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Calcium in PDB 4x0p: Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog

Enzymatic activity of Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog, PDB code: 4x0p was solved by K.E.Zahn, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 3.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.921, 136.971, 247.991, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 30.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog (pdb code 4x0p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog, PDB code: 4x0p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4x0p

Go back to Calcium Binding Sites List in 4x0p
Calcium binding site 1 out of 4 in the Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog


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 Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2603

b:0.7
occ:1.00
 O1G A:DDS2604 1.8 0.9 1.0
O1B A:DDS2604 2.1 1.0 1.0
O1A A:DDS2604 2.2 0.9 1.0
OD1 A:ASP2540 2.2 0.6 1.0
OD2 A:ASP2330 2.5 0.0 1.0
OD1 A:ASP2330 2.5 0.8 1.0
CG A:ASP2330 2.8 0.1 1.0
O A:TYR2331 3.0 0.6 1.0
PB A:DDS2604 3.1 0.9 1.0
PG A:DDS2604 3.1 0.5 1.0
PA A:DDS2604 3.3 0.4 1.0
CG A:ASP2540 3.3 0.9 1.0
O3A A:DDS2604 3.3 0.8 1.0
O3B A:DDS2604 3.5 0.3 1.0
OD2 A:ASP2540 3.6 0.8 1.0
O2G A:DDS2604 3.7 0.6 1.0
O5' A:DDS2604 4.1 0.2 1.0
C A:TYR2331 4.1 0.1 1.0
C5' A:DDS2604 4.3 0.4 1.0
O3G A:DDS2604 4.3 0.9 1.0
CB A:ASP2330 4.3 0.2 1.0
N A:TYR2331 4.4 0.2 1.0
O2B A:DDS2604 4.5 0.8 1.0
O2A A:DDS2604 4.5 0.5 1.0
CB A:ASP2540 4.6 0.7 1.0
O3' F:DC13 4.8 0.7 1.0
CA A:TYR2331 4.8 0.2 1.0
OE1 A:GLU2541 4.8 0.3 1.0
N A:GLN2333 4.9 0.4 1.0
C A:ASP2330 4.9 0.9 1.0
CA A:ASP2330 4.9 0.8 1.0

Calcium binding site 2 out of 4 in 4x0p

Go back to Calcium Binding Sites List in 4x0p
Calcium binding site 2 out of 4 in the Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog


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 Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2603

b:0.6
occ:1.00
 OD1 B:ASP2540 1.8 0.8 1.0
O1B B:DDS2604 2.0 0.2 1.0
O B:TYR2331 2.0 0.8 1.0
O1G B:DDS2604 2.2 0.3 1.0
OD1 B:ASP2330 2.3 0.3 1.0
O1A B:DDS2604 2.6 0.3 1.0
CG B:ASP2330 3.0 0.9 1.0
OD2 B:ASP2330 3.0 0.7 1.0
CG B:ASP2540 3.1 0.1 1.0
C B:TYR2331 3.2 0.2 1.0
PB B:DDS2604 3.2 0.5 1.0
PG B:DDS2604 3.4 0.5 1.0
O3B B:DDS2604 3.6 0.4 1.0
N B:GLN2333 3.6 0.1 1.0
PA B:DDS2604 3.7 0.0 1.0
OD2 B:ASP2540 3.8 0.0 1.0
N B:TYR2331 3.8 0.1 1.0
O3A B:DDS2604 3.9 0.0 1.0
CA B:TYR2331 4.0 0.3 1.0
CA B:SER2332 4.1 0.4 1.0
CB B:ASP2540 4.1 0.6 1.0
N B:SER2332 4.1 0.1 1.0
O5' B:DDS2604 4.2 0.2 1.0
C5' B:DDS2604 4.2 0.6 1.0
O2G B:DDS2604 4.2 0.3 1.0
C B:SER2332 4.3 0.2 1.0
CB B:ASP2330 4.4 0.3 1.0
CA B:GLN2333 4.4 0.4 1.0
CB B:TYR2331 4.4 0.8 1.0
C B:ASP2330 4.5 0.0 1.0
O2B B:DDS2604 4.5 0.8 1.0
O3G B:DDS2604 4.6 0.7 1.0
CA B:ASP2330 4.8 0.8 1.0
N B:LEU2334 5.0 0.1 1.0

Calcium binding site 3 out of 4 in 4x0p

Go back to Calcium Binding Sites List in 4x0p
Calcium binding site 3 out of 4 in the Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog


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 Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2603

b:0.4
occ:1.00
 OD1 C:ASP2540 1.7 0.4 1.0
O1B C:DDS2604 1.8 0.8 1.0
O1G C:DDS2604 2.0 0.9 1.0
O C:TYR2331 2.2 0.7 1.0
OD1 C:ASP2330 2.3 0.0 1.0
CG C:ASP2540 2.9 0.8 1.0
PB C:DDS2604 3.0 0.8 1.0
CG C:ASP2330 3.0 0.7 1.0
OD2 C:ASP2330 3.1 0.3 1.0
O1A C:DDS2604 3.1 0.2 1.0
PG C:DDS2604 3.2 0.0 1.0
O3B C:DDS2604 3.3 0.6 1.0
C C:TYR2331 3.3 0.3 1.0
OD2 C:ASP2540 3.6 0.8 1.0
N C:TYR2331 3.7 0.8 1.0
CA C:TYR2331 3.9 0.6 1.0
CB C:ASP2540 4.0 0.8 1.0
O2B C:DDS2604 4.1 0.8 1.0
O3A C:DDS2604 4.1 0.9 1.0
CB C:TYR2331 4.2 0.3 1.0
PA C:DDS2604 4.2 0.8 1.0
O2G C:DDS2604 4.2 0.6 1.0
O3G C:DDS2604 4.3 0.7 1.0
N C:GLN2333 4.3 0.7 1.0
C5' C:DDS2604 4.4 0.7 1.0
CB C:ASP2330 4.4 0.2 1.0
N C:SER2332 4.4 0.2 1.0
C C:ASP2330 4.5 0.2 1.0
CA C:SER2332 4.7 0.9 1.0
O5' C:DDS2604 4.7 0.2 1.0
CA C:ASP2330 4.8 0.6 1.0
C C:SER2332 4.9 0.6 1.0

Calcium binding site 4 out of 4 in 4x0p

Go back to Calcium Binding Sites List in 4x0p
Calcium binding site 4 out of 4 in the Ternary Complex of Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog


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 Human Dna Polymerase Theta C-Terminal Domain Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2603

b:0.6
occ:1.00
 O1B D:DDS2604 1.8 0.6 1.0
O1A D:DDS2604 2.1 1.0 1.0
OD1 D:ASP2330 2.1 0.3 1.0
OD1 D:ASP2540 2.2 0.6 1.0
OD2 D:ASP2330 2.4 0.0 1.0
O1G D:DDS2604 2.5 0.8 1.0
CG D:ASP2330 2.6 0.1 1.0
O D:TYR2331 2.9 0.5 1.0
PB D:DDS2604 3.1 0.3 1.0
CG D:ASP2540 3.2 0.3 1.0
PA D:DDS2604 3.3 0.7 1.0
PG D:DDS2604 3.4 0.3 1.0
O3G D:DDS2604 3.4 0.1 1.0
O3A D:DDS2604 3.5 0.1 1.0
OD2 D:ASP2540 3.6 0.7 1.0
O3B D:DDS2604 3.7 0.2 1.0
C D:TYR2331 4.0 0.5 1.0
CB D:ASP2330 4.1 0.7 1.0
O5' D:DDS2604 4.1 0.4 1.0
C5' D:DDS2604 4.2 0.1 1.0
N D:TYR2331 4.2 0.2 1.0
O2B D:DDS2604 4.4 1.0 1.0
CB D:ASP2540 4.5 0.3 1.0
O2A D:DDS2604 4.6 1.0 1.0
O3' L:DC13 4.6 0.2 1.0
CA D:TYR2331 4.7 0.6 1.0
C D:ASP2330 4.7 0.3 1.0
CA D:ASP2330 4.8 0.5 1.0
N D:GLN2333 4.8 0.8 1.0
O2G D:DDS2604 4.9 0.5 1.0
N D:SER2332 5.0 0.1 1.0

Reference:

K.E.Zahn, A.M.Averil, P.Aller, R.D.Wood, S.Doublie. Human Dna Polymerase Theta Grasps the Primer Terminus to Mediate Dna Repair Nat.Struct.Mol.Biol. 2015.
ISSN: ESSN 1545-9985
DOI: 10.1038/NSMB.2993
Page generated: Sun Jul 14 14:26:54 2024

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