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Calcium in PDB 4m3t: RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-2 of Primer/Template Duplex

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-2 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-2 of Primer/Template Duplex, PDB code: 4m3t 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) 49.31 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.913, 120.230, 130.784, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.9

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-2 of Primer/Template Duplex (pdb code 4m3t). 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-2 of Primer/Template Duplex, PDB code: 4m3t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4m3t

Go back to Calcium Binding Sites List in 4m3t
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-2 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:21.2
occ:1.00
 OD2 A:ASP411 2.2 22.0 1.0
O2B A:ATP1001 2.3 21.4 1.0
O1G A:ATP1001 2.3 18.4 1.0
OD2 A:ASP623 2.3 18.7 1.0
O A:LEU412 2.4 20.1 1.0
O2A A:ATP1001 2.4 21.0 1.0
PB A:ATP1001 3.4 21.5 1.0
CG A:ASP623 3.4 20.0 1.0
CG A:ASP411 3.4 27.7 1.0
C A:LEU412 3.5 20.0 1.0
PG A:ATP1001 3.6 21.1 1.0
PA A:ATP1001 3.6 22.1 1.0
CA A:CA1003 3.7 50.7 1.0
O A:HOH1588 3.7 38.1 1.0
O3A A:ATP1001 3.8 22.8 1.0
O3B A:ATP1001 3.9 22.2 1.0
OD1 A:ASP623 3.9 17.8 1.0
O A:HOH1102 3.9 35.4 1.0
N A:LEU412 4.0 23.0 1.0
CB A:ASP411 4.1 27.4 1.0
O2G A:ATP1001 4.2 20.5 1.0
CA A:LEU412 4.3 21.1 1.0
C5' A:ATP1001 4.3 17.4 1.0
C A:ASP411 4.4 21.5 1.0
OD1 A:ASP411 4.4 26.8 1.0
O5' A:ATP1001 4.5 19.8 1.0
N A:THR413 4.6 22.2 1.0
N A:SER414 4.6 21.0 1.0
N A:ALA415 4.7 19.0 1.0
CB A:ASP623 4.7 19.2 1.0
CB A:ALA415 4.7 16.7 1.0
CB A:LEU412 4.7 21.8 1.0
O3G A:ATP1001 4.8 22.3 1.0
O1B A:ATP1001 4.8 22.7 1.0
CA A:THR413 4.8 23.6 1.0
O A:ASP411 4.8 25.8 1.0
O1A A:ATP1001 4.8 19.4 1.0
CA A:ASP411 4.9 22.8 1.0
C A:THR413 4.9 21.0 1.0

Calcium binding site 2 out of 5 in 4m3t

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

b:50.7
occ:1.00
 O P:HOH222 2.6 34.1 1.0
OD1 A:ASP623 2.6 17.8 1.0
O2A A:ATP1001 2.8 21.0 1.0
CG A:ASP623 3.5 20.0 1.0
OD2 A:ASP411 3.6 22.0 1.0
C3' P:DC115 3.6 24.9 1.0
OD2 A:ASP623 3.7 18.7 1.0
CA A:CA1002 3.7 21.2 1.0
CG A:ASP411 3.8 27.7 1.0
CB A:ASP411 3.9 27.4 1.0
O A:HOH1588 3.9 38.1 1.0
CB A:SER624 3.9 23.2 1.0
PA A:ATP1001 4.0 22.1 1.0
C5' P:DC115 4.1 32.9 1.0
C4' P:DC115 4.4 28.1 1.0
O A:ASP621 4.4 22.5 1.0
O5' A:ATP1001 4.5 19.8 1.0
O1A A:ATP1001 4.5 19.4 1.0
OG A:SER624 4.5 27.7 1.0
C5' A:ATP1001 4.5 17.4 1.0
OD1 A:ASP411 4.6 26.8 1.0
O P:HOH205 4.6 26.3 1.0
O A:HOH1328 4.6 36.2 1.0
N A:SER624 4.7 21.7 1.0
O P:HOH204 4.8 28.7 1.0
CA A:SER624 4.8 22.9 1.0
C A:ASP623 4.8 22.5 1.0
CB A:ASP623 4.9 19.2 1.0
C2' P:DC115 5.0 24.4 1.0

Calcium binding site 3 out of 5 in 4m3t

Go back to Calcium Binding Sites List in 4m3t
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-2 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:36.1
occ:1.00
 O A:HOH1309 2.0 35.3 1.0
O A:LYS531 2.1 38.4 1.0
OD1 A:ASN507 2.2 42.1 1.0
O A:ASN505 2.3 34.2 1.0
O A:HOH1287 2.5 33.4 1.0
O A:HOH1299 2.6 34.6 1.0
C A:LYS531 3.2 39.2 1.0
CG A:ASN507 3.4 42.5 1.0
C A:ASN505 3.5 35.2 1.0
CA A:LYS531 3.9 37.4 1.0
ND2 A:ASN507 4.0 40.2 1.0
N A:LYS532 4.1 34.7 1.0
CB A:ASN505 4.2 39.8 1.0
C A:PRO506 4.2 42.4 1.0
N A:ASN507 4.3 43.6 1.0
CA A:PRO506 4.3 38.0 1.0
CA A:LYS532 4.3 36.1 1.0
N A:PRO506 4.4 34.8 1.0
CA A:ASN505 4.5 40.8 1.0
O A:LEU533 4.5 34.1 1.0
CB A:ASN507 4.6 42.5 1.0
O A:HOH1360 4.6 37.2 1.0
CB A:LYS531 4.6 41.2 1.0
O A:ALA502 4.6 35.8 1.0
C A:LYS532 4.7 36.3 1.0
O A:PRO506 4.8 41.1 1.0
CA A:ASN507 4.8 40.3 1.0
N A:LEU533 4.8 33.2 1.0
O A:ILE530 4.9 30.0 1.0

Calcium binding site 4 out of 5 in 4m3t

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

b:44.3
occ:1.00
 O A:HOH1607 2.3 44.1 1.0
O A:HOH1624 2.4 39.5 1.0
O A:HOH1337 2.6 35.9 1.0
O A:HOH1260 2.6 32.5 1.0
O A:HOH1102 3.2 35.4 1.0
OE1 A:GLU716 3.2 41.0 1.0
O A:HOH1315 3.6 35.2 1.0
O A:HOH1538 4.2 48.0 1.0
NZ A:LYS486 4.2 32.1 1.0
CD A:GLU716 4.2 40.6 1.0
CB A:ASP684 4.3 38.5 1.0
OG1 A:THR413 4.4 27.4 1.0
CG A:GLU716 4.5 34.5 1.0
O A:ASP411 4.5 25.8 1.0
OD1 A:ASP411 4.5 26.8 1.0
O A:HOH1618 4.7 36.6 1.0
O A:ASP684 4.7 25.1 1.0
OD2 A:ASP684 4.8 52.5 1.0
OD2 A:ASP411 5.0 22.0 1.0

Calcium binding site 5 out of 5 in 4m3t

Go back to Calcium Binding Sites List in 4m3t
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg 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 Dt/Dg at Position N-2 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:54.5
occ:1.00
 O A:HOH1478 2.2 37.4 1.0
O A:HOH1104 2.4 28.3 1.0
O A:HOH1559 2.5 45.2 1.0
OE1 A:GLU116 2.6 30.7 1.0
OE2 A:GLU116 2.6 28.6 1.0
CD A:GLU116 3.0 29.0 1.0
OD2 A:ASP114 4.2 46.6 1.0
O A:HOH1584 4.4 42.9 1.0
CG A:GLU116 4.5 23.9 1.0
O A:ILE115 4.6 25.1 1.0
O A:HOH1563 4.7 54.5 1.0
CD1 A:ILE309 5.0 53.5 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 09:59:38 2024

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