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

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside, PDB code: 3qer 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 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.269, 118.705, 130.523, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.7

Other elements in 3qer:

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

Calcium binding site 1 out of 4 in 3qer

Go back to Calcium Binding Sites List in 3qer
Calcium binding site 1 out of 4 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Datp 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 Datp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:21.8
occ:1.00
 OD1 A:ASP623 2.3 19.1 1.0
O1G A:DTP904 2.3 4.7 1.0
O2B A:DTP904 2.3 3.0 1.0
O2A A:DTP904 2.3 4.9 1.0
O A:LEU412 2.4 16.6 1.0
OD1 A:ASP411 2.5 26.5 1.0
OD2 A:ASP411 2.7 28.5 1.0
CG A:ASP411 2.9 20.1 1.0
CG A:ASP623 3.3 15.2 1.0
PB A:DTP904 3.4 4.5 1.0
C A:LEU412 3.5 15.5 1.0
PA A:DTP904 3.5 5.8 1.0
PG A:DTP904 3.6 6.5 1.0
CA A:CA906 3.6 43.2 1.0
O3A A:DTP904 3.7 6.1 1.0
OD2 A:ASP623 3.7 18.4 1.0
O A:HOH1134 3.8 26.3 1.0
O3B A:DTP904 3.9 4.7 1.0
N A:LEU412 4.0 14.1 1.0
C5' A:DTP904 4.1 4.3 1.0
CA A:LEU412 4.3 14.4 1.0
O2G A:DTP904 4.3 2.0 1.0
O A:HOH1524 4.3 34.4 1.0
O5' A:DTP904 4.3 6.1 1.0
CB A:ASP411 4.4 18.3 1.0
N A:SER414 4.4 13.3 1.0
N A:THR413 4.5 13.9 1.0
C A:ASP411 4.6 12.8 1.0
CB A:ASP623 4.6 13.7 1.0
N A:LEU415 4.7 12.4 1.0
O3G A:DTP904 4.7 5.1 1.0
C A:THR413 4.7 14.9 1.0
CA A:THR413 4.7 16.2 1.0
O1A A:DTP904 4.8 4.6 1.0
O1B A:DTP904 4.8 5.0 1.0
CB A:LEU412 4.8 13.4 1.0
CA A:ASP411 5.0 13.6 1.0

Calcium binding site 2 out of 4 in 3qer

Go back to Calcium Binding Sites List in 3qer
Calcium binding site 2 out of 4 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Datp 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 Datp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:43.2
occ:1.00
 OD2 A:ASP411 2.3 28.5 1.0
O A:HOH1020 2.4 23.0 1.0
O2A A:DTP904 2.5 4.9 1.0
OD2 A:ASP623 2.5 18.4 1.0
O A:HOH1230 3.2 32.3 1.0
O A:HOH1250 3.4 21.7 1.0
CG A:ASP623 3.4 15.2 1.0
CG A:ASP411 3.4 20.1 1.0
CA A:CA905 3.6 21.8 1.0
OD1 A:ASP623 3.6 19.1 1.0
PA A:DTP904 3.7 5.8 1.0
C3' P:DOC115 3.8 3.7 1.0
CB A:SER624 4.0 18.0 1.0
OD1 A:ASP411 4.1 26.5 1.0
O A:HOH1134 4.1 26.3 1.0
C5' P:DOC115 4.2 11.7 1.0
O1A A:DTP904 4.2 4.6 1.0
O5' A:DTP904 4.2 6.1 1.0
C4' P:DOC115 4.4 3.6 1.0
O A:HOH967 4.4 22.5 1.0
CB A:ASP411 4.5 18.3 1.0
C5' A:DTP904 4.5 4.3 1.0
O A:ASP621 4.6 14.2 1.0
OG A:SER624 4.6 20.6 1.0
N A:SER624 4.6 15.4 1.0
C A:ASP623 4.7 15.5 1.0
CB A:ASP623 4.8 13.7 1.0
O A:HOH1458 4.8 36.8 1.0
CA A:SER624 4.8 16.8 1.0
O A:ASP623 4.9 14.2 1.0
O1G A:DTP904 4.9 4.7 1.0

Calcium binding site 3 out of 4 in 3qer

Go back to Calcium Binding Sites List in 3qer
Calcium binding site 3 out of 4 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Datp 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 Datp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:43.1
occ:1.00
 O A:LYS531 2.3 22.5 1.0
O A:ASN505 2.3 24.2 1.0
O A:HOH1726 2.3 26.3 1.0
OD1 A:ASN507 2.4 24.5 1.0
O A:HOH937 2.5 19.6 1.0
O A:HOH1116 2.5 23.2 1.0
O A:HOH975 2.6 26.5 1.0
C A:LYS531 3.3 22.8 1.0
C A:ASN505 3.5 26.7 1.0
CG A:ASN507 3.5 24.5 1.0
CA A:LYS531 4.0 22.2 1.0
ND2 A:ASN507 4.2 24.4 1.0
N A:ASN507 4.2 26.4 1.0
CB A:ASN505 4.2 29.2 1.0
N A:LYS532 4.2 23.2 1.0
CA A:PRO506 4.3 26.9 1.0
C A:PRO506 4.3 27.3 1.0
N A:PRO506 4.4 26.4 1.0
CA A:LYS532 4.5 24.0 1.0
CA A:ASN505 4.5 28.4 1.0
O A:LEU533 4.6 17.9 1.0
O A:HOH1620 4.6 26.9 1.0
O A:ALA502 4.6 23.9 1.0
CB A:LYS531 4.6 23.5 1.0
CB A:ASN507 4.7 25.3 1.0
C A:LYS532 4.8 24.0 1.0
CA A:ASN507 4.9 26.2 1.0
O A:ILE530 4.9 20.6 1.0
N A:LEU533 4.9 21.0 1.0
O A:PRO506 5.0 28.3 1.0

Calcium binding site 4 out of 4 in 3qer

Go back to Calcium Binding Sites List in 3qer
Calcium binding site 4 out of 4 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Datp 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 Datp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:43.3
occ:1.00
 O A:HOH1594 2.3 33.0 1.0
O A:HOH1536 2.5 49.8 1.0
O A:HOH970 2.5 24.4 1.0
O A:HOH1619 2.6 33.5 1.0
OE2 A:GLU116 2.6 20.2 1.0
OE1 A:GLU116 2.6 19.1 1.0
CD A:GLU116 2.9 18.2 1.0
O A:HOH1490 4.2 30.8 1.0
O A:HOH1392 4.2 26.1 1.0
O A:HOH1208 4.3 35.0 1.0
OD2 A:ASP114 4.3 29.8 1.0
CG A:GLU116 4.4 16.3 1.0
O A:ILE115 4.5 15.8 1.0

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 15:56:07 2025

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