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Calcium in PDB 4m3z: RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-2 of Primer/Template Duplex

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-2 of Primer/Template Duplex

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-2 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-2 of Primer/Template Duplex, PDB code: 4m3z 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) 49.37 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.006, 120.615, 130.910, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.7

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-2 of Primer/Template Duplex (pdb code 4m3z). 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-2 of Primer/Template Duplex, PDB code: 4m3z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4m3z

Go back to Calcium Binding Sites List in 4m3z
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-2 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-2 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:19.0
occ:1.00
 OD2 A:ASP411 2.3 21.6 1.0
OD1 A:ASP623 2.3 19.9 1.0
O2B A:ATP1001 2.3 18.0 1.0
O1G A:ATP1001 2.3 20.5 1.0
O A:LEU412 2.3 17.7 1.0
O2A A:ATP1001 2.4 20.1 1.0
CG A:ASP623 3.4 20.3 1.0
PB A:ATP1001 3.4 20.2 1.0
CG A:ASP411 3.4 25.3 1.0
C A:LEU412 3.5 19.7 1.0
PG A:ATP1001 3.6 21.2 1.0
PA A:ATP1001 3.6 20.4 1.0
CA A:CA1003 3.7 45.5 1.0
O3A A:ATP1001 3.8 19.9 1.0
OD2 A:ASP623 3.8 20.1 1.0
O3B A:ATP1001 3.9 22.3 1.0
O A:HOH1685 3.9 32.0 1.0
O A:HOH1106 3.9 32.3 1.0
N A:LEU412 4.0 18.9 1.0
CB A:ASP411 4.0 22.2 1.0
O2G A:ATP1001 4.2 20.9 1.0
C5' A:ATP1001 4.2 18.0 1.0
CA A:LEU412 4.2 19.4 1.0
C A:ASP411 4.4 19.6 1.0
O5' A:ATP1001 4.5 19.0 1.0
OD1 A:ASP411 4.5 25.5 1.0
N A:THR413 4.6 19.5 1.0
N A:SER414 4.6 19.6 1.0
N A:ALA415 4.6 16.4 1.0
CB A:ASP623 4.7 19.4 1.0
CB A:ALA415 4.7 16.4 1.0
CB A:LEU412 4.7 18.4 1.0
O3G A:ATP1001 4.8 21.6 1.0
O1B A:ATP1001 4.8 20.4 1.0
CA A:THR413 4.8 20.4 1.0
O1A A:ATP1001 4.8 18.7 1.0
O A:ASP411 4.8 21.2 1.0
CA A:ASP411 4.9 21.5 1.0
C A:THR413 4.9 19.2 1.0

Calcium binding site 2 out of 5 in 4m3z

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

b:45.5
occ:1.00
 O A:HOH1328 2.5 30.0 1.0
O A:HOH1362 2.6 39.3 1.0
OD2 A:ASP623 2.6 20.1 1.0
O2A A:ATP1001 2.7 20.1 1.0
OD2 A:ASP411 3.4 21.6 1.0
CG A:ASP623 3.5 20.3 1.0
CG A:ASP411 3.6 25.3 1.0
CA A:CA1002 3.7 19.0 1.0
OD1 A:ASP623 3.7 19.9 1.0
CB A:ASP411 3.7 22.2 1.0
C3' P:DC115 3.7 25.1 1.0
PA A:ATP1001 4.0 20.4 1.0
CB A:SER624 4.0 20.2 1.0
O A:HOH1685 4.0 32.0 1.0
OD1 A:ASP411 4.4 25.5 1.0
C5' P:DC115 4.4 33.7 1.0
O1A A:ATP1001 4.5 18.7 1.0
O A:HOH1270 4.5 35.0 1.0
O5' A:ATP1001 4.5 19.0 1.0
OG A:SER624 4.5 22.3 1.0
O P:HOH209 4.6 32.2 1.0
O A:ASP621 4.6 19.7 1.0
C4' P:DC115 4.6 26.0 1.0
C5' A:ATP1001 4.6 18.0 1.0
O A:HOH1281 4.7 29.4 1.0
N A:SER624 4.7 21.0 1.0
O5' P:DC115 4.8 38.7 1.0
C A:ASP623 4.8 20.5 1.0
CA A:SER624 4.8 20.8 1.0
CB A:ASP623 4.9 19.4 1.0
O1G A:ATP1001 4.9 20.5 1.0

Calcium binding site 3 out of 5 in 4m3z

Go back to Calcium Binding Sites List in 4m3z
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-2 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-2 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:39.7
occ:1.00
 O A:LYS531 2.2 44.7 1.0
O A:HOH1247 2.2 40.3 1.0
OD1 A:ASN507 2.3 46.7 1.0
O A:ASN505 2.3 38.2 1.0
O A:HOH1285 2.5 33.1 1.0
O A:HOH1376 2.5 36.6 1.0
C A:LYS531 3.3 42.1 1.0
CG A:ASN507 3.4 43.6 1.0
C A:ASN505 3.6 41.5 1.0
ND2 A:ASN507 4.0 40.7 1.0
CA A:LYS531 4.1 39.5 1.0
CB A:ASN505 4.2 43.4 1.0
N A:LYS532 4.2 40.2 1.0
N A:ASN507 4.2 41.0 1.0
C A:PRO506 4.3 41.9 1.0
O A:HOH1808 4.3 57.9 1.0
CA A:PRO506 4.3 40.8 1.0
CA A:LYS532 4.4 41.6 1.0
N A:PRO506 4.4 40.7 1.0
CA A:ASN505 4.5 45.4 1.0
O A:HOH1873 4.6 40.5 1.0
O A:LEU533 4.6 35.3 1.0
CB A:ASN507 4.6 43.5 1.0
O A:ALA502 4.7 36.6 1.0
C A:LYS532 4.7 41.5 1.0
CB A:LYS531 4.7 44.7 1.0
O A:PRO506 4.8 43.2 1.0
CA A:ASN507 4.9 43.4 1.0
N A:LEU533 4.9 37.9 1.0
O A:ILE530 4.9 32.1 1.0

Calcium binding site 4 out of 5 in 4m3z

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-2 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-2 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:37.5
occ:1.00
 O A:HOH1656 2.2 50.7 1.0
O A:HOH1139 2.4 26.6 1.0
O A:HOH1344 2.5 36.5 1.0
O A:HOH1305 2.5 33.2 1.0
O A:HOH1496 2.5 40.2 1.0
O A:HOH1461 2.7 43.2 1.0
O A:HOH1106 3.2 32.3 1.0
O A:HOH1609 3.8 32.6 1.0
OE1 A:GLU716 4.2 32.5 1.0
CB A:ASP684 4.3 31.8 1.0
NZ A:LYS486 4.3 29.7 1.0
OG1 A:THR413 4.4 22.4 1.0
O A:HOH1612 4.5 47.5 1.0
O A:ASP411 4.5 21.2 1.0
OD1 A:ASP411 4.6 25.5 1.0
O A:HOH1590 4.6 31.7 1.0
O A:ASP684 4.7 22.7 1.0
OD2 A:ASP411 4.9 21.6 1.0
CG A:GLU716 5.0 34.0 1.0
O A:ARG685 5.0 23.5 1.0
OD2 A:ASP684 5.0 49.5 1.0

Calcium binding site 5 out of 5 in 4m3z

Go back to Calcium Binding Sites List in 4m3z
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-2 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-2 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:45.7
occ:1.00
 O A:HOH1219 2.4 31.3 1.0
O A:HOH1507 2.4 40.0 1.0
O A:HOH1116 2.4 24.0 1.0
OE1 A:GLU116 2.6 28.9 1.0
OE2 A:GLU116 2.7 29.1 1.0
CD A:GLU116 3.0 27.6 1.0
O A:HOH1618 4.3 35.4 1.0
O A:HOH1705 4.3 37.3 1.0
OD2 A:ASP114 4.3 36.1 1.0
CG A:GLU116 4.5 22.0 1.0
O A:ILE115 4.6 21.1 1.0
O A:HOH1595 4.7 58.8 1.0
CD1 A:ILE309 4.7 46.0 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 10:02:37 2024

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