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Calcium in PDB 3cfr: Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2

Enzymatic activity of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2

All present enzymatic activity of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2:
2.7.7.7;

Protein crystallography data

The structure of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2, PDB code: 3cfr was solved by J.Wang, D.Klimenko, M.Wang, T.A.Steitz, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.958, 119.769, 130.430, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 26.6

Other elements in 3cfr:

The structure of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2 (pdb code 3cfr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2, PDB code: 3cfr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3cfr

Go back to Calcium Binding Sites List in 3cfr
Calcium binding site 1 out of 5 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:48.9
occ:1.00
 OD1 A:ASP623 2.0 32.9 1.0
O A:LEU412 2.2 29.2 1.0
O2B A:TTP916 2.2 31.6 1.0
O A:HOH1019 2.3 21.6 1.0
O1G A:TTP916 2.3 31.5 1.0
OD1 A:ASP411 2.6 40.1 1.0
OD2 A:ASP411 3.1 40.9 1.0
O2A A:TTP916 3.1 29.4 1.0
CG A:ASP411 3.1 37.5 1.0
CG A:ASP623 3.2 30.8 1.0
PB A:TTP916 3.3 32.7 1.0
C A:LEU412 3.4 27.8 1.0
PG A:TTP916 3.5 28.9 1.0
O3A A:TTP916 3.7 31.5 1.0
O3B A:TTP916 3.7 30.8 1.0
CA A:CA911 3.9 57.0 1.0
PA A:TTP916 4.0 28.1 1.0
OD2 A:ASP623 4.0 30.8 1.0
N A:LEU412 4.0 28.0 1.0
O2G A:TTP916 4.2 29.0 1.0
CA A:LEU412 4.2 26.9 1.0
CB A:ASP623 4.2 29.4 1.0
C5' A:TTP916 4.3 25.0 1.0
N A:SER414 4.4 28.0 1.0
N A:THR413 4.4 28.1 1.0
O A:HOH1258 4.5 29.9 1.0
C A:ASP411 4.5 31.5 1.0
CB A:ASP411 4.5 34.3 1.0
CA A:THR413 4.6 27.4 1.0
O3G A:TTP916 4.6 29.5 1.0
CB A:LEU412 4.7 24.6 1.0
O5' A:TTP916 4.7 28.6 1.0
O1B A:TTP916 4.7 31.8 1.0
N A:LEU415 4.7 25.3 1.0
C A:THR413 4.7 28.1 1.0
CA A:CA912 4.9 91.6 1.0
CB A:LEU415 5.0 23.6 1.0
O A:ASP623 5.0 30.5 1.0
CA A:ASP411 5.0 31.9 1.0

Calcium binding site 2 out of 5 in 3cfr

Go back to Calcium Binding Sites List in 3cfr
Calcium binding site 2 out of 5 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca911

b:57.0
occ:1.00
 O A:HOH1019 2.4 21.6 1.0
O2A A:TTP916 2.5 29.4 1.0
OD2 A:ASP411 2.7 40.9 1.0
OD2 A:ASP623 2.7 30.8 1.0
OG A:SER624 3.1 39.5 1.0
OD1 A:ASP623 3.5 32.9 1.0
CG A:ASP623 3.5 30.8 1.0
CG A:ASP411 3.6 37.5 1.0
C3' P:DOC115 3.7 18.8 1.0
PA A:TTP916 3.9 28.1 1.0
CA A:CA910 3.9 48.9 1.0
O A:HOH1258 4.0 29.9 1.0
C5' P:DOC115 4.0 19.7 1.0
OD1 A:ASP411 4.1 40.1 1.0
CB A:SER624 4.3 33.2 1.0
O1A A:TTP916 4.3 29.0 1.0
C4' P:DOC115 4.4 18.3 1.0
O P:HOH261 4.5 31.0 1.0
O5' A:TTP916 4.6 28.6 1.0
C5' A:TTP916 4.7 25.0 1.0
CB A:ASP411 4.8 34.3 1.0
O1G A:TTP916 4.8 31.5 1.0
O5' P:DOC115 4.9 20.5 1.0
N A:SER624 4.9 30.8 1.0
O A:ASP621 4.9 27.3 1.0
OE2 A:GLU686 4.9 46.2 1.0
CB A:ASP623 4.9 29.4 1.0
C2' P:DOC115 4.9 21.1 1.0
C A:ASP623 5.0 30.0 1.0
O3A A:TTP916 5.0 31.5 1.0

Calcium binding site 3 out of 5 in 3cfr

Go back to Calcium Binding Sites List in 3cfr
Calcium binding site 3 out of 5 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca912

b:91.6
occ:1.00
 O A:HOH1121 3.1 29.3 1.0
OD1 A:ASP411 3.2 40.1 1.0
OE1 A:GLU686 3.3 49.4 1.0
NZ A:LYS486 3.5 26.9 1.0
OE1 A:GLU716 3.8 35.7 1.0
O2G A:TTP916 3.9 29.0 1.0
O1G A:TTP916 3.9 31.5 1.0
CD A:GLU716 4.1 33.5 1.0
CG A:ASP411 4.2 37.5 1.0
CD A:GLU686 4.3 46.0 1.0
O A:HOH1258 4.4 29.9 1.0
O A:ASP411 4.4 31.8 1.0
OE2 A:GLU716 4.4 31.1 1.0
PG A:TTP916 4.5 28.9 1.0
CB A:ASP411 4.5 34.3 1.0
OE2 A:GLU686 4.7 46.2 1.0
O A:LEU412 4.8 29.2 1.0
CG A:GLU716 4.8 33.0 1.0
O A:HOH1019 4.9 21.6 1.0
CE A:LYS486 4.9 27.0 1.0
CA A:CA910 4.9 48.9 1.0
O3G A:TTP916 4.9 29.5 1.0
CA A:THR413 4.9 27.4 1.0
C A:ASP411 5.0 31.5 1.0

Calcium binding site 4 out of 5 in 3cfr

Go back to Calcium Binding Sites List in 3cfr
Calcium binding site 4 out of 5 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca913

b:48.4
occ:1.00
 OD1 A:ASN507 2.1 49.5 1.0
O A:ASN505 2.3 47.3 1.0
O A:LYS531 2.4 41.0 1.0
C A:LYS531 3.2 40.6 1.0
CG A:ASN507 3.3 49.3 1.0
C A:ASN505 3.6 47.7 1.0
CA A:LYS531 3.7 40.6 1.0
CB A:ASN505 3.9 47.7 1.0
CB A:ASN507 4.2 50.5 1.0
N A:LYS532 4.2 39.4 1.0
ND2 A:ASN507 4.2 46.0 1.0
CB A:LYS531 4.3 40.7 1.0
CA A:ASN505 4.4 47.3 1.0
O A:ALA502 4.5 34.4 1.0
N A:PRO506 4.5 48.5 1.0
CA A:LYS532 4.6 38.5 1.0
CA A:PRO506 4.6 49.7 1.0
O A:HOH1319 4.7 59.8 1.0
O A:ILE530 4.8 38.6 1.0
N A:LEU533 4.9 37.9 1.0

Calcium binding site 5 out of 5 in 3cfr

Go back to Calcium Binding Sites List in 3cfr
Calcium binding site 5 out of 5 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca914

b:61.9
occ:1.00
 O A:ASN676 3.1 24.6 1.0
O A:HOH1457 3.1 25.7 1.0
SG A:CYS671 3.4 31.3 1.0
O A:CYS671 3.7 27.6 1.0
N A:ASN676 3.7 23.5 1.0
C A:CYS671 3.9 28.8 1.0
CA A:GLU672 3.9 31.1 1.0
N A:GLU672 3.9 28.9 1.0
C A:ASN676 4.1 26.0 1.0
C A:ASN675 4.2 23.5 1.0
NZ A:LYS465 4.4 15.8 1.0
CA A:ASN675 4.4 23.9 1.0
CA A:ASN676 4.4 24.1 1.0
CB A:CYS671 4.5 30.2 1.0
CG A:GLU672 4.5 37.0 1.0
CA A:CYS671 4.8 29.2 1.0
CB A:GLU672 4.8 33.2 1.0
OD1 A:ASN675 4.9 25.4 1.0
O A:ASN675 4.9 25.5 1.0
C A:GLU672 5.0 28.8 1.0
CB A:ASN676 5.0 22.3 1.0

Reference:

D.Klimenko, M.Wang, T.A.Steitz, W.H.Konigsberg, J.Wang. Insights Into Base Selectivity From the Structures of An RB69 Dna Polymerase Triple Mutant To Be Published.
Page generated: Tue Jul 8 11:21:06 2025

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