Calcium in PDB 7f4y: Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes

Enzymatic activity of Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes

All present enzymatic activity of Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes, PDB code: 7f4y was solved by H.-S.Youn, J.Park, J.Y.An, Y.Lee, S.H.Eom, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.44, 164.44, 165.601, 90, 90, 120
R / Rfree (%) 19.4 / 24.5

Other elements in 7f4y:

The structure of Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes (pdb code 7f4y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes, PDB code: 7f4y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7f4y

Go back to Calcium Binding Sites List in 7f4y
Calcium binding site 1 out of 2 in the Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:63.8
occ:1.00
O2B A:DUP1001 2.0 34.7 1.0
O A:LEU412 2.1 31.0 1.0
O3G A:DUP1001 2.1 40.6 1.0
OD1 A:ASP623 2.2 101.8 1.0
OD1 A:ASP411 2.3 43.3 1.0
O2A A:DUP1001 2.9 50.4 1.0
PB A:DUP1001 3.1 38.5 1.0
CG A:ASP623 3.2 46.2 1.0
PG A:DUP1001 3.3 40.1 1.0
C A:LEU412 3.3 27.5 1.0
O3B A:DUP1001 3.4 36.7 1.0
CG A:ASP411 3.6 53.8 1.0
N3A A:DUP1001 3.6 43.3 1.0
PA A:DUP1001 3.6 52.6 1.0
O A:HOH1189 3.8 40.8 1.0
O5' A:DUP1001 3.9 45.4 1.0
N A:LEU412 3.9 27.8 1.0
O2G A:DUP1001 3.9 34.0 1.0
CB A:ASP623 4.0 37.2 1.0
CA A:LEU412 4.1 30.3 1.0
OD2 A:ASP623 4.1 51.5 1.0
N A:SER414 4.2 19.9 1.0
C A:ASP411 4.3 29.2 1.0
N A:THR413 4.3 27.9 1.0
N A:LEU415 4.4 24.1 1.0
CB A:ASP411 4.4 40.6 1.0
OD2 A:ASP411 4.4 70.1 1.0
O1G A:DUP1001 4.4 38.8 1.0
O1B A:DUP1001 4.5 49.4 1.0
C A:THR413 4.5 22.2 1.0
CB A:LEU412 4.6 28.4 1.0
CA A:THR413 4.6 27.7 1.0
CA A:ASP411 4.8 30.7 1.0
O A:ASP623 4.8 25.7 1.0
O A:ASP411 4.8 26.2 1.0
CB A:LEU415 4.8 22.1 1.0
CA A:SER414 4.8 23.5 1.0
O A:HOH1578 4.9 65.5 1.0

Calcium binding site 2 out of 2 in 7f4y

Go back to Calcium Binding Sites List in 7f4y
Calcium binding site 2 out of 2 in the Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:108.5
occ:1.00
O B:HOH1698 2.8 76.7 1.0
O B:HOH1702 3.4 62.8 1.0
O B:HOH1402 3.5 59.6 1.0
O B:MET900 3.8 63.9 1.0
O B:PHE901 4.3 70.7 1.0
C B:MET900 4.5 65.3 1.0
C B:PHE901 4.6 62.1 1.0

Reference:

H.-S.Youn, J.Park, J.Y.An, Y.Lee, S.H.Eom, J.Wang. Crystal Structure of Replisomal Dimer of Dna Polymerase From Bacteriophage RB69 with Dna Duplexes To Be Published.
Page generated: Sat Aug 21 12:37:57 2021

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