Atomistry » Sodium » PDB 5syu-5tde » 5tba
Atomistry »
  Sodium »
    PDB 5syu-5tde »
      5tba »

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

Go back to Sodium Binding Sites List in 5tba
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

Go back to Sodium Binding Sites List in 5tba
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

Go back to Sodium Binding Sites List in 5tba
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

Go back to Sodium Binding Sites List in 5tba
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

Last articles

Cl in 5QTW
Cl in 5QTY
Cl in 5QTX
Cl in 5QTV
Cl in 5QTT
Cl in 5QTU
Cl in 5QTQ
Cl in 5QTO
Cl in 5QTS
Cl in 5QTJ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy