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Calcium in PDB 3cfp: Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 1

Enzymatic activity of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 1

All present enzymatic activity of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 1:
2.7.7.7;

Protein crystallography data

The structure of Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 1, PDB code: 3cfp 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 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.726, 117.281, 126.813, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 26.7

Other elements in 3cfp:

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

Calcium binding site 1 out of 4 in 3cfp

Go back to Calcium Binding Sites List in 3cfp
Calcium binding site 1 out of 4 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:56.3
occ:1.00
 OD1 A:ASP623 2.1 66.3 1.0
O1G A:TTP1006 2.2 33.2 1.0
OD1 A:ASP411 2.2 70.3 1.0
O2B A:TTP1006 2.4 38.3 1.0
O2A A:TTP1006 2.5 41.8 1.0
O A:LEU412 2.5 52.6 1.0
CG A:ASP411 3.1 68.0 1.0
CG A:ASP623 3.2 63.9 1.0
PB A:TTP1006 3.2 40.6 1.0
O3A A:TTP1006 3.3 39.9 1.0
PA A:TTP1006 3.4 41.0 1.0
PG A:TTP1006 3.4 39.0 1.0
OD2 A:ASP411 3.4 69.7 1.0
O3B A:TTP1006 3.7 40.8 1.0
C A:LEU412 3.7 53.7 1.0
OD2 A:ASP623 3.8 65.4 1.0
CA A:CA1002 3.9 0.5 1.0
C5' A:TTP1006 4.0 34.0 1.0
O5' A:TTP1006 4.2 39.0 1.0
N A:LEU412 4.2 56.8 1.0
O3G A:TTP1006 4.3 34.1 1.0
O2G A:TTP1006 4.4 34.7 1.0
CB A:ASP623 4.4 60.1 1.0
CB A:ASP411 4.5 63.3 1.0
CA A:LEU412 4.5 55.0 1.0
N A:SER414 4.6 53.5 1.0
O1B A:TTP1006 4.7 40.2 1.0
O1A A:TTP1006 4.7 39.8 1.0
N A:THR413 4.7 53.3 1.0
CA A:THR413 4.9 53.7 1.0
O A:ASP623 4.9 57.6 1.0
C A:ASP411 4.9 58.5 1.0
N A:LEU415 5.0 47.5 1.0
C A:THR413 5.0 52.2 1.0
CB A:LEU412 5.0 52.9 1.0

Calcium binding site 2 out of 4 in 3cfp

Go back to Calcium Binding Sites List in 3cfp
Calcium binding site 2 out of 4 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:0.5
occ:1.00
 OD2 A:ASP411 2.5 69.7 1.0
O2A A:TTP1006 2.6 41.8 1.0
OD2 A:ASP623 2.8 65.4 1.0
CG A:ASP411 3.5 68.0 1.0
CG A:ASP623 3.7 63.9 1.0
OD1 A:ASP623 3.8 66.3 1.0
OD1 A:ASP411 3.8 70.3 1.0
C3' P:DOC115 3.9 32.5 1.0
PA A:TTP1006 3.9 41.0 1.0
CA A:CA1001 3.9 56.3 1.0
C5' P:DOC115 3.9 35.9 1.0
CB A:SER624 4.1 56.6 1.0
C4' P:DOC115 4.2 33.6 1.0
O1A A:TTP1006 4.3 39.8 1.0
OG A:SER624 4.6 60.2 1.0
O5' A:TTP1006 4.7 39.0 1.0
O A:ASP621 4.7 47.4 1.0
C5' A:TTP1006 4.7 34.0 1.0
O5' P:DOC115 4.8 37.5 1.0
CB A:ASP411 4.8 63.3 1.0
C A:ASP623 4.9 56.5 1.0
O A:ASP623 4.9 57.6 1.0

Calcium binding site 3 out of 4 in 3cfp

Go back to Calcium Binding Sites List in 3cfp
Calcium binding site 3 out of 4 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:94.4
occ:1.00
 OE2 A:GLU716 2.7 61.4 1.0
CD A:GLU716 3.4 61.5 1.0
OD2 A:ASP684 3.5 71.0 1.0
OE2 A:GLU686 3.6 77.3 1.0
CG A:GLU716 4.1 60.7 1.0
O A:HOH1148 4.1 65.0 1.0
OE1 A:GLU716 4.1 61.5 1.0
CG A:GLU686 4.1 70.6 1.0
NZ A:LYS486 4.2 50.5 1.0
CD A:GLU686 4.3 75.7 1.0
CB A:ASP411 4.4 63.3 1.0
OD1 A:ASP411 4.4 70.3 1.0
O A:ASP411 4.7 57.9 1.0
CG A:ASP684 4.7 70.7 1.0
O1G A:TTP1006 4.7 33.2 1.0
CG A:ASP411 4.9 68.0 1.0
O A:ASP684 4.9 60.9 1.0
O2G A:TTP1006 5.0 34.7 1.0

Calcium binding site 4 out of 4 in 3cfp

Go back to Calcium Binding Sites List in 3cfp
Calcium binding site 4 out of 4 in the Structure of the Replicating Complex of A Pol Alpha Family Dna Polymerase, Ternary Complex 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:85.0
occ:1.00
 OE1 A:GLU116 2.4 63.3 1.0
O A:HOH1076 2.6 65.0 1.0
O A:HOH1145 2.6 48.9 1.0
O A:HOH1066 2.9 56.1 1.0
OE2 A:GLU116 3.0 61.0 1.0
CD A:GLU116 3.1 61.8 1.0
O A:HOH1235 4.3 53.5 1.0
O A:HOH1262 4.4 52.7 1.0
OD2 A:ASP114 4.5 64.3 1.0
CG A:GLU116 4.6 59.5 1.0
CD1 A:ILE309 4.6 72.5 1.0
O A:ILE115 4.7 52.4 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: Sat Jul 13 08:37:13 2024

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