Calcium in PDB 3rwu: RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside, PDB code: 3rwu 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 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.913, 120.103, 130.596, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.6

Other elements in 3rwu:

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

Calcium binding site 1 out of 4 in 3rwu

Go back to Calcium Binding Sites List in 3rwu
Calcium binding site 1 out of 4 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:38.1
occ:1.00
 O1G A:ATP902 2.2 34.0 1.0
OD1 A:ASP623 2.2 36.9 1.0
O2B A:ATP902 2.3 27.6 1.0
O A:LEU412 2.3 29.5 1.0
O2A A:ATP902 2.4 34.2 1.0
OD1 A:ASP411 2.5 34.6 1.0
OD2 A:ASP411 2.6 40.7 1.0
CG A:ASP411 2.9 34.3 1.0
CG A:ASP623 3.3 33.9 1.0
PB A:ATP902 3.4 30.9 1.0
PG A:ATP902 3.5 35.5 1.0
C A:LEU412 3.5 28.5 1.0
PA A:ATP902 3.6 31.2 1.0
O3A A:ATP902 3.7 30.5 1.0
CA A:CA904 3.8 65.5 1.0
O3B A:ATP902 3.8 29.8 1.0
OD2 A:ASP623 3.9 35.0 1.0
N A:LEU412 4.1 28.0 1.0
O2G A:ATP902 4.3 27.2 1.0
N A:SER414 4.3 28.6 1.0
CA A:LEU412 4.3 26.6 1.0
CB A:ASP411 4.3 30.9 1.0
C5' A:ATP902 4.4 26.2 1.0
O A:HOH1008 4.4 40.2 1.0
O5' A:ATP902 4.4 31.9 1.0
N A:THR413 4.5 30.1 1.0
CB A:ASP623 4.5 32.6 1.0
C A:ASP411 4.5 29.7 1.0
CA A:THR413 4.6 28.8 1.0
O3G A:ATP902 4.6 36.8 1.0
O1B A:ATP902 4.8 33.0 1.0
C A:THR413 4.8 28.5 1.0
N A:LEU415 4.8 23.7 1.0
O1A A:ATP902 4.8 33.1 1.0
CB A:LEU412 4.9 26.6 1.0
CA A:ASP411 4.9 30.1 1.0

Calcium binding site 2 out of 4 in 3rwu

Go back to Calcium Binding Sites List in 3rwu
Calcium binding site 2 out of 4 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:65.5
occ:1.00
 OD2 A:ASP411 2.5 40.7 1.0
O2A A:ATP902 2.7 34.2 1.0
OD2 A:ASP623 2.7 35.0 1.0
CG A:ASP411 3.5 34.3 1.0
CG A:ASP623 3.6 33.9 1.0
OD1 A:ASP623 3.7 36.9 1.0
CB A:SER624 3.8 30.5 1.0
CA A:CA903 3.8 38.1 1.0
C3' P:DOC115 3.8 33.2 1.0
PA A:ATP902 3.9 31.2 1.0
C5' P:DOC115 3.9 33.8 1.0
O P:HOH148 4.1 33.8 1.0
OD1 A:ASP411 4.2 34.6 1.0
O1A A:ATP902 4.3 33.1 1.0
CB A:ASP411 4.3 30.9 1.0
C4' P:DOC115 4.5 34.5 1.0
OG A:SER624 4.5 28.8 1.0
O5' A:ATP902 4.7 31.9 1.0
N A:SER624 4.8 30.3 1.0
O A:ASP621 4.8 25.1 1.0
CA A:SER624 4.8 29.8 1.0
C5' A:ATP902 4.9 26.2 1.0
O5' P:DOC115 4.9 30.0 1.0
C A:ASP623 4.9 33.2 1.0
O1G A:ATP902 4.9 34.0 1.0
CB A:ASP623 5.0 32.6 1.0

Calcium binding site 3 out of 4 in 3rwu

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

b:62.5
occ:1.00
 O A:LYS531 2.2 49.6 1.0
OD1 A:ASN507 2.2 58.1 1.0
O A:ASN505 2.3 59.5 1.0
C A:LYS531 3.2 49.7 1.0
CG A:ASN507 3.4 58.5 1.0
C A:ASN505 3.5 60.7 1.0
CA A:LYS531 3.9 49.3 1.0
N A:ASN507 4.0 61.9 1.0
N A:LYS532 4.1 49.0 1.0
CA A:PRO506 4.2 59.6 1.0
ND2 A:ASN507 4.2 58.2 1.0
C A:PRO506 4.3 61.0 1.0
N A:PRO506 4.3 59.7 1.0
CA A:LYS532 4.4 50.2 1.0
CB A:ASN505 4.4 65.0 1.0
CB A:ASN507 4.5 61.9 1.0
CB A:LYS531 4.6 49.4 1.0
CA A:ASN505 4.6 63.0 1.0
O A:ALA502 4.6 56.0 1.0
CA A:ASN507 4.7 63.1 1.0
O A:LEU533 4.7 50.8 1.0
N A:LEU533 4.7 48.5 1.0
C A:LYS532 4.8 49.9 1.0
O A:ILE530 4.9 42.7 1.0

Calcium binding site 4 out of 4 in 3rwu

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

b:91.6
occ:1.00
 O A:HOH1017 2.2 38.9 1.0
O A:HOH1018 2.6 31.7 1.0
OE2 A:GLU116 2.6 39.1 1.0
OD2 A:ASP114 3.3 45.0 1.0
CD A:GLU116 3.5 34.6 1.0
OE1 A:GLU116 3.7 43.8 1.0
CG A:ASP114 4.5 41.2 1.0
O A:ILE115 4.5 22.6 1.0
OD1 A:ASP114 4.9 38.8 1.0
CG A:GLU116 4.9 29.7 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: Sat Dec 12 04:29:00 2020

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