Atomistry » Calcium » PDB 3q4y-3qgo » 3qer
Atomistry »
  Calcium »
    PDB 3q4y-3qgo »
      3qer »

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: Sat Jul 13 17:27:25 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy