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Calcium in PDB 3qep: RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside

Enzymatic activity of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside

All present enzymatic activity of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside, PDB code: 3qep was solved by S.Xia, W.H.Konigsberg, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.133, 119.774, 130.481, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.4

Other elements in 3qep:

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside (pdb code 3qep). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside, PDB code: 3qep:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3qep

Go back to Calcium Binding Sites List in 3qep
Calcium binding site 1 out of 7 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


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 (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:17.6
occ:1.00
 OD1 A:ASP623 2.2 18.0 1.0
OD2 A:ASP411 2.3 22.3 1.0
O2B A:TTP904 2.3 12.6 1.0
O1G A:TTP904 2.3 16.8 1.0
O A:LEU412 2.3 8.9 1.0
O2A A:TTP904 2.4 18.9 1.0
OD1 A:ASP411 2.8 27.6 1.0
CG A:ASP411 2.9 17.9 1.0
CG A:ASP623 3.3 14.3 1.0
PB A:TTP904 3.3 15.8 1.0
C A:LEU412 3.5 9.2 1.0
PA A:TTP904 3.5 18.4 1.0
PG A:TTP904 3.6 17.9 1.0
OD2 A:ASP623 3.7 13.7 1.0
CA A:CA906 3.7 42.8 1.0
O3A A:TTP904 3.7 19.1 1.0
O A:HOH1531 3.8 23.0 1.0
O3B A:TTP904 3.8 17.6 1.0
N A:LEU412 4.0 10.0 1.0
O2G A:TTP904 4.3 15.4 1.0
CA A:LEU412 4.3 8.7 1.0
CB A:ASP411 4.3 14.3 1.0
C5' A:TTP904 4.4 13.8 1.0
N A:SER414 4.4 7.0 1.0
O5' A:TTP904 4.4 15.7 1.0
O A:HOH1710 4.5 31.6 1.0
N A:THR413 4.5 8.9 1.0
C A:ASP411 4.5 10.7 1.0
N A:LEU415 4.6 7.1 1.0
CB A:ASP623 4.6 10.9 1.0
O1B A:TTP904 4.7 18.7 1.0
O1A A:TTP904 4.7 16.5 1.0
O A:HOH968 4.7 36.2 1.0
CA A:THR413 4.7 8.1 1.0
C A:THR413 4.7 8.5 1.0
O3G A:TTP904 4.7 19.0 1.0
CB A:LEU412 4.8 8.1 1.0
CB A:LEU415 4.9 8.2 1.0
CA A:ASP411 4.9 10.8 1.0

Calcium binding site 2 out of 7 in 3qep

Go back to Calcium Binding Sites List in 3qep
Calcium binding site 2 out of 7 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


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 (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:42.8
occ:1.00
 O A:HOH1232 2.3 18.0 1.0
O A:HOH968 2.4 36.2 1.0
OD2 A:ASP623 2.6 13.7 1.0
O2A A:TTP904 2.6 18.9 1.0
OD2 A:ASP411 2.7 22.3 1.0
O A:HOH1210 3.3 38.3 1.0
CG A:ASP623 3.5 14.3 1.0
CG A:ASP411 3.7 17.9 1.0
CA A:CA905 3.7 17.6 1.0
OD1 A:ASP623 3.8 18.0 1.0
C3' P:DOC115 3.8 9.1 1.0
PA A:TTP904 3.8 18.4 1.0
CB A:SER624 3.9 14.3 1.0
O A:HOH1531 4.0 23.0 1.0
O1A A:TTP904 4.1 16.5 1.0
CB A:ASP411 4.4 14.3 1.0
O5' A:TTP904 4.4 15.7 1.0
O A:ASP621 4.5 7.3 1.0
N A:SER624 4.5 10.7 1.0
OG A:SER624 4.5 17.2 1.0
O P:HOH117 4.5 18.3 1.0
C A:ASP623 4.6 10.8 1.0
OD1 A:ASP411 4.6 27.6 1.0
O A:HOH1711 4.7 25.9 1.0
C5' A:TTP904 4.7 13.8 1.0
CA A:SER624 4.7 11.3 1.0
O5' P:DOC115 4.7 14.0 1.0
C4' P:DOC115 4.8 7.4 1.0
O A:ASP623 4.8 9.5 1.0
CB A:ASP623 4.8 10.9 1.0
C5' P:DOC115 4.9 14.9 1.0
O1G A:TTP904 5.0 16.8 1.0
C2' P:DOC115 5.0 6.4 1.0
N A:ASP623 5.0 8.3 1.0

Calcium binding site 3 out of 7 in 3qep

Go back to Calcium Binding Sites List in 3qep
Calcium binding site 3 out of 7 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


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 (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:31.5
occ:1.00
 O A:LYS531 2.3 18.4 1.0
O A:ASN505 2.3 16.2 1.0
OD1 A:ASN507 2.3 18.0 1.0
O A:HOH1708 2.4 23.6 1.0
O A:HOH1347 2.5 14.0 1.0
O A:HOH1213 2.6 29.5 1.0
O A:HOH1585 2.6 12.2 1.0
C A:LYS531 3.3 18.4 1.0
CG A:ASN507 3.4 17.8 1.0
C A:ASN505 3.5 17.0 1.0
ND2 A:ASN507 4.0 14.8 1.0
CA A:LYS531 4.0 17.4 1.0
CB A:ASN505 4.2 17.5 1.0
N A:LYS532 4.2 18.0 1.0
N A:ASN507 4.2 17.0 1.0
C A:PRO506 4.3 16.9 1.0
CA A:PRO506 4.3 16.7 1.0
CA A:LYS532 4.4 17.7 1.0
N A:PRO506 4.4 16.3 1.0
CA A:ASN505 4.5 17.8 1.0
CB A:ASN507 4.6 17.3 1.0
O A:LEU533 4.6 12.2 1.0
O A:HOH1682 4.7 15.6 1.0
O A:ALA502 4.7 14.1 1.0
CB A:LYS531 4.7 19.5 1.0
C A:LYS532 4.8 17.4 1.0
CA A:ASN507 4.8 16.4 1.0
N A:LEU533 4.9 15.6 1.0
O A:PRO506 4.9 15.7 1.0
O A:ILE530 4.9 10.8 1.0

Calcium binding site 4 out of 7 in 3qep

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Calcium binding site 4 out of 7 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


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 (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:38.1
occ:1.00
 O A:HOH1234 2.2 24.5 1.0
O A:HOH1697 2.4 27.2 1.0
O A:HOH1256 2.4 11.9 1.0
O A:HOH1221 2.5 41.6 1.0
O A:HOH1174 2.5 39.0 1.0
OE2 A:GLU116 2.6 18.3 1.0
OE1 A:GLU116 2.6 16.8 1.0
CD A:GLU116 3.0 17.9 1.0
OD2 A:ASP114 4.1 24.1 1.0
O A:HOH1712 4.2 24.7 1.0
O A:HOH1857 4.3 25.1 1.0
O A:HOH1695 4.4 22.8 1.0
O A:HOH1069 4.4 32.3 1.0
CG A:GLU116 4.5 12.0 1.0
O A:ILE115 4.6 9.5 1.0
CD1 A:ILE309 4.8 28.8 1.0
O A:HOH1228 4.8 39.5 1.0

Calcium binding site 5 out of 7 in 3qep

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Calcium binding site 5 out of 7 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


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 (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:83.9
occ:1.00
 O A:HOH1878 2.4 28.7 1.0
O A:ASP792 2.5 19.7 1.0
O A:HOH1879 2.5 22.8 1.0
O A:HOH1703 2.7 20.8 1.0
C A:ASP792 3.7 18.3 1.0
O A:ALA789 4.1 17.0 1.0
CA A:VAL793 4.3 17.2 1.0
N A:VAL793 4.4 18.3 1.0
CA A:ASP792 4.8 17.7 1.0
N A:GLY794 5.0 18.3 1.0
CG2 A:VAL793 5.0 17.2 1.0
CB A:ASP792 5.0 17.5 1.0

Calcium binding site 6 out of 7 in 3qep

Go back to Calcium Binding Sites List in 3qep
Calcium binding site 6 out of 7 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


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 (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:53.8
occ:1.00
 OD1 A:ASP684 2.3 21.6 1.0
O A:HOH1194 2.4 26.5 1.0
O A:HOH1784 2.5 31.6 1.0
O A:HOH1090 3.1 30.4 1.0
OE1 A:GLU660 3.4 19.4 1.0
CG A:ASP684 3.4 20.9 1.0
CD A:GLU660 4.0 17.9 1.0
OD2 A:ASP684 4.0 26.3 1.0
OD1 A:ASP664 4.4 11.2 0.5
OD2 A:ASP664 4.4 11.3 0.5
O A:MET683 4.4 17.3 1.0
CB A:GLU660 4.5 12.8 1.0
CG A:GLU660 4.5 13.2 1.0
CB A:ASP684 4.5 16.5 1.0
OE2 A:GLU660 4.6 20.1 1.0
CA A:ASP684 4.7 14.9 1.0
CG A:ASP664 4.9 10.2 0.5
C A:MET683 4.9 13.8 1.0

Calcium binding site 7 out of 7 in 3qep

Go back to Calcium Binding Sites List in 3qep
Calcium binding site 7 out of 7 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca5

b:57.4
occ:1.00
 O T:HOH588 2.5 20.1 1.0
O T:HOH773 2.5 25.1 1.0
O P:HOH771 2.5 38.6 1.0
O T:HOH772 2.6 22.0 1.0
O T:HOH608 2.7 34.1 1.0
O T:HOH834 4.3 26.5 1.0
O6 T:DG12 4.5 9.4 1.0
N7 T:DG12 4.6 13.1 1.0
N7 P:DG105 4.6 30.5 1.0
O4 T:DT13 4.7 14.9 1.0
C8 P:DG105 4.8 32.0 1.0
O6 P:DG106 4.8 13.7 1.0
N6 P:DA107 4.8 12.0 1.0
N7 P:DG106 5.0 18.4 1.0

Reference:

S.Xia, W.H.Konigsberg, J.Wang. Hydrogen-Bonding Capability of A Templating Difluorotoluene Nucleotide Residue in An RB69 Dna Polymerase Ternary Complex. J.Am.Chem.Soc. V. 133 10003 2011.
ISSN: ISSN 0002-7863
PubMed: 21667997
DOI: 10.1021/JA2021735
Page generated: Tue Jul 8 15:56:07 2025

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