Atomistry » Calcium » PDB 4m18-4m8u » 4m3w
Atomistry »
  Calcium »
    PDB 4m18-4m8u »
      4m3w »

Calcium in PDB 4m3w: RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-4 of Primer/Template Duplex

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-4 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-4 of Primer/Template Duplex, PDB code: 4m3w 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) 47.41 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.518, 118.774, 129.773, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-4 of Primer/Template Duplex (pdb code 4m3w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-4 of Primer/Template Duplex, PDB code: 4m3w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4m3w

Go back to Calcium Binding Sites List in 4m3w
Calcium binding site 1 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:23.0
occ:1.00
 O1G A:ATP1001 2.3 19.5 1.0
O2B A:ATP1001 2.3 20.4 1.0
OD1 A:ASP623 2.3 18.9 1.0
O A:LEU412 2.3 23.1 1.0
O2A A:ATP1001 2.3 19.5 1.0
OD2 A:ASP411 2.4 22.7 1.0
CG A:ASP623 3.4 21.0 1.0
PB A:ATP1001 3.4 22.1 1.0
CA A:CA1003 3.4 58.2 1.0
CG A:ASP411 3.5 24.0 1.0
C A:LEU412 3.5 24.5 1.0
PG A:ATP1001 3.5 21.3 1.0
PA A:ATP1001 3.6 20.4 1.0
O3A A:ATP1001 3.7 21.4 1.0
OD2 A:ASP623 3.8 21.5 1.0
O A:HOH1107 3.9 32.1 1.0
O3B A:ATP1001 3.9 23.1 1.0
O A:HOH1266 3.9 41.3 1.0
N A:LEU412 3.9 23.1 1.0
CB A:ASP411 4.1 24.8 1.0
C5' A:ATP1001 4.2 18.6 1.0
O2G A:ATP1001 4.2 21.1 1.0
CA A:LEU412 4.2 24.5 1.0
O5' A:ATP1001 4.4 19.2 1.0
C A:ASP411 4.4 25.1 1.0
OD1 A:ASP411 4.5 24.9 1.0
N A:SER414 4.6 20.4 1.0
N A:THR413 4.6 21.6 1.0
CB A:ASP623 4.7 22.2 1.0
N A:ALA415 4.7 19.1 1.0
CB A:LEU412 4.7 23.9 1.0
CB A:ALA415 4.7 21.6 1.0
O3G A:ATP1001 4.7 22.2 1.0
O1B A:ATP1001 4.8 23.2 1.0
O1A A:ATP1001 4.8 21.4 1.0
CA A:THR413 4.8 22.5 1.0
C A:THR413 4.9 22.0 1.0
CA A:ASP411 4.9 24.4 1.0

Calcium binding site 2 out of 6 in 4m3w

Go back to Calcium Binding Sites List in 4m3w
Calcium binding site 2 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:58.2
occ:1.00
 O2A A:ATP1001 2.5 19.5 1.0
OD2 A:ASP623 2.6 21.5 1.0
O A:HOH1193 2.8 25.8 1.0
OD2 A:ASP411 3.4 22.7 1.0
CA A:CA1002 3.4 23.0 1.0
CG A:ASP623 3.5 21.0 1.0
OD1 A:ASP623 3.5 18.9 1.0
O A:HOH1267 3.6 45.2 1.0
PA A:ATP1001 3.7 20.4 1.0
CG A:ASP411 3.7 24.0 1.0
C3' P:DC115 3.7 21.6 1.0
CB A:ASP411 3.8 24.8 1.0
O A:HOH1266 4.0 41.3 1.0
C5' P:DC115 4.1 25.7 1.0
O1A A:ATP1001 4.2 21.4 1.0
CB A:SER624 4.2 20.6 1.0
O5' A:ATP1001 4.3 19.2 1.0
C4' P:DC115 4.3 23.4 1.0
C5' A:ATP1001 4.4 18.6 1.0
O A:HOH1138 4.5 21.0 1.0
OD1 A:ASP411 4.5 24.9 1.0
O1G A:ATP1001 4.6 19.5 1.0
O A:ASP621 4.7 21.3 1.0
O A:HOH1167 4.8 25.1 1.0
OG A:SER624 4.8 23.8 1.0
O A:HOH1232 4.8 24.3 1.0
N A:SER624 4.8 21.8 1.0
CB A:ASP623 4.9 22.2 1.0
C A:ASP623 4.9 22.2 1.0
O3A A:ATP1001 5.0 21.4 1.0
CA A:SER624 5.0 20.7 1.0

Calcium binding site 3 out of 6 in 4m3w

Go back to Calcium Binding Sites List in 4m3w
Calcium binding site 3 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:45.0
occ:1.00
 O A:LYS531 2.1 36.1 1.0
O A:HOH1317 2.2 43.6 1.0
OD1 A:ASN507 2.3 47.3 1.0
O A:ASN505 2.3 36.5 1.0
O A:HOH1195 2.5 36.5 1.0
O A:HOH1319 2.7 46.4 1.0
C A:LYS531 3.2 39.2 1.0
CG A:ASN507 3.4 46.4 1.0
C A:ASN505 3.6 42.4 1.0
CA A:LYS531 4.0 40.5 1.0
O A:HOH1318 4.0 44.8 1.0
ND2 A:ASN507 4.0 50.3 1.0
N A:LYS532 4.1 41.4 1.0
CB A:ASN505 4.2 50.9 1.0
CA A:LYS532 4.3 43.4 1.0
N A:ASN507 4.3 50.8 1.0
C A:PRO506 4.3 50.1 1.0
CA A:PRO506 4.4 44.1 1.0
N A:PRO506 4.5 41.9 1.0
CA A:ASN505 4.5 49.4 1.0
O A:LEU533 4.5 38.4 1.0
O A:ALA502 4.6 37.6 1.0
CB A:LYS531 4.6 43.9 1.0
CB A:ASN507 4.6 48.8 1.0
C A:LYS532 4.7 43.4 1.0
O A:PRO506 4.8 58.8 1.0
O A:ILE530 4.8 36.4 1.0
CA A:ASN507 4.9 50.0 1.0
N A:LEU533 4.9 40.5 1.0

Calcium binding site 4 out of 6 in 4m3w

Go back to Calcium Binding Sites List in 4m3w
Calcium binding site 4 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:38.7
occ:1.00
 O A:HOH1240 2.6 29.4 1.0
OE1 A:GLU716 2.6 44.9 1.0
O A:HOH1239 2.6 30.6 1.0
O A:HOH1401 2.8 47.4 1.0
O A:HOH1107 2.8 32.1 1.0
O A:HOH1216 2.9 29.0 1.0
O A:HOH1241 3.3 39.1 1.0
CD A:GLU716 3.6 40.3 1.0
NZ A:LYS486 4.2 35.6 1.0
OE2 A:GLU716 4.3 36.6 1.0
CG A:GLU716 4.4 36.5 1.0
OD1 A:ASP411 4.4 24.9 1.0
OG1 A:THR413 4.4 23.1 1.0
CB A:ASP684 4.5 31.2 1.0
O A:ASP684 4.6 24.4 1.0
O A:ASP411 4.6 23.4 1.0
OD2 A:ASP411 4.7 22.7 1.0
CG A:ASP411 4.9 24.0 1.0
O A:ARG685 4.9 23.2 1.0
O2G A:ATP1001 5.0 21.1 1.0
O A:HOH1403 5.0 44.9 1.0

Calcium binding site 5 out of 6 in 4m3w

Go back to Calcium Binding Sites List in 4m3w
Calcium binding site 5 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:55.0
occ:1.00
 O A:HOH1454 2.4 46.1 1.0
O A:HOH1290 2.5 46.5 1.0
OE1 A:GLU116 2.5 34.6 1.0
O A:HOH1289 2.6 47.2 1.0
OE2 A:GLU116 2.6 30.0 1.0
CD A:GLU116 2.9 29.3 1.0
OD2 A:ASP114 4.2 62.1 1.0
CG A:GLU116 4.5 31.8 1.0
O A:ILE115 4.6 25.0 1.0

Calcium binding site 6 out of 6 in 4m3w

Go back to Calcium Binding Sites List in 4m3w
Calcium binding site 6 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 6 of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-4 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:87.0
occ:1.00
 OD1 A:ASP861 2.4 68.4 1.0
O A:LEU857 2.8 63.6 1.0
OD2 A:ASP860 3.0 61.5 1.0
OD1 A:ASP860 3.2 89.5 1.0
CG A:ASP861 3.3 59.5 1.0
CG A:ASP860 3.5 67.3 1.0
CB A:ASP861 4.0 56.8 1.0
C A:LEU857 4.0 60.1 1.0
OD2 A:ASP861 4.2 55.4 1.0
CA A:ILE858 4.3 54.6 1.0
N A:ASP861 4.4 47.1 1.0
N A:ILE858 4.7 57.2 1.0
CA A:ASP861 4.8 49.8 1.0
C A:ILE858 4.9 47.1 1.0
CB A:ASP860 4.9 57.2 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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy