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Calcium in PDB 3cq8: Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase

Enzymatic activity of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase

All present enzymatic activity of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase, PDB code: 3cq8 was solved by X.Zhong, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.70 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.840, 117.006, 127.823, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 28.1

Other elements in 3cq8:

The structure of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase (pdb code 3cq8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase, PDB code: 3cq8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3cq8

Go back to Calcium Binding Sites List in 3cq8
Calcium binding site 1 out of 6 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:36.0
occ:1.00
 OD2 A:ASP411 2.3 41.9 1.0
O A:LEU412 2.4 40.0 1.0
OD1 A:ASP623 2.4 35.4 1.0
O2A A:TTP1010 2.4 33.6 1.0
O1G A:TTP1010 2.5 29.7 1.0
O2B A:TTP1010 2.5 38.3 1.0
OD1 A:ASP411 2.8 40.9 1.0
CG A:ASP411 2.9 39.9 1.0
PB A:TTP1010 3.3 35.7 1.0
CA A:CA1002 3.3 87.8 1.0
CG A:ASP623 3.4 35.2 1.0
PG A:TTP1010 3.5 36.6 1.0
PA A:TTP1010 3.5 34.8 1.0
O3A A:TTP1010 3.5 35.7 1.0
C A:LEU412 3.5 39.5 1.0
O3B A:TTP1010 3.6 34.7 1.0
OD2 A:ASP623 3.7 33.2 1.0
N A:LEU412 3.9 38.3 1.0
C5' A:TTP1010 4.1 32.5 1.0
O5' A:TTP1010 4.1 33.5 1.0
O2G A:TTP1010 4.2 33.2 1.0
CA A:LEU412 4.3 38.6 1.0
CB A:ASP411 4.4 39.0 1.0
N A:THR413 4.6 40.4 1.0
O1B A:TTP1010 4.6 36.2 1.0
O3G A:TTP1010 4.6 35.6 1.0
N A:SER414 4.7 39.6 1.0
CB A:LEU412 4.7 38.6 1.0
CB A:PHE415 4.8 31.6 1.0
O1A A:TTP1010 4.8 33.9 1.0
N A:PHE415 4.8 32.3 1.0
O A:HOH1484 4.8 50.0 1.0
CB A:ASP623 4.8 30.7 1.0
CA A:THR413 4.8 40.4 1.0
C A:ASP411 4.8 37.6 1.0
C A:THR413 4.9 40.7 1.0

Calcium binding site 2 out of 6 in 3cq8

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Calcium binding site 2 out of 6 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:87.8
occ:1.00
 OD2 A:ASP411 2.7 41.9 1.0
O2A A:TTP1010 2.8 33.6 1.0
CG A:ASP411 3.0 39.9 1.0
OD2 A:ASP623 3.0 33.2 1.0
CA A:CA1001 3.3 36.0 1.0
OD1 A:ASP411 3.4 40.9 1.0
CB A:ASP411 3.7 39.0 1.0
CG A:ASP623 3.9 35.2 1.0
OD1 A:ASP623 3.9 35.4 1.0
PA A:TTP1010 4.0 34.8 1.0
CB A:SER624 4.2 27.1 1.0
OE2 A:GLU686 4.4 58.9 1.0
O1G A:TTP1010 4.5 29.7 1.0
C3' P:DC115 4.6 33.2 1.0
O1A A:TTP1010 4.6 33.9 1.0
CA A:ASP411 4.7 37.2 1.0
O5' A:TTP1010 4.7 33.5 1.0
OG A:SER624 4.8 30.1 1.0

Calcium binding site 3 out of 6 in 3cq8

Go back to Calcium Binding Sites List in 3cq8
Calcium binding site 3 out of 6 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:55.7
occ:1.00
 O A:HOH1484 2.1 50.0 1.0
O A:HOH1300 2.2 42.2 1.0
O A:HOH1298 2.6 41.6 1.0
OE1 A:GLU686 2.8 59.3 1.0
OE1 A:GLU716 3.1 49.9 1.0
O A:HOH1385 3.4 39.2 1.0
CD A:GLU716 3.6 49.1 1.0
O A:HOH1351 3.7 43.9 1.0
CD A:GLU686 3.8 57.4 1.0
OD1 A:ASP411 3.9 40.9 1.0
CG A:GLU716 4.0 49.5 1.0
OE2 A:GLU686 4.1 58.9 1.0
OE2 A:GLU716 4.3 49.7 1.0
NZ A:LYS486 4.4 46.3 1.0
O A:ARG685 4.6 41.8 1.0
CB A:ASP411 4.7 39.0 1.0
CG A:ASP411 4.7 39.9 1.0
CB A:ASP684 4.8 46.8 1.0
OG1 A:THR413 4.9 41.3 1.0

Calcium binding site 4 out of 6 in 3cq8

Go back to Calcium Binding Sites List in 3cq8
Calcium binding site 4 out of 6 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:56.1
occ:1.00
 O A:HOH1360 2.3 44.9 1.0
SG A:CYS671 2.6 41.7 1.0
CB A:CYS671 3.6 42.9 1.0
C A:CYS671 3.9 43.8 1.0
N A:GLU672 3.9 45.6 1.0
CD A:GLU672 3.9 57.1 1.0
O A:ASN676 4.0 44.0 1.0
OE1 A:GLU672 4.0 60.0 1.0
O A:CYS671 4.1 44.5 1.0
OE2 A:GLU672 4.2 58.2 1.0
CG A:GLU672 4.2 52.3 1.0
CA A:GLU672 4.2 46.0 1.0
CA A:CYS671 4.4 43.0 1.0
O A:ARG668 4.7 49.4 1.0
N A:HIS679 4.8 41.4 1.0
CB A:GLU672 4.9 47.9 1.0
CB A:HIS679 4.9 40.3 1.0
N A:ASN676 4.9 40.4 1.0
C A:ASN676 4.9 43.3 1.0

Calcium binding site 5 out of 6 in 3cq8

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Calcium binding site 5 out of 6 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:72.3
occ:1.00
 O A:HOH1401 2.5 41.5 1.0
O A:HOH1435 2.6 44.5 1.0
OE2 A:GLU116 2.7 45.0 1.0
O A:HOH1387 2.8 37.6 1.0
OD2 A:ASP114 3.0 41.1 1.0
O A:ILE115 3.0 38.5 1.0
O A:HOH1370 3.3 25.4 1.0
CD A:GLU116 3.3 46.4 1.0
OD1 A:ASP114 3.4 36.5 1.0
OE1 A:GLU116 3.4 45.3 1.0
CG A:ASP114 3.5 37.3 1.0
O A:HOH1414 3.7 33.5 1.0
C A:ILE115 4.1 38.1 1.0
N A:ILE115 4.6 33.0 1.0
CG A:GLU116 4.6 45.1 1.0
CA A:GLU116 4.8 40.6 1.0
ND2 A:ASN324 4.8 28.0 1.0
N A:GLU116 4.9 40.5 1.0
CB A:ASP114 5.0 34.4 1.0
O A:HOH1434 5.0 43.5 1.0

Calcium binding site 6 out of 6 in 3cq8

Go back to Calcium Binding Sites List in 3cq8
Calcium binding site 6 out of 6 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:70.8
occ:1.00
 OD2 A:ASP684 2.4 50.3 1.0
O A:HOH1310 2.5 39.4 1.0
OE1 A:GLU660 2.6 53.6 1.0
O A:HOH1311 3.4 47.3 1.0
CG A:ASP684 3.4 50.0 1.0
CD A:GLU660 3.7 52.9 1.0
OD1 A:ASP684 4.0 52.3 1.0
O A:MET683 4.2 45.2 1.0
CG A:GLU660 4.3 52.7 1.0
CB A:ASP684 4.4 46.8 1.0
CB A:GLU660 4.5 54.2 1.0
OE2 A:GLU660 4.6 52.3 1.0
CA A:ASP684 4.6 43.6 1.0
C A:MET683 4.7 44.7 1.0
N A:ASP684 4.9 44.5 1.0

Reference:

X.Zhong, L.C.Pedersen, T.A.Kunkel. Characterization of A Replicative Dna Polymerase Mutant with Reduced Fidelity and Increased Translesion Synthesis Capacity. Nucleic Acids Res. V. 36 3892 2008.
ISSN: ISSN 0305-1048
PubMed: 18503083
DOI: 10.1093/NAR/GKN312
Page generated: Sat Dec 12 04:07:53 2020

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