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

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Difluorotoluene Nucleoside, PDB code: 3qei 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 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.345, 118.231, 130.854, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.8

Other elements in 3qei:

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

Calcium binding site 1 out of 4 in 3qei

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

b:29.9
occ:1.00
 O1G A:DCP904 2.2 5.7 1.0
OD1 A:ASP623 2.2 26.5 1.0
OD1 A:ASP411 2.3 24.2 1.0
O2B A:DCP904 2.4 5.4 1.0
O A:LEU412 2.4 21.4 1.0
O2A A:DCP904 2.5 10.8 1.0
OD2 A:ASP411 2.8 28.9 1.0
CG A:ASP411 2.9 19.6 1.0
PB A:DCP904 3.4 6.2 1.0
CG A:ASP623 3.4 23.6 1.0
PG A:DCP904 3.5 4.8 1.0
C A:LEU412 3.6 19.4 1.0
PA A:DCP904 3.6 6.2 1.0
O3A A:DCP904 3.8 10.2 1.0
CA A:CA906 3.8 55.5 1.0
O3B A:DCP904 3.8 8.1 1.0
OD2 A:ASP623 3.9 25.1 1.0
N A:LEU412 4.1 18.2 1.0
O2G A:DCP904 4.3 5.6 1.0
O A:HOH960 4.3 35.8 1.0
C5' A:DCP904 4.3 4.8 1.0
CB A:ASP411 4.4 19.9 1.0
CA A:LEU412 4.4 18.4 1.0
N A:SER414 4.4 13.4 1.0
O5' A:DCP904 4.5 9.8 1.0
N A:THR413 4.5 18.6 1.0
O3G A:DCP904 4.6 4.7 1.0
CB A:ASP623 4.6 19.3 1.0
C A:ASP411 4.6 18.3 1.0
CA A:THR413 4.7 18.0 1.0
O1B A:DCP904 4.7 9.2 1.0
C A:THR413 4.7 15.7 1.0
O1A A:DCP904 4.8 10.8 1.0
N A:LEU415 4.8 14.5 1.0
CB A:LEU412 4.9 17.3 1.0
CA A:ASP411 5.0 17.4 1.0

Calcium binding site 2 out of 4 in 3qei

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

b:55.5
occ:1.00
 O A:HOH1146 2.5 32.8 1.0
OD2 A:ASP411 2.5 28.9 1.0
O A:HOH1145 2.6 18.9 1.0
O2A A:DCP904 2.6 10.8 1.0
OD2 A:ASP623 2.7 25.1 1.0
CG A:ASP411 3.6 19.6 1.0
CG A:ASP623 3.6 23.6 1.0
OD1 A:ASP623 3.7 26.5 1.0
CA A:CA905 3.8 29.9 1.0
C3' P:DOC115 3.8 6.1 1.0
PA A:DCP904 3.8 6.2 1.0
CB A:SER624 4.1 21.1 1.0
OD1 A:ASP411 4.1 24.2 1.0
O1A A:DCP904 4.1 10.8 1.0
O A:HOH1085 4.2 27.2 1.0
O5' A:DCP904 4.4 9.8 1.0
OG A:SER624 4.5 25.6 1.0
C5' P:DOC115 4.6 11.8 1.0
CB A:ASP411 4.6 19.9 1.0
C5' A:DCP904 4.7 4.8 1.0
O5' P:DOC115 4.7 9.0 1.0
C4' P:DOC115 4.8 6.7 1.0
N A:SER624 4.8 16.2 1.0
O A:ASP621 4.8 16.6 1.0
C A:ASP623 5.0 17.9 1.0
CA A:SER624 5.0 19.3 1.0
OE2 A:GLU686 5.0 41.4 1.0
CB A:ASP623 5.0 19.3 1.0

Calcium binding site 3 out of 4 in 3qei

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

b:65.8
occ:1.00
 O A:HOH1312 2.2 18.9 1.0
O A:LYS531 2.3 33.8 1.0
O A:ASN505 2.3 31.4 1.0
OD1 A:ASN507 2.4 28.9 1.0
O A:HOH1095 2.4 41.6 1.0
O A:HOH1096 2.5 41.8 1.0
O A:HOH1097 2.8 21.4 1.0
C A:LYS531 3.2 33.4 1.0
C A:ASN505 3.5 32.0 1.0
CG A:ASN507 3.5 30.7 1.0
CA A:LYS531 4.0 34.0 1.0
N A:LYS532 4.0 33.0 1.0
N A:ASN507 4.2 33.8 1.0
CA A:PRO506 4.2 32.6 1.0
ND2 A:ASN507 4.2 28.4 1.0
C A:PRO506 4.2 33.6 1.0
CA A:LYS532 4.2 33.0 1.0
CB A:ASN505 4.3 32.2 0.5
N A:PRO506 4.3 32.2 1.0
O A:LEU533 4.4 28.1 1.0
O A:ALA502 4.5 31.8 1.0
CA A:ASN505 4.5 32.7 0.5
C A:LYS532 4.7 32.1 1.0
CB A:ASN507 4.7 31.8 1.0
O A:ILE530 4.7 31.7 1.0
N A:LEU533 4.7 30.9 1.0
CB A:LYS531 4.7 34.6 1.0
O A:PRO506 4.8 34.5 1.0
CA A:ASN507 4.9 32.9 1.0

Calcium binding site 4 out of 4 in 3qei

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

b:52.6
occ:1.00
 O A:HOH1036 2.5 26.1 1.0
OE1 A:GLU116 2.5 20.1 1.0
O A:HOH1035 2.6 29.5 1.0
OE2 A:GLU116 2.7 21.7 1.0
CD A:GLU116 3.0 20.4 1.0
O A:HOH1037 3.1 38.9 1.0
O A:HOH1038 3.8 22.7 1.0
CG A:GLU116 4.5 17.7 1.0
O A:ILE115 4.7 19.1 1.0
OD2 A:ASP114 4.7 32.7 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 15:55:45 2025

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