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

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp Opposite Difluorotoluene Nucleoside, PDB code: 3qes 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) 46.81 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.824, 119.979, 130.068, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.8

Other elements in 3qes:

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp 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 Dgtp Opposite Difluorotoluene Nucleoside (pdb code 3qes). 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 (L561A/S565G/Y567A) Ternary Complex with Dgtp Opposite Difluorotoluene Nucleoside, PDB code: 3qes:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3qes

Go back to Calcium Binding Sites List in 3qes
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp 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 Dgtp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:22.6
occ:1.00
 OD1 A:ASP623 2.2 28.6 1.0
O1G A:DGT904 2.2 19.0 1.0
O2B A:DGT904 2.3 18.3 1.0
O A:LEU412 2.4 17.5 1.0
O2A A:DGT904 2.5 23.7 1.0
OD1 A:ASP411 2.6 36.4 1.0
OD2 A:ASP411 2.6 33.5 1.0
CG A:ASP411 2.9 27.4 1.0
CG A:ASP623 3.3 26.0 1.0
PB A:DGT904 3.3 21.3 1.0
PG A:DGT904 3.5 20.8 1.0
C A:LEU412 3.5 19.3 1.0
PA A:DGT904 3.6 23.9 1.0
O A:HOH1389 3.7 44.4 1.0
CA A:CA906 3.7 47.3 1.0
OD2 A:ASP623 3.7 26.2 1.0
O3A A:DGT904 3.7 24.5 1.0
O3B A:DGT904 3.8 23.7 1.0
N A:LEU412 4.1 19.6 1.0
O2G A:DGT904 4.2 21.3 1.0
N A:SER414 4.3 17.6 1.0
C5' A:DGT904 4.3 20.3 1.0
O A:HOH1374 4.3 44.3 1.0
CA A:LEU412 4.3 18.9 1.0
CB A:ASP411 4.4 26.0 1.0
O5' A:DGT904 4.5 24.5 1.0
CB A:ASP623 4.5 22.6 1.0
N A:THR413 4.5 18.1 1.0
C A:ASP411 4.6 20.9 1.0
O3G A:DGT904 4.7 24.3 1.0
O1B A:DGT904 4.7 23.0 1.0
N A:LEU415 4.7 16.0 1.0
CA A:THR413 4.7 18.2 1.0
C A:THR413 4.7 18.3 1.0
O1A A:DGT904 4.8 21.6 1.0
CB A:LEU412 4.9 16.9 1.0
CA A:ASP411 4.9 22.2 1.0
O A:ASP623 5.0 19.9 1.0

Calcium binding site 2 out of 5 in 3qes

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp 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 Dgtp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:47.3
occ:1.00
 O A:HOH1285 2.4 50.9 1.0
OD2 A:ASP411 2.5 33.5 1.0
O2A A:DGT904 2.6 23.7 1.0
OD2 A:ASP623 2.7 26.2 1.0
O A:HOH1408 2.9 37.6 1.0
O A:HOH1622 3.0 41.8 1.0
CG A:ASP411 3.6 27.4 1.0
CG A:ASP623 3.6 26.0 1.0
CA A:CA905 3.7 22.6 1.0
OD1 A:ASP623 3.8 28.6 1.0
PA A:DGT904 3.8 23.9 1.0
C3' P:DOC115 3.8 20.3 1.0
O A:HOH1389 3.9 44.4 1.0
CB A:SER624 4.0 19.3 1.0
C5' P:DOC115 4.0 25.1 1.0
O1A A:DGT904 4.1 21.6 1.0
OD1 A:ASP411 4.2 36.4 1.0
O A:HOH1155 4.3 21.4 1.0
C4' P:DOC115 4.4 19.8 1.0
OG A:SER624 4.4 25.4 1.0
CB A:ASP411 4.5 26.0 1.0
O5' A:DGT904 4.5 24.5 1.0
O A:ASP621 4.7 16.0 1.0
O P:HOH217 4.7 31.4 1.0
C5' A:DGT904 4.8 20.3 1.0
N A:SER624 4.9 19.1 1.0
C A:ASP623 4.9 20.4 1.0
O1G A:DGT904 4.9 19.0 1.0
CA A:SER624 5.0 19.1 1.0
OE2 A:GLU686 5.0 45.3 1.0
O5' P:DOC115 5.0 25.3 1.0

Calcium binding site 3 out of 5 in 3qes

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp 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 Dgtp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:41.8
occ:1.00
 OD1 A:ASN507 2.2 45.3 1.0
O A:ASN505 2.3 45.7 1.0
O A:LYS531 2.4 39.5 1.0
O A:HOH1421 2.5 45.0 1.0
O A:HOH1047 2.5 28.1 1.0
O A:HOH1147 2.5 36.8 1.0
C A:LYS531 3.3 39.6 1.0
CG A:ASN507 3.4 46.7 1.0
C A:ASN505 3.6 47.0 1.0
CA A:LYS531 4.0 39.3 1.0
CB A:ASN505 4.1 48.7 1.0
ND2 A:ASN507 4.1 41.4 1.0
N A:ASN507 4.1 48.0 1.0
N A:LYS532 4.2 39.5 1.0
C A:PRO506 4.4 48.1 1.0
CA A:LYS532 4.4 40.4 1.0
CA A:ASN505 4.5 48.2 1.0
CA A:PRO506 4.5 46.6 1.0
O A:LEU533 4.5 38.5 1.0
O A:HOH1448 4.5 34.6 1.0
N A:PRO506 4.5 46.2 1.0
CB A:ASN507 4.5 47.7 1.0
O A:ALA502 4.6 38.2 1.0
CA A:ASN507 4.8 49.1 1.0
CB A:LYS531 4.8 41.1 1.0
C A:LYS532 4.8 40.6 1.0
N A:LEU533 4.8 38.8 1.0
O A:ILE530 4.8 33.3 1.0

Calcium binding site 4 out of 5 in 3qes

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp 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 Dgtp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:44.0
occ:1.00
 O A:HOH1547 2.3 30.6 1.0
O A:HOH1452 2.4 34.1 1.0
O A:HOH922 2.5 21.4 1.0
OE1 A:GLU116 2.5 23.4 1.0
OE2 A:GLU116 2.6 25.3 1.0
CD A:GLU116 2.9 21.6 1.0
OD2 A:ASP114 4.2 34.5 1.0
O A:HOH1414 4.2 31.8 1.0
O A:HOH1511 4.4 38.6 1.0
O A:HOH1557 4.4 35.2 1.0
CG A:GLU116 4.4 19.7 1.0
O A:HOH1304 4.5 45.4 1.0
O A:HOH1453 4.5 48.1 1.0
O A:ILE115 4.6 20.0 1.0
CD1 A:ILE309 4.8 40.5 1.0

Calcium binding site 5 out of 5 in 3qes

Go back to Calcium Binding Sites List in 3qes
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp 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 Dgtp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:60.2
occ:1.00
 O A:HOH1540 2.4 46.8 1.0
OD1 A:ASP684 2.4 34.8 1.0
OE1 A:GLU660 3.1 33.8 1.0
CG A:ASP684 3.5 35.0 1.0
CD A:GLU660 3.8 30.4 1.0
OD2 A:ASP684 4.1 36.8 1.0
CG A:GLU660 4.3 25.4 1.0
CB A:GLU660 4.4 25.8 1.0
O A:MET683 4.4 27.6 1.0
OD2 A:ASP664 4.5 26.1 0.5
CB A:ASP684 4.5 29.4 1.0
OD1 A:ASP664 4.5 24.0 0.5
OE2 A:GLU660 4.6 31.6 1.0
CA A:ASP684 4.7 28.1 1.0
C A:MET683 4.9 25.9 1.0
CG A:ASP664 5.0 23.1 0.5

Reference:

S.Xia, S.H.Eom, W.H.Konigsberg, J.Wang. Structural Basis For Differential Insertion Kinetics of Dnmps Opposite A Difluorotoluene Nucleotide Residue. Biochemistry V. 51 1476 2012.
ISSN: ISSN 0006-2960
PubMed: 22304682
DOI: 10.1021/BI2016487
Page generated: Tue Jul 8 15:56:39 2025

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