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Calcium in PDB 4fk0: RB69 Dna Polymerase Ternary Complex with Dctp/Dg

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dctp/Dg

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dctp/Dg:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Dctp/Dg, PDB code: 4fk0 was solved by S.Xia, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.21 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.846, 120.149, 130.619, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.2

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dctp/Dg (pdb code 4fk0). 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 Dctp/Dg, PDB code: 4fk0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4fk0

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Calcium binding site 1 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dg


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 Dctp/Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:26.4
occ:1.00
 O1G A:DCP1001 2.2 25.6 1.0
O A:LEU412 2.2 26.3 1.0
O2B A:DCP1001 2.3 27.6 1.0
OD1 A:ASP623 2.3 24.3 1.0
OD1 A:ASP411 2.3 33.1 1.0
O2A A:DCP1001 2.3 28.4 1.0
OD2 A:ASP411 2.8 80.5 1.0
CG A:ASP411 2.9 41.0 1.0
PB A:DCP1001 3.4 26.6 1.0
C A:LEU412 3.4 28.6 1.0
CG A:ASP623 3.4 30.6 1.0
PG A:DCP1001 3.5 26.6 1.0
PA A:DCP1001 3.6 30.6 1.0
CA A:CA1003 3.7 60.1 1.0
O3A A:DCP1001 3.8 31.0 1.0
O3B A:DCP1001 3.9 27.8 1.0
OD2 A:ASP623 3.9 23.5 1.0
N A:LEU412 3.9 26.1 1.0
O A:HOH1102 4.1 36.2 1.0
CA A:LEU412 4.2 26.1 1.0
CB A:ASP411 4.2 37.2 1.0
O2G A:DCP1001 4.2 27.1 1.0
C5' A:DCP1001 4.3 27.9 1.0
C A:ASP411 4.3 28.4 1.0
O5' A:DCP1001 4.4 31.5 1.0
N A:THR413 4.5 29.4 1.0
N A:SER414 4.5 28.2 1.0
N A:ALA415 4.6 25.9 1.0
CB A:LEU412 4.6 25.6 1.0
O3G A:DCP1001 4.7 29.1 1.0
CB A:ASP623 4.7 22.8 1.0
CA A:THR413 4.7 26.9 1.0
CA A:ASP411 4.7 31.7 1.0
O1B A:DCP1001 4.8 32.8 1.0
O A:ASP411 4.8 30.9 1.0
CB A:ALA415 4.8 20.8 1.0
O1A A:DCP1001 4.8 32.3 1.0
C A:THR413 4.9 31.3 1.0

Calcium binding site 2 out of 6 in 4fk0

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Calcium binding site 2 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dg


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 Dctp/Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:60.1
occ:1.00
 OD2 A:ASP411 2.2 80.5 1.0
O P:HOH211 2.5 33.3 1.0
O2A A:DCP1001 2.8 28.4 1.0
OD2 A:ASP623 2.8 23.5 1.0
CG A:ASP411 3.3 41.0 1.0
CG A:ASP623 3.7 30.6 1.0
C3' P:DOC115 3.7 31.7 1.0
CA A:CA1002 3.7 26.4 1.0
OD1 A:ASP623 3.8 24.3 1.0
OD1 A:ASP411 3.9 33.1 1.0
PA A:DCP1001 3.9 30.6 1.0
CB A:SER624 4.0 22.8 1.0
O P:HOH203 4.2 29.8 1.0
CB A:ASP411 4.3 37.2 1.0
O1A A:DCP1001 4.3 32.3 1.0
O A:HOH1240 4.4 41.3 1.0
O5' A:DCP1001 4.5 31.5 1.0
OG A:SER624 4.6 28.9 1.0
C5' P:DOC115 4.6 35.5 1.0
C5' A:DCP1001 4.6 27.9 1.0
O P:HOH207 4.6 24.1 1.0
C4' P:DOC115 4.7 32.3 1.0
O A:ASP621 4.8 27.3 1.0
N A:SER624 4.8 28.2 1.0
CA A:SER624 4.9 24.3 1.0
C A:ASP623 4.9 30.3 1.0
O5' P:DOC115 4.9 36.4 1.0
C2' P:DOC115 4.9 33.7 1.0
O1G A:DCP1001 5.0 25.6 1.0

Calcium binding site 3 out of 6 in 4fk0

Go back to Calcium Binding Sites List in 4fk0
Calcium binding site 3 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dg


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 Dctp/Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:42.8
occ:1.00
 O A:HOH1281 2.0 36.2 1.0
O A:LYS531 2.2 55.6 1.0
OD1 A:ASN507 2.3 52.1 1.0
O A:ASN505 2.4 50.2 1.0
O A:HOH1193 2.5 41.7 1.0
O A:HOH1273 2.6 35.1 1.0
C A:LYS531 3.2 50.4 1.0
CG A:ASN507 3.4 59.7 1.0
C A:ASN505 3.6 46.2 1.0
CA A:LYS531 3.9 53.6 1.0
ND2 A:ASN507 4.0 48.9 1.0
CB A:ASN505 4.1 47.9 1.0
N A:LYS532 4.1 43.2 1.0
N A:ASN507 4.2 54.8 1.0
CA A:LYS532 4.4 48.3 1.0
C A:PRO506 4.4 53.9 1.0
CA A:PRO506 4.5 49.9 1.0
CA A:ASN505 4.5 53.1 1.0
N A:PRO506 4.5 43.4 1.0
CB A:LYS531 4.5 50.1 1.0
O A:LEU533 4.6 40.1 1.0
CB A:ASN507 4.6 53.4 1.0
O A:ALA502 4.7 46.2 1.0
C A:LYS532 4.8 44.5 1.0
CA A:ASN507 4.8 51.3 1.0
N A:LEU533 4.9 50.8 1.0
O A:ILE530 5.0 40.5 1.0

Calcium binding site 4 out of 6 in 4fk0

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Calcium binding site 4 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dg


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 Dctp/Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:51.6
occ:1.00
 O A:HOH1353 2.3 54.5 1.0
O A:HOH1267 2.6 45.3 1.0
O A:HOH1102 2.8 36.2 1.0
O A:HOH1150 3.0 37.6 1.0
O A:HOH1144 3.0 30.6 1.0
OE1 A:GLU716 3.3 44.5 1.0
NZ A:LYS486 4.1 29.0 1.0
CD A:GLU716 4.2 55.1 1.0
OD1 A:ASP411 4.3 33.1 1.0
OG1 A:THR413 4.4 31.1 1.0
CB A:ASP684 4.5 40.8 1.0
CG A:GLU716 4.5 53.5 1.0
O A:ASP411 4.5 30.9 1.0
OD2 A:ASP684 4.8 52.8 1.0
O2G A:DCP1001 4.9 27.1 1.0
O1G A:DCP1001 5.0 25.6 1.0
O A:HOH1331 5.0 40.1 1.0

Calcium binding site 5 out of 6 in 4fk0

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Calcium binding site 5 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dg


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 Dctp/Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:71.1
occ:1.00
 O A:HOH1347 2.3 39.8 1.0
O A:HOH1368 2.4 47.5 1.0
O A:HOH1114 2.6 37.0 1.0
OE2 A:GLU116 2.7 54.6 1.0
OE1 A:GLU116 2.8 42.3 1.0
CD A:GLU116 3.1 37.6 1.0
O A:HOH1313 4.4 39.5 1.0
OD2 A:ASP114 4.4 63.4 1.0
CG A:GLU116 4.6 29.6 1.0
O A:ILE115 4.7 32.7 1.0
CD1 A:ILE309 4.7 51.1 1.0

Calcium binding site 6 out of 6 in 4fk0

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Calcium binding site 6 out of 6 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dg


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 Dctp/Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca101

b:87.9
occ:1.00
 O6 T:DG12 4.0 54.4 1.0
N7 T:DG12 4.2 50.3 1.0
C6 T:DG12 4.8 48.8 1.0
O4 T:DT13 4.8 57.7 1.0
C5 T:DG12 4.9 51.7 1.0
N7 T:DA11 4.9 38.3 1.0
N6 P:DA107 4.9 48.2 1.0

Reference:

S.Xia, J.Wang, W.H.Konigsberg. Dna Mismatch Synthesis Complexes Provide Insights Into Base Selectivity of A B Family Dna Polymerase. J.Am.Chem.Soc. V. 135 193 2013.
ISSN: ISSN 0002-7863
PubMed: 23214497
DOI: 10.1021/JA3079048
Page generated: Sun Jul 14 00:23:46 2024

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