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Calcium in PDB 4m41: RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-3 of Primer/Template Duplex

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

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-3 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-3 of Primer/Template Duplex, PDB code: 4m41 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) 47.50 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.193, 119.408, 130.119, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.7

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dg/Dt at Position N-3 of Primer/Template Duplex (pdb code 4m41). 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-3 of Primer/Template Duplex, PDB code: 4m41:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4m41

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Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:33.8
occ:1.00
 O1G A:ATP1001 2.3 31.6 1.0
OD1 A:ASP623 2.3 29.5 1.0
O A:LEU412 2.3 36.8 1.0
O2B A:ATP1001 2.3 32.8 1.0
OD2 A:ASP411 2.3 37.0 1.0
O2A A:ATP1001 2.4 31.9 1.0
CG A:ASP623 3.4 34.6 1.0
PB A:ATP1001 3.4 33.7 1.0
CG A:ASP411 3.5 34.2 1.0
C A:LEU412 3.5 37.2 1.0
PG A:ATP1001 3.5 32.1 1.0
CA A:CA1003 3.6 72.7 1.0
PA A:ATP1001 3.6 33.5 1.0
O A:HOH1144 3.8 39.1 1.0
O3A A:ATP1001 3.8 38.8 1.0
OD2 A:ASP623 3.8 32.8 1.0
O3B A:ATP1001 3.9 33.9 1.0
N A:LEU412 4.0 36.9 1.0
CB A:ASP411 4.0 33.8 1.0
O2G A:ATP1001 4.1 34.7 1.0
C5' A:ATP1001 4.2 30.8 1.0
CA A:LEU412 4.2 34.1 1.0
C A:ASP411 4.4 38.3 1.0
O5' A:ATP1001 4.4 33.1 1.0
O A:HOH1243 4.4 51.4 1.0
N A:SER414 4.4 31.8 1.0
OD1 A:ASP411 4.5 40.3 1.0
N A:THR413 4.5 30.9 1.0
N A:ALA415 4.6 28.9 1.0
CB A:LEU412 4.6 35.1 1.0
CB A:ASP623 4.7 30.9 1.0
CB A:ALA415 4.7 24.9 1.0
CA A:THR413 4.8 37.1 1.0
O1B A:ATP1001 4.8 33.7 1.0
O3G A:ATP1001 4.8 35.3 1.0
O1A A:ATP1001 4.8 36.2 1.0
C A:THR413 4.8 33.2 1.0
CA A:ASP411 4.9 34.4 1.0
O A:ASP411 5.0 32.4 1.0

Calcium binding site 2 out of 5 in 4m41

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:72.7
occ:1.00
 O2A A:ATP1001 2.6 31.9 1.0
O A:HOH1206 2.6 38.3 1.0
OD2 A:ASP623 2.7 32.8 1.0
OD2 A:ASP411 3.4 37.0 1.0
CG A:ASP623 3.5 34.6 1.0
CA A:CA1002 3.6 33.8 1.0
OD1 A:ASP623 3.7 29.5 1.0
O A:HOH1242 3.7 49.2 1.0
CG A:ASP411 3.7 34.2 1.0
C3' P:DC115 3.7 30.1 1.0
PA A:ATP1001 3.8 33.5 1.0
CB A:ASP411 3.8 33.8 1.0
C5' P:DC115 4.1 34.7 1.0
CB A:SER624 4.2 27.5 1.0
O1A A:ATP1001 4.2 36.2 1.0
O5' A:ATP1001 4.3 33.1 1.0
O A:HOH1243 4.3 51.4 1.0
C4' P:DC115 4.3 32.2 1.0
C5' A:ATP1001 4.4 30.8 1.0
OD1 A:ASP411 4.4 40.3 1.0
O P:HOH201 4.5 40.1 1.0
OG A:SER624 4.5 35.7 1.0
O P:HOH202 4.6 31.5 1.0
O A:HOH1136 4.6 32.6 1.0
O A:ASP621 4.7 34.8 1.0
O1G A:ATP1001 4.7 31.6 1.0
N A:SER624 4.8 32.1 1.0
C A:ASP623 4.9 36.2 1.0
CB A:ASP623 5.0 30.9 1.0

Calcium binding site 3 out of 5 in 4m41

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

b:63.4
occ:1.00
 O A:HOH1294 2.1 48.9 1.0
OD1 A:ASN507 2.2 61.0 1.0
O A:LYS531 2.3 53.6 1.0
O A:ASN505 2.4 56.9 1.0
O A:HOH1119 2.4 48.3 1.0
O A:HOH1202 2.6 57.5 1.0
O A:HOH1289 3.1 54.4 1.0
CG A:ASN507 3.3 54.9 1.0
C A:LYS531 3.4 51.5 1.0
C A:ASN505 3.6 54.0 1.0
ND2 A:ASN507 3.9 56.0 1.0
CA A:LYS531 4.1 50.0 1.0
N A:ASN507 4.2 64.0 1.0
C A:PRO506 4.3 59.6 1.0
CB A:ASN505 4.3 63.9 1.0
N A:LYS532 4.3 54.4 1.0
CA A:PRO506 4.4 58.3 1.0
O A:LEU533 4.4 54.7 1.0
CA A:LYS532 4.5 52.1 1.0
N A:PRO506 4.5 57.1 1.0
CB A:ASN507 4.5 54.3 1.0
CA A:ASN505 4.6 59.6 1.0
O A:ALA502 4.6 53.9 1.0
CB A:LYS531 4.8 49.6 1.0
CA A:ASN507 4.8 60.0 1.0
C A:LYS532 4.8 53.9 1.0
O A:PRO506 4.8 68.3 1.0
N A:LEU533 4.9 52.0 1.0
O A:ILE530 4.9 46.2 1.0

Calcium binding site 4 out of 5 in 4m41

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:65.7
occ:1.00
 OE1 A:GLU716 2.6 56.6 1.0
O A:HOH1197 2.7 45.1 1.0
O A:HOH1144 3.3 39.1 1.0
CD A:GLU716 3.7 53.9 1.0
CG A:GLU716 4.1 49.2 1.0
CB A:ASP684 4.2 51.3 1.0
NZ A:LYS486 4.2 37.2 1.0
OG1 A:THR413 4.5 39.8 1.0
O A:ASP684 4.6 37.0 1.0
OD1 A:ASP411 4.7 40.3 1.0
O A:ASP411 4.7 32.4 1.0
OE2 A:GLU716 4.8 52.3 1.0
OD2 A:ASP684 4.8 63.4 1.0
O A:ARG685 4.9 40.4 1.0
CG A:ASP684 5.0 59.6 1.0
OD2 A:ASP411 5.0 37.0 1.0

Calcium binding site 5 out of 5 in 4m41

Go back to Calcium Binding Sites List in 4m41
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dg/Dt 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 Dg/Dt at Position N-3 of Primer/Template Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:66.2
occ:1.00
 O A:HOH1132 2.4 43.2 1.0
OE1 A:GLU116 2.5 44.7 1.0
OE2 A:GLU116 2.8 45.1 1.0
CD A:GLU116 3.0 44.1 1.0
OD2 A:ASP114 4.3 68.2 1.0
CG A:GLU116 4.5 41.4 1.0
O A:ILE115 4.5 38.4 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 10:03:02 2024

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