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Calcium in PDB 4m3y: RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-1 of Primer/Template Duplex

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-1 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-1 of Primer/Template Duplex, PDB code: 4m3y 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 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.004, 120.181, 130.624, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-1 of Primer/Template Duplex (pdb code 4m3y). 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-1 of Primer/Template Duplex, PDB code: 4m3y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4m3y

Go back to Calcium Binding Sites List in 4m3y
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:22.0
occ:1.00
 O2B A:ATP1001 2.3 21.7 1.0
OD2 A:ASP411 2.3 22.0 1.0
OD1 A:ASP623 2.3 17.7 1.0
O A:LEU412 2.3 19.3 1.0
O2A A:ATP1001 2.4 20.4 1.0
O1G A:ATP1001 2.4 20.4 1.0
CG A:ASP623 3.4 19.1 1.0
PB A:ATP1001 3.4 21.9 1.0
CG A:ASP411 3.4 24.7 1.0
CA A:CA1003 3.5 51.0 1.0
C A:LEU412 3.5 19.5 1.0
PA A:ATP1001 3.6 21.1 1.0
PG A:ATP1001 3.6 19.9 1.0
O3A A:ATP1001 3.7 20.8 1.0
OD2 A:ASP623 3.8 18.0 1.0
O3B A:ATP1001 3.9 22.2 1.0
O A:HOH1721 3.9 34.6 1.0
CB A:ASP411 3.9 22.8 1.0
N A:LEU412 4.0 19.1 1.0
O A:HOH1661 4.1 33.0 1.0
C5' A:ATP1001 4.2 19.0 1.0
CA A:LEU412 4.2 19.1 1.0
O2G A:ATP1001 4.2 21.0 1.0
C A:ASP411 4.3 21.5 1.0
O5' A:ATP1001 4.4 19.9 1.0
OD1 A:ASP411 4.5 25.0 1.0
N A:SER414 4.6 21.5 1.0
N A:THR413 4.6 20.8 1.0
N A:ALA415 4.6 19.1 1.0
CB A:ALA415 4.6 17.3 1.0
CB A:ASP623 4.7 18.5 1.0
CB A:LEU412 4.7 17.5 1.0
O1B A:ATP1001 4.8 21.1 1.0
CA A:ASP411 4.8 22.5 1.0
O3G A:ATP1001 4.8 22.0 1.0
CA A:THR413 4.8 20.6 1.0
O1A A:ATP1001 4.8 21.4 1.0
O A:ASP411 4.9 21.9 1.0
C A:THR413 4.9 21.5 1.0

Calcium binding site 2 out of 5 in 4m3y

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:51.0
occ:1.00
 O A:HOH1177 2.5 29.3 1.0
OD2 A:ASP623 2.6 18.0 1.0
O2A A:ATP1001 2.7 20.4 1.0
OD2 A:ASP411 3.5 22.0 1.0
CG A:ASP623 3.5 19.1 1.0
CA A:CA1002 3.5 22.0 1.0
CB A:ASP411 3.6 22.8 1.0
CG A:ASP411 3.6 24.7 1.0
OD1 A:ASP623 3.6 17.7 1.0
C3' P:DG115 3.8 22.8 1.0
O A:HOH1472 3.8 32.2 1.0
O A:HOH1721 3.9 34.6 1.0
PA A:ATP1001 3.9 21.1 1.0
CB A:SER624 4.0 20.5 1.0
C5' P:DG115 4.2 25.1 1.0
O P:HOH204 4.3 23.5 1.0
OD1 A:ASP411 4.4 25.0 1.0
C4' P:DG115 4.4 23.3 1.0
O1A A:ATP1001 4.4 21.4 1.0
O A:HOH1636 4.5 33.3 1.0
O5' A:ATP1001 4.5 19.9 1.0
OG A:SER624 4.6 21.0 1.0
C5' A:ATP1001 4.6 19.0 1.0
O A:ASP621 4.6 20.1 1.0
O P:HOH202 4.8 23.4 1.0
N A:SER624 4.8 19.1 1.0
C A:ASP623 4.8 19.1 1.0
O1G A:ATP1001 4.8 20.4 1.0
CA A:SER624 4.9 21.1 1.0
CB A:ASP623 4.9 18.5 1.0
O A:ASP623 5.0 19.1 1.0

Calcium binding site 3 out of 5 in 4m3y

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:37.5
occ:1.00
 O A:HOH1131 2.0 36.5 1.0
OD1 A:ASN507 2.3 46.1 1.0
O A:LYS531 2.3 41.5 1.0
O A:ASN505 2.3 39.2 1.0
O A:HOH1394 2.5 39.1 1.0
O A:HOH1637 2.6 31.1 1.0
C A:LYS531 3.2 41.8 1.0
CG A:ASN507 3.4 44.9 1.0
C A:ASN505 3.5 41.4 1.0
ND2 A:ASN507 3.9 41.9 1.0
CA A:LYS531 4.0 39.4 1.0
CB A:ASN505 4.1 45.4 1.0
N A:ASN507 4.1 42.0 1.0
N A:LYS532 4.1 38.1 1.0
C A:PRO506 4.3 41.0 1.0
CA A:LYS532 4.3 39.2 1.0
CA A:PRO506 4.3 38.6 1.0
N A:PRO506 4.4 39.1 1.0
CA A:ASN505 4.4 45.1 1.0
O A:LEU533 4.5 32.2 1.0
CB A:ASN507 4.6 45.6 1.0
CB A:LYS531 4.6 44.4 1.0
O A:HOH1422 4.7 38.9 1.0
C A:LYS532 4.7 38.6 1.0
CA A:ASN507 4.7 45.8 1.0
O A:ALA502 4.7 36.4 1.0
N A:LEU533 4.8 32.5 1.0
O A:ILE530 4.9 33.2 1.0

Calcium binding site 4 out of 5 in 4m3y

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:40.1
occ:1.00
 O A:HOH1663 2.5 44.7 1.0
O A:HOH1277 2.5 32.5 1.0
O A:HOH1105 2.5 26.7 1.0
O A:HOH1315 2.5 34.8 1.0
O A:HOH1662 2.6 44.0 1.0
O A:HOH1661 2.8 33.0 1.0
OE1 A:GLU716 4.0 32.7 1.0
O A:HOH1716 4.1 46.4 1.0
CB A:ASP684 4.2 31.9 1.0
NZ A:LYS486 4.3 30.3 1.0
OG1 A:THR413 4.4 24.3 1.0
OD1 A:ASP411 4.5 25.0 1.0
O A:ASP411 4.5 21.9 1.0
O A:HOH1409 4.7 35.2 1.0
CG A:GLU716 4.7 32.1 1.0
O A:ASP684 4.7 23.7 1.0
OD2 A:ASP684 4.8 41.8 1.0
OD2 A:ASP411 4.8 22.0 1.0
CD A:GLU716 4.9 37.8 1.0
CG A:ASP411 5.0 24.7 1.0
O A:ARG685 5.0 24.4 1.0

Calcium binding site 5 out of 5 in 4m3y

Go back to Calcium Binding Sites List in 4m3y
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-1 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:51.4
occ:1.00
 O A:HOH1707 2.2 32.9 1.0
O A:HOH1709 2.4 56.8 1.0
O A:HOH1101 2.5 26.6 1.0
O A:HOH1708 2.5 49.5 1.0
OE1 A:GLU116 2.5 31.9 1.0
OE2 A:GLU116 2.7 32.0 1.0
CD A:GLU116 3.0 28.4 1.0
CD1 A:ILE309 4.1 50.6 1.0
OD2 A:ASP114 4.3 38.5 1.0
O A:HOH1506 4.3 34.5 1.0
O A:HOH1481 4.5 37.9 1.0
CG A:GLU116 4.5 24.3 1.0
O A:ILE115 4.6 21.0 1.0
OD1 A:ASP114 5.0 30.4 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 10:02:18 2024

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