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Calcium in PDB 4m42: RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-4 of Primer/Template Duplex

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-4 of Primer/Template Duplex

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-4 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-4 of Primer/Template Duplex, PDB code: 4m42 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) 47.38 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.538, 118.657, 130.651, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-4 of Primer/Template Duplex (pdb code 4m42). 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-4 of Primer/Template Duplex, PDB code: 4m42:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4m42

Go back to Calcium Binding Sites List in 4m42
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-4 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-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:25.2
occ:1.00
 OD1 A:ASP623 2.3 21.9 1.0
O1G A:ATP1001 2.3 26.3 1.0
O2B A:ATP1001 2.3 25.9 1.0
O2A A:ATP1001 2.3 26.7 1.0
OD2 A:ASP411 2.4 28.2 1.0
O A:LEU412 2.4 24.2 1.0
PB A:ATP1001 3.4 25.1 1.0
CG A:ASP623 3.4 26.6 1.0
CA A:CA1003 3.4 56.6 1.0
CG A:ASP411 3.5 28.5 1.0
PA A:ATP1001 3.5 28.3 1.0
PG A:ATP1001 3.6 27.8 1.0
C A:LEU412 3.6 29.5 1.0
O3A A:ATP1001 3.7 25.9 1.0
O3B A:ATP1001 3.9 26.9 1.0
OD2 A:ASP623 3.9 24.6 1.0
O A:HOH1174 4.0 37.6 1.0
N A:LEU412 4.0 23.4 1.0
CB A:ASP411 4.0 22.3 1.0
C5' A:ATP1001 4.2 27.1 1.0
O2G A:ATP1001 4.3 25.2 1.0
CA A:LEU412 4.3 27.3 1.0
O5' A:ATP1001 4.4 29.0 1.0
C A:ASP411 4.4 24.7 1.0
N A:SER414 4.5 26.4 1.0
OD1 A:ASP411 4.5 31.6 1.0
N A:ALA415 4.6 24.0 1.0
CB A:ALA415 4.6 23.4 1.0
N A:THR413 4.6 26.9 1.0
CB A:ASP623 4.7 25.2 1.0
CB A:LEU412 4.7 26.0 1.0
O3G A:ATP1001 4.7 27.9 1.0
O1A A:ATP1001 4.7 27.4 1.0
O1B A:ATP1001 4.7 25.4 1.0
CA A:THR413 4.9 27.4 1.0
CA A:ASP411 4.9 24.7 1.0
C A:THR413 4.9 24.7 1.0
O A:ASP411 4.9 24.0 1.0

Calcium binding site 2 out of 5 in 4m42

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-4 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-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:56.6
occ:1.00
 O2A A:ATP1001 2.6 26.7 1.0
OD2 A:ASP623 2.7 24.6 1.0
O P:HOH212 2.8 25.9 1.0
CA A:CA1002 3.4 25.2 1.0
CG A:ASP623 3.4 26.6 1.0
OD2 A:ASP411 3.5 28.2 1.0
OD1 A:ASP623 3.5 21.9 1.0
O A:HOH1367 3.5 40.1 1.0
CG A:ASP411 3.7 28.5 1.0
CB A:ASP411 3.7 22.3 1.0
PA A:ATP1001 3.8 28.3 1.0
C3' P:DC115 3.8 24.9 1.0
CB A:SER624 4.1 24.3 1.0
C5' P:DC115 4.2 28.4 1.0
O1A A:ATP1001 4.3 27.4 1.0
O5' A:ATP1001 4.4 29.0 1.0
OD1 A:ASP411 4.4 31.6 1.0
C4' P:DC115 4.4 26.1 1.0
C5' A:ATP1001 4.5 27.1 1.0
O A:HOH1109 4.5 28.8 1.0
O A:HOH1288 4.7 27.9 1.0
OG A:SER624 4.7 23.7 1.0
O1G A:ATP1001 4.7 26.3 1.0
O A:ASP621 4.7 24.6 1.0
O P:HOH206 4.8 28.8 1.0
N A:SER624 4.8 22.4 1.0
C A:ASP623 4.9 26.7 1.0
CB A:ASP623 4.9 25.2 1.0
CA A:SER624 5.0 24.8 1.0

Calcium binding site 3 out of 5 in 4m42

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-4 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-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:48.1
occ:1.00
 O A:LYS531 2.3 43.1 1.0
O A:HOH1206 2.3 41.5 1.0
OD1 A:ASN507 2.4 50.0 1.0
O A:ASN505 2.4 45.7 1.0
O A:HOH1165 2.5 42.6 1.0
O A:HOH1278 2.5 54.3 1.0
C A:LYS531 3.2 44.8 1.0
CG A:ASN507 3.5 49.9 1.0
C A:ASN505 3.6 48.5 1.0
CA A:LYS531 4.0 42.7 1.0
N A:LYS532 4.1 48.4 1.0
ND2 A:ASN507 4.2 52.5 1.0
CA A:LYS532 4.2 48.3 1.0
CB A:ASN505 4.2 53.5 1.0
N A:ASN507 4.3 58.6 1.0
C A:PRO506 4.3 60.3 1.0
CA A:PRO506 4.4 51.5 1.0
O A:LEU533 4.5 46.4 1.0
N A:PRO506 4.5 45.8 1.0
CA A:ASN505 4.6 50.7 1.0
C A:LYS532 4.6 48.8 1.0
CB A:ASN507 4.7 52.7 1.0
O A:ALA502 4.7 46.4 1.0
CB A:LYS531 4.7 44.1 1.0
O A:PRO506 4.8 68.9 1.0
N A:LEU533 4.8 47.5 1.0
O A:ILE530 4.9 42.1 1.0
CA A:ASN507 4.9 55.4 1.0

Calcium binding site 4 out of 5 in 4m42

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

b:43.8
occ:1.00
 O A:HOH1378 2.5 32.8 1.0
O A:HOH1383 2.6 48.5 1.0
O A:HOH1226 2.6 32.3 1.0
O A:HOH1225 2.6 31.2 1.0
OE1 A:GLU716 2.6 46.4 1.0
O A:HOH1174 2.7 37.6 1.0
CD A:GLU716 3.6 44.6 1.0
O A:HOH1409 4.1 55.2 1.0
CG A:GLU716 4.1 36.2 1.0
CB A:ASP684 4.2 35.6 1.0
OG1 A:THR413 4.3 30.2 1.0
NZ A:LYS486 4.4 39.7 1.0
OD1 A:ASP411 4.5 31.6 1.0
O A:ASP411 4.5 24.0 1.0
O A:ASP684 4.6 25.5 1.0
OE2 A:GLU716 4.6 36.0 1.0
OD2 A:ASP684 4.8 48.5 1.0
OD2 A:ASP411 4.8 28.2 1.0
CG A:ASP411 4.9 28.5 1.0
O A:ARG685 5.0 26.2 1.0
C A:ASP684 5.0 30.8 1.0

Calcium binding site 5 out of 5 in 4m42

Go back to Calcium Binding Sites List in 4m42
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-4 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-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:51.2
occ:1.00
 OE1 A:GLU116 2.5 28.7 1.0
O A:HOH1241 2.6 37.6 1.0
OE2 A:GLU116 2.8 31.0 1.0
CD A:GLU116 3.0 32.4 1.0
OD2 A:ASP114 4.2 62.6 1.0
CG A:GLU116 4.5 27.2 1.0
O A:ILE115 4.6 28.4 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 10:03:07 2024

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