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Sodium in PDB 5tba: Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi.

Enzymatic activity of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi.

All present enzymatic activity of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi.:
2.7.7.7;

Protein crystallography data

The structure of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi., PDB code: 5tba 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) 25.18 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.697, 79.325, 54.947, 90.00, 107.03, 90.00
R / Rfree (%) 20.5 / 27.3

Sodium Binding Sites:

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

Sodium binding site 1 out of 5 in 5tba

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Sodium binding site 1 out of 5 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi.


Mono view


Stereo pair view

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

b:42.1
occ:1.00
 O2A A:42E407 2.3 70.3 1.0
O21 A:PPV401 2.4 81.5 1.0
OD1 A:ASP190 2.4 35.4 1.0
OD2 A:ASP192 2.8 51.4 1.0
O11 A:PPV401 3.1 86.7 1.0
P1 A:PPV401 3.1 85.7 1.0
O32 A:PPV401 3.3 72.8 1.0
OPP A:PPV401 3.4 77.8 1.0
CG A:ASP190 3.4 33.6 1.0
PA A:42E407 3.4 67.0 1.0
OD2 A:ASP190 3.7 39.8 1.0
C5' A:42E407 3.7 64.6 1.0
NA A:NA406 3.8 59.1 1.0
O5' A:42E407 3.8 64.9 1.0
CG A:ASP192 4.0 43.4 1.0
O1A A:42E407 4.0 59.4 1.0
P2 A:PPV401 4.0 74.8 1.0
O31 A:PPV401 4.6 74.9 1.0
O3' P:DC10 4.7 39.9 1.0
CB A:ASP192 4.8 36.5 1.0
N A:ASP190 4.8 28.5 1.0
CB A:ASP190 4.8 31.1 1.0
OD1 A:ASP192 4.9 52.2 1.0
O A:ASP190 4.9 29.3 1.0
O A:HOH526 4.9 29.6 1.0
O22 A:PPV401 4.9 66.5 1.0
C A:ASP190 5.0 29.4 1.0
CA A:GLY179 5.0 36.0 1.0

Sodium binding site 2 out of 5 in 5tba

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Sodium binding site 2 out of 5 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi.


Mono view


Stereo pair view

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

b:19.8
occ:1.00
 O A:THR101 2.2 18.7 1.0
O A:ILE106 2.2 15.5 1.0
OP1 P:DG9 2.3 17.5 1.0
O P:HOH103 2.3 16.9 1.0
O A:HOH538 2.5 17.8 1.0
O A:VAL103 2.5 19.4 1.0
C A:THR101 3.2 18.6 1.0
C A:ILE106 3.3 16.1 1.0
P P:DG9 3.3 16.8 1.0
O A:HOH519 3.3 17.8 1.0
C A:VAL103 3.5 18.3 1.0
OP2 P:DG9 3.6 17.5 1.0
N A:ILE106 3.7 17.0 1.0
CA A:THR101 3.8 18.4 1.0
N A:GLY105 3.9 17.3 1.0
CA A:SER104 3.9 17.7 1.0
CA A:ILE106 4.0 16.4 1.0
N A:SER104 4.1 17.9 1.0
N A:GLY107 4.2 16.7 1.0
N A:VAL103 4.3 17.6 1.0
C A:SER104 4.3 17.4 1.0
CB A:THR101 4.3 17.8 1.0
O3' P:DC8 4.3 18.4 1.0
N A:ARG102 4.3 19.1 1.0
C A:ARG102 4.4 19.0 1.0
CB A:ILE106 4.4 16.6 1.0
O5' P:DG9 4.5 18.3 1.0
CA A:GLY107 4.5 17.4 1.0
C A:GLY105 4.5 16.7 1.0
CA A:VAL103 4.5 18.0 1.0
CA A:ARG102 4.6 18.0 1.0
CA A:GLY105 4.8 16.8 1.0
O A:ARG102 4.8 20.6 1.0
O A:LEU100 4.9 20.6 1.0

Sodium binding site 3 out of 5 in 5tba

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Sodium binding site 3 out of 5 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi.


Mono view


Stereo pair view

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

b:38.5
occ:1.00
 O D:HOH101 2.3 24.1 1.0
O A:LYS60 2.5 36.8 1.0
O A:VAL65 2.5 24.8 1.0
O A:LEU62 2.6 32.2 1.0
OP1 D:DC3 2.9 27.2 1.0
C A:LEU62 3.5 30.8 1.0
C A:LYS60 3.6 33.5 1.0
OP2 D:DC3 3.7 23.8 1.0
C A:VAL65 3.7 25.8 1.0
P D:DC3 3.8 27.7 1.0
C A:LYS61 3.9 32.4 1.0
N A:LEU62 3.9 30.5 1.0
CA A:PRO63 4.1 31.0 1.0
O A:LYS61 4.1 31.4 1.0
N A:PRO63 4.1 30.6 1.0
N A:VAL65 4.2 24.2 1.0
CA A:LYS61 4.4 34.9 1.0
CA A:LEU62 4.4 29.9 1.0
N A:LYS61 4.4 33.5 1.0
CA A:VAL65 4.4 24.5 1.0
N A:GLY64 4.5 29.1 1.0
CA A:LYS60 4.5 33.1 1.0
CG A:LYS60 4.6 36.9 1.0
CB A:VAL65 4.7 24.6 1.0
N A:GLY66 4.7 24.7 1.0
C A:PRO63 4.7 30.1 1.0
O3' D:DT2 4.8 26.3 1.0
CA A:GLY66 5.0 24.0 1.0

Sodium binding site 4 out of 5 in 5tba

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Sodium binding site 4 out of 5 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi.


Mono view


Stereo pair view

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

b:31.4
occ:1.00
 O A:HOH516 2.2 22.3 1.0
O A:SER30 2.4 17.2 1.0
C A:SER30 3.6 17.4 1.0
O A:GLN31 4.3 15.9 1.0
CA A:SER30 4.3 17.1 1.0
C A:GLN31 4.5 17.1 1.0
CB A:GLN31 4.6 18.4 1.0
N A:GLN31 4.6 16.9 1.0
CB A:SER30 4.7 18.2 1.0
CA A:GLN31 4.8 17.5 1.0

Sodium binding site 5 out of 5 in 5tba

Go back to Sodium Binding Sites List in 5tba
Sodium binding site 5 out of 5 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC and Ppi.


Mono view


Stereo pair view

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

b:59.1
occ:1.00
 O21 A:PPV401 2.3 81.5 1.0
O1A A:42E407 2.8 59.4 1.0
P1 A:PPV401 3.7 85.7 1.0
NA A:NA402 3.8 42.1 1.0
PA A:42E407 3.8 67.0 1.0
O2A A:42E407 3.8 70.3 1.0
OD1 A:ASP190 4.0 35.4 1.0
O32 A:PPV401 4.0 72.8 1.0
O31 A:PPV401 4.1 74.9 1.0
CA A:GLY189 4.3 28.2 1.0
CG A:ASP190 4.4 33.6 1.0
OD2 A:ASP190 4.5 39.8 1.0
OPP A:PPV401 4.6 77.8 1.0
C A:GLY189 4.6 29.1 1.0
O11 A:PPV401 4.7 86.7 1.0
O12 A:PPV401 4.7 64.2 1.0
O5' A:42E407 4.7 64.9 1.0
P2 A:PPV401 4.7 74.8 1.0
N A:ASP190 4.8 28.5 1.0
N A:GLY189 4.9 27.2 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 00:06:29 2024

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