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Sodium in PDB 5tbc: Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide., PDB code: 5tbc was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.76 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.330, 79.530, 55.330, 90.00, 107.39, 90.00
R / Rfree (%) 22.8 / 27.9

Other elements in 5tbc:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. (pdb code 5tbc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide., PDB code: 5tbc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5tbc

Go back to Sodium Binding Sites List in 5tbc
Sodium binding site 1 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:40.9
occ:1.00
 O A:HOH521 2.2 45.6 1.0
OD1 A:ASP190 2.2 37.0 1.0
O2B A:1RZ401 2.2 49.5 1.0
O3G A:1RZ401 2.2 51.8 1.0
OD2 A:ASP190 2.3 36.1 1.0
O1A A:42E408 2.5 44.6 1.0
CG A:ASP190 2.6 33.0 1.0
PB A:1RZ401 3.6 52.6 1.0
PG A:1RZ401 3.7 55.6 1.0
PA A:42E408 3.8 40.0 1.0
O3B A:1RZ401 4.1 53.7 1.0
CB A:ASP190 4.1 29.2 1.0
O2A A:42E408 4.2 40.2 1.0
O1A A:1RZ401 4.2 47.4 1.0
O1G A:1RZ401 4.3 55.1 1.0
N A:ASP190 4.4 24.4 1.0
O5' A:42E408 4.5 40.8 1.0
O1B A:1RZ401 4.5 54.0 1.0
C5' A:42E408 4.6 39.3 1.0
OD1 A:ASP192 4.8 39.2 1.0
CA A:ASP190 4.8 26.3 1.0
O3' P:DC10 4.8 31.7 1.0
O3A A:1RZ401 4.8 51.6 1.0
O2C A:1RZ401 4.8 55.3 1.0
O A:ASP190 4.8 22.6 1.0
N A:GLY189 4.9 26.1 1.0
C A:GLY189 5.0 25.1 1.0
CA A:GLY189 5.0 25.4 1.0

Sodium binding site 2 out of 6 in 5tbc

Go back to Sodium Binding Sites List in 5tbc
Sodium binding site 2 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:13.8
occ:1.00
 O A:THR101 2.3 15.4 1.0
O A:HOH572 2.3 17.6 1.0
O A:ILE106 2.3 12.2 1.0
O A:HOH561 2.3 17.9 1.0
OP1 P:DG9 2.3 13.7 1.0
O A:VAL103 2.3 12.8 1.0
NA A:NA406 3.2 21.1 1.0
C A:THR101 3.2 13.9 1.0
C A:ILE106 3.3 11.9 1.0
C A:VAL103 3.3 12.8 1.0
P P:DG9 3.5 14.0 1.0
N A:ILE106 3.7 11.5 1.0
OP2 P:DG9 3.8 14.0 1.0
CA A:THR101 3.8 13.8 1.0
N A:GLY105 4.0 12.4 1.0
CA A:SER104 4.0 12.9 1.0
N A:SER104 4.0 13.1 1.0
CA A:ILE106 4.0 11.7 1.0
N A:VAL103 4.1 13.2 1.0
N A:GLY107 4.3 12.0 1.0
C A:ARG102 4.3 14.6 1.0
N A:ARG102 4.3 14.9 1.0
C A:SER104 4.3 12.4 1.0
CA A:VAL103 4.4 13.0 1.0
CB A:THR101 4.4 13.6 1.0
O3' P:DC8 4.4 13.5 1.0
CB A:ILE106 4.5 11.4 1.0
O P:HOH118 4.6 37.9 1.0
CA A:GLY107 4.6 11.8 1.0
C A:GLY105 4.6 12.2 1.0
CA A:ARG102 4.6 14.9 1.0
O5' P:DG9 4.6 14.2 1.0
O A:ARG102 4.7 15.6 1.0
O A:HOH669 4.8 26.9 1.0
O A:HOH611 4.8 25.4 1.0
O A:LEU100 4.8 13.1 1.0
CA A:GLY105 4.9 12.0 1.0
O A:HOH509 4.9 18.6 1.0
O A:HOH659 5.0 26.1 1.0

Sodium binding site 3 out of 6 in 5tbc

Go back to Sodium Binding Sites List in 5tbc
Sodium binding site 3 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:26.7
occ:1.00
 O A:LEU62 2.2 28.3 1.0
O A:VAL65 2.2 25.5 1.0
O A:HOH637 2.2 30.5 1.0
O A:HOH618 2.3 26.1 1.0
O A:LYS60 2.3 29.0 1.0
OP1 D:DC3 2.3 24.9 1.0
C A:LEU62 3.3 28.4 1.0
C A:VAL65 3.3 23.9 1.0
C A:LYS60 3.5 29.0 1.0
P D:DC3 3.5 23.8 1.0
N A:VAL65 3.6 22.6 1.0
OP2 D:DC3 3.9 20.7 1.0
N A:GLY64 3.9 26.3 1.0
CA A:PRO63 3.9 28.1 1.0
CA A:VAL65 3.9 23.1 1.0
N A:PRO63 4.0 28.7 1.0
N A:LEU62 4.1 28.2 1.0
C A:LYS61 4.3 29.3 1.0
CA A:LYS60 4.3 28.1 1.0
C A:PRO63 4.3 27.1 1.0
CA A:LEU62 4.3 28.9 1.0
CB A:VAL65 4.3 22.4 1.0
N A:GLY66 4.4 23.2 1.0
O3' D:DT2 4.4 20.9 1.0
N A:LYS61 4.5 29.1 1.0
CG A:LYS60 4.6 31.5 1.0
O A:LYS61 4.6 29.0 1.0
C A:GLY64 4.6 24.1 1.0
CA A:LYS61 4.8 30.0 1.0
CA A:GLY66 4.8 23.7 1.0
O5' D:DC3 4.8 23.5 1.0
CA A:GLY64 4.8 24.7 1.0
O A:ALA59 4.9 26.0 1.0

Sodium binding site 4 out of 6 in 5tbc

Go back to Sodium Binding Sites List in 5tbc
Sodium binding site 4 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:20.9
occ:1.00
 O A:HOH623 2.2 24.7 1.0
O A:HOH639 2.3 22.8 1.0
O A:SER30 2.3 16.2 1.0
C A:SER30 3.5 16.3 1.0
O A:HOH606 4.1 20.0 1.0
CA A:SER30 4.2 16.2 1.0
O A:GLN31 4.3 16.2 1.0
C A:GLN31 4.5 16.1 1.0
N A:GLN31 4.5 16.4 1.0
CB A:SER30 4.6 17.5 1.0
CB A:GLN31 4.7 18.7 1.0
CA A:GLN31 4.8 16.7 1.0

Sodium binding site 5 out of 6 in 5tbc

Go back to Sodium Binding Sites List in 5tbc
Sodium binding site 5 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:21.1
occ:1.00
 O A:HOH669 2.3 26.9 1.0
O A:HOH659 2.3 26.1 1.0
O A:HOH561 2.3 17.9 1.0
O A:HOH611 2.3 25.4 1.0
O A:HOH572 2.3 17.6 1.0
O A:THR101 2.3 15.4 1.0
NA A:NA403 3.2 13.8 1.0
C A:THR101 3.3 13.9 1.0
CA A:ARG102 4.0 14.9 1.0
N A:ARG102 4.0 14.9 1.0
O P:HOH126 4.1 37.1 1.0
O A:HOH509 4.3 18.6 1.0
OG1 A:THR101 4.4 14.4 1.0
CB A:THR101 4.4 13.6 1.0
C A:ARG102 4.4 14.6 1.0
CA A:THR101 4.4 13.8 1.0
O P:HOH118 4.5 37.9 1.0
O A:HOH667 4.6 32.0 1.0
OP1 P:DG9 4.6 13.7 1.0
NZ A:LYS27 4.6 24.5 1.0
O A:ARG102 4.7 15.6 1.0
OP2 P:DG9 4.8 14.0 1.0
O A:ILE106 4.8 12.2 1.0
O A:VAL103 4.9 12.8 1.0
O P:HOH104 4.9 22.4 1.0

Sodium binding site 6 out of 6 in 5tbc

Go back to Sodium Binding Sites List in 5tbc
Sodium binding site 6 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na101

b:35.4
occ:1.00
 O T:HOH238 2.2 37.5 1.0
OP2 T:DC10 2.3 25.2 1.0
O5' T:DC10 3.3 22.2 1.0
P T:DC10 3.4 23.0 1.0
C2' T:DG9 3.4 23.1 1.0
O T:HOH210 3.6 26.5 1.0
C3' T:DG9 3.9 23.7 1.0
C6 T:DC10 4.1 17.8 1.0
O3' T:DG9 4.1 22.2 1.0
O A:HOH525 4.4 34.1 1.0
C5 T:DC10 4.6 16.8 1.0
OP1 T:DC10 4.7 23.8 1.0
C5' T:DC10 4.7 21.6 1.0
C2' T:DC10 4.7 19.7 1.0
O4' T:DC10 4.8 19.9 1.0
C1' T:DG9 4.8 21.9 1.0
O T:HOH214 4.9 27.1 1.0
C3' T:DC10 5.0 20.8 1.0

Reference:

A.J.Reed, R.Vyas, A.T.Raper, Z.Suo. Structural Insights Into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed By A Dna Polymerase. J. Am. Chem. Soc. V. 139 465 2017.
ISSN: ESSN 1520-5126
PubMed: 27959534
DOI: 10.1021/JACS.6B11258
Page generated: Tue Oct 8 00:06:45 2024

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