23.9 1.0
CB A:ASP623 4.9 21.4 1.0
O A:ASP623 5.0 20.7 1.0

Calcium binding site 3 out of 5 in 4m3x

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg 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:LYS531 2.1 38.7 1.0
O A:HOH1203 2.1 40.4 1.0
OD1 A:ASN507 2.2 51.5 1.0
O A:ASN505 2.4 36.4 1.0
O A:HOH1202 2.6 38.1 1.0
O A:HOH1302 2.6 36.6 1.0
C A:LYS531 3.1 44.0 1.0
CG A:ASN507 3.3 48.3 1.0
C A:ASN505 3.6 43.6 1.0
ND2 A:ASN507 3.8 50.6 1.0
CA A:LYS531 3.8 45.4 1.0
N A:LYS532 4.0 39.4 1.0
CA A:LYS532 4.3 44.5 1.0
CB A:ASN505 4.3 53.4 1.0
N A:ASN507 4.3 47.9 1.0
C A:PRO506 4.4 44.1 1.0
CA A:PRO506 4.4 43.1 1.0
N A:PRO506 4.5 42.1 1.0
CB A:LYS531 4.5 45.8 1.0
CB A:ASN507 4.5 48.0 1.0
CA A:ASN505 4.6 53.1 1.0
O A:LEU533 4.6 32.8 1.0
C A:LYS532 4.7 46.6 1.0
O A:ALA502 4.7 36.6 1.0
N A:LEU533 4.7 44.0 1.0
O A:ILE530 4.8 32.9 1.0
CA A:ASN507 4.8 48.9 1.0
O A:PRO506 4.9 42.0 1.0
O A:HOH1204 5.0 42.6 1.0

Calcium binding site 4 out of 5 in 4m3x

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:44.4
occ:1.00
 O A:HOH1198 2.0 38.6 1.0
O A:HOH1199 2.3 29.8 1.0
OE1 A:GLU716 2.5 46.3 1.0
O A:HOH1197 2.6 39.4 1.0
O A:HOH1195 2.9 37.1 1.0
O A:HOH1102 3.0 32.5 1.0
CD A:GLU716 3.6 45.4 1.0
CB A:ASP684 4.1 39.8 1.0
CG A:GLU716 4.2 44.4 1.0
NZ A:LYS486 4.2 26.9 1.0
OG1 A:THR413 4.3 29.1 1.0
OD1 A:ASP411 4.4 31.3 1.0
OD2 A:ASP684 4.5 50.0 1.0
O A:ASP411 4.5 29.1 1.0
OE2 A:GLU716 4.6 45.0 1.0
O A:ASP684 4.7 26.9 1.0
O A:HOH1196 4.7 35.8 1.0
OD2 A:ASP411 4.8 28.4 1.0
CG A:ASP684 4.8 42.8 1.0
O A:ARG685 4.9 22.7 1.0
CG A:ASP411 4.9 31.7 1.0

Calcium binding site 5 out of 5 in 4m3x

Go back to Calcium Binding Sites List in 4m3x
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-5 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:63.3
occ:1.00
 O A:HOH1229 2.4 36.9 1.0
O A:HOH1121 2.5 31.1 1.0
OE2 A:GLU116 2.6 35.1 1.0
OE1 A:GLU116 2.7 35.2 1.0
O A:HOH1228 2.8 60.9 1.0
CD A:GLU116 3.0 33.2 1.0
OD2 A:ASP114 4.3 48.5 1.0
CG A:GLU116 4.5 27.3 1.0
O A:ILE115 4.6 24.9 1.0
CD1 A:ILE309 4.8 50.9 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: Sun Jul 14 09:59:45 2024

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