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Calcium in PDB 4m3u: RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 of Primer/Template Duplex

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 of Primer/Template Duplex

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 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-3 of Primer/Template Duplex, PDB code: 4m3u 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) 46.21 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.109, 118.536, 130.721, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 of Primer/Template Duplex (pdb code 4m3u). 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-3 of Primer/Template Duplex, PDB code: 4m3u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4m3u

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Calcium binding site 1 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 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-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:28.1
occ:1.00
 O2B A:ATP1001 2.2 28.4 1.0
O1G A:ATP1001 2.3 27.0 1.0
OD2 A:ASP411 2.3 27.7 1.0
OD2 A:ASP623 2.3 28.2 1.0
O2A A:ATP1001 2.4 23.9 1.0
O A:LEU412 2.4 28.0 1.0
PB A:ATP1001 3.4 29.6 1.0
CG A:ASP623 3.4 29.9 1.0
CG A:ASP411 3.4 28.6 1.0
CA A:CA1003 3.5 62.1 1.0
PG A:ATP1001 3.5 29.9 1.0
PA A:ATP1001 3.5 30.3 1.0
C A:LEU412 3.6 30.8 1.0
O3A A:ATP1001 3.8 30.8 1.0
O A:HOH1104 3.8 37.7 1.0
OD1 A:ASP623 3.8 26.2 1.0
O3B A:ATP1001 3.9 29.9 1.0
CB A:ASP411 4.0 28.8 1.0
N A:LEU412 4.0 29.8 1.0
O2G A:ATP1001 4.2 26.6 1.0
C5' A:ATP1001 4.2 29.5 1.0
CA A:LEU412 4.3 28.4 1.0
O5' A:ATP1001 4.4 28.9 1.0
C A:ASP411 4.4 27.8 1.0
OD1 A:ASP411 4.5 32.6 1.0
N A:SER414 4.5 29.6 1.0
N A:THR413 4.6 29.4 1.0
N A:ALA415 4.7 25.8 1.0
CB A:ALA415 4.7 27.2 1.0
CB A:ASP623 4.7 29.1 1.0
CB A:LEU412 4.7 29.9 1.0
O1B A:ATP1001 4.8 31.7 1.0
O3G A:ATP1001 4.8 28.6 1.0
O1A A:ATP1001 4.8 28.1 1.0
CA A:THR413 4.8 31.0 1.0
CA A:ASP411 4.9 30.6 1.0
C A:THR413 4.9 29.4 1.0

Calcium binding site 2 out of 6 in 4m3u

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Calcium binding site 2 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 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-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:62.1
occ:1.00
 OD1 A:ASP623 2.5 26.2 1.0
O2A A:ATP1001 2.6 23.9 1.0
O A:HOH1232 2.8 36.1 1.0
CG A:ASP623 3.4 29.9 1.0
CA A:CA1002 3.5 28.1 1.0
OD2 A:ASP411 3.5 27.7 1.0
OD2 A:ASP623 3.5 28.2 1.0
C3' P:DC115 3.6 26.0 1.0
PA A:ATP1001 3.8 30.3 1.0
O A:HOH1347 3.8 49.2 1.0
CG A:ASP411 3.8 28.6 1.0
CB A:ASP411 3.8 28.8 1.0
C5' P:DC115 4.1 30.2 1.0
CB A:SER624 4.1 31.6 1.0
O5' A:ATP1001 4.2 28.9 1.0
C4' P:DC115 4.3 28.1 1.0
O1A A:ATP1001 4.3 28.1 1.0
C5' A:ATP1001 4.3 29.5 1.0
O A:ASP621 4.5 33.0 1.0
OG A:SER624 4.5 35.5 1.0
O A:HOH1125 4.5 31.4 1.0
OD1 A:ASP411 4.6 32.6 1.0
N A:SER624 4.7 27.2 1.0
O A:HOH1281 4.7 30.7 1.0
C A:ASP623 4.8 27.1 1.0
O1G A:ATP1001 4.8 27.0 1.0
O P:HOH201 4.8 30.9 1.0
CB A:ASP623 4.8 29.1 1.0
CA A:SER624 4.9 32.1 1.0
C2' P:DC115 5.0 27.5 1.0

Calcium binding site 3 out of 6 in 4m3u

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

b:54.9
occ:1.00
 O A:LYS531 2.2 42.1 1.0
O A:ASN505 2.3 44.4 1.0
O A:HOH1126 2.3 51.2 1.0
O A:HOH1239 2.5 51.6 1.0
OD1 A:ASN507 2.5 52.9 1.0
O A:HOH1473 2.6 50.9 1.0
O A:HOH1112 2.8 54.5 1.0
C A:LYS531 3.3 41.8 1.0
C A:ASN505 3.5 43.6 1.0
CG A:ASN507 3.6 57.6 1.0
CA A:LYS531 4.0 50.9 1.0
CB A:ASN505 4.0 57.7 1.0
ND2 A:ASN507 4.2 62.6 1.0
N A:LYS532 4.2 40.5 1.0
N A:ASN507 4.3 66.7 1.0
CA A:ASN505 4.4 53.2 1.0
C A:PRO506 4.4 68.8 1.0
O A:HOH1474 4.5 50.1 1.0
N A:PRO506 4.5 43.3 1.0
CA A:PRO506 4.5 53.1 1.0
CA A:LYS532 4.5 42.0 1.0
O A:ALA502 4.6 54.6 1.0
CB A:LYS531 4.6 52.4 1.0
O A:LEU533 4.7 44.0 1.0
CB A:ASN507 4.8 64.9 1.0
O A:ILE530 4.9 49.0 1.0
C A:LYS532 4.9 48.5 1.0
CA A:ASN507 4.9 68.6 1.0

Calcium binding site 4 out of 6 in 4m3u

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Calcium binding site 4 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 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-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:46.1
occ:1.00
 OE1 A:GLU716 2.4 48.2 1.0
O A:HOH1197 2.6 39.7 1.0
O A:HOH1342 2.6 40.1 1.0
O A:HOH1341 2.7 38.2 1.0
O A:HOH1104 3.0 37.7 1.0
O A:HOH1249 3.3 47.1 1.0
CD A:GLU716 3.4 45.5 1.0
CG A:GLU716 4.1 37.9 1.0
CB A:ASP684 4.3 41.7 1.0
OG1 A:THR413 4.3 35.4 1.0
OE2 A:GLU716 4.3 37.9 1.0
OD1 A:ASP411 4.5 32.6 1.0
NZ A:LYS486 4.6 45.4 1.0
O A:ASP411 4.6 31.6 1.0
O A:ASP684 4.7 33.9 1.0
OD2 A:ASP411 4.9 27.7 1.0
O A:HOH1343 4.9 41.6 1.0
O A:ARG685 4.9 26.9 1.0
CG A:ASP411 5.0 28.6 1.0
OD2 A:ASP684 5.0 54.1 1.0

Calcium binding site 5 out of 6 in 4m3u

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Calcium binding site 5 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 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-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:59.2
occ:1.00
 OE1 A:GLU116 2.5 35.6 1.0
O A:HOH1436 2.5 55.2 1.0
O A:HOH1267 2.6 49.9 1.0
O A:HOH1205 2.7 48.1 1.0
OE2 A:GLU116 2.8 33.5 1.0
CD A:GLU116 3.0 35.4 1.0
CG A:GLU116 4.5 33.6 1.0
O A:ILE115 4.7 29.8 1.0
OD2 A:ASP114 4.7 57.5 1.0
O A:HOH1437 4.9 50.1 1.0

Calcium binding site 6 out of 6 in 4m3u

Go back to Calcium Binding Sites List in 4m3u
Calcium binding site 6 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dt/Dg at Position N-3 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-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:79.0
occ:1.00
 OD2 A:ASP861 2.2 71.0 1.0
O A:LEU857 2.7 76.5 1.0
OD2 A:ASP860 2.9 83.9 1.0
OD1 A:ASP860 3.1 67.5 1.0
CG A:ASP861 3.3 61.2 1.0
CG A:ASP860 3.3 67.0 1.0
OD1 A:ASP861 3.8 51.2 1.0
C A:LEU857 3.9 68.9 1.0
CB A:ASP861 4.4 54.3 1.0
CA A:ILE858 4.4 54.5 1.0
N A:ASP861 4.5 44.8 1.0
N A:ILE858 4.6 62.7 1.0
CB A:ASP860 4.8 55.2 1.0
CA A:LEU857 4.9 65.9 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 09:59:42 2024

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