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Sodium in PDB 5tb9: Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+., PDB code: 5tb9 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) 46.87 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.190, 82.310, 54.280, 90.00, 110.97, 90.00
R / Rfree (%) 20.5 / 26.7

Other elements in 5tb9:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. also contains other interesting chemical elements:

Fluorine (F) 1 atom
Manganese (Mn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. (pdb code 5tb9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+., PDB code: 5tb9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5tb9

Go back to Sodium Binding Sites List in 5tb9
Sodium binding site 1 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


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 in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:17.1
occ:1.00
 O A:HOH544 2.1 47.8 1.0
OD2 A:ASP130 2.5 48.6 1.0
OD1 A:ASP130 2.6 43.8 1.0
CG A:ASP130 2.9 46.5 1.0
OD1 A:ASN128 4.3 39.5 1.0
O A:LYS127 4.4 36.2 1.0
CB A:ASP130 4.4 45.5 1.0
CA A:ASN128 4.5 39.3 1.0
CG A:ASN128 4.8 40.4 1.0
CB A:ASN128 4.9 39.9 1.0

Sodium binding site 2 out of 4 in 5tb9

Go back to Sodium Binding Sites List in 5tb9
Sodium binding site 2 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


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 in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:28.7
occ:1.00
 O A:HOH504 2.2 28.9 1.0
OD2 A:ASP145 2.2 26.2 1.0
ND1 A:HIS252 2.9 30.9 1.0
CG A:ASP145 3.3 26.4 1.0
CE1 A:HIS252 3.6 30.5 1.0
CG A:HIS252 3.8 29.3 1.0
CD1 A:TYR142 3.8 25.4 1.0
CE1 A:TYR142 3.9 25.4 1.0
OD1 A:ASP145 4.0 27.0 1.0
CB A:HIS252 4.1 27.1 1.0
N A:HIS252 4.3 26.4 1.0
CB A:ASP145 4.4 26.1 1.0
NE2 A:HIS252 4.6 30.5 1.0
CD2 A:HIS252 4.7 30.0 1.0
CA A:HIS252 4.9 26.3 1.0

Sodium binding site 3 out of 4 in 5tb9

Go back to Sodium Binding Sites List in 5tb9
Sodium binding site 3 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


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 in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:38.5
occ:1.00
 O A:LYS60 2.4 33.2 1.0
OP1 D:DC3 2.6 34.8 1.0
O A:VAL65 2.7 27.1 1.0
O A:LEU62 3.0 30.2 1.0
OP2 D:DC3 3.5 35.9 1.0
P D:DC3 3.6 34.8 1.0
C A:LYS60 3.6 34.8 1.0
C A:VAL65 3.8 27.8 1.0
C A:LEU62 3.9 31.4 1.0
N A:VAL65 4.1 27.9 1.0
N A:GLY64 4.2 28.8 1.0
C A:LYS61 4.2 36.0 1.0
O A:LYS61 4.3 33.9 1.0
CA A:PRO63 4.3 29.2 1.0
N A:PRO63 4.4 29.4 1.0
CA A:LYS60 4.5 35.4 1.0
N A:LEU62 4.5 35.6 1.0
CG A:LYS60 4.5 35.4 1.0
CA A:VAL65 4.5 27.6 1.0
N A:LYS61 4.5 35.7 1.0
CA A:LYS61 4.6 36.8 1.0
O3' D:DT2 4.6 33.5 1.0
C A:PRO63 4.7 29.3 1.0
O5' D:DC3 4.7 35.0 1.0
N A:GLY66 4.8 27.2 1.0
CA A:LEU62 4.8 33.7 1.0
CB A:VAL65 4.9 28.0 1.0

Sodium binding site 4 out of 4 in 5tb9

Go back to Sodium Binding Sites List in 5tb9
Sodium binding site 4 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


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 in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:20.0
occ:1.00
 OP1 P:DG9 2.1 25.2 1.0
O A:THR101 2.3 21.8 1.0
O P:HOH203 2.3 16.1 1.0
O A:ILE106 2.4 19.1 1.0
O A:VAL103 2.5 20.9 1.0
O P:HOH205 2.6 35.8 1.0
P P:DG9 3.2 24.8 1.0
C A:THR101 3.3 20.5 1.0
C A:ILE106 3.4 19.5 1.0
OP2 P:DG9 3.4 23.8 1.0
C A:VAL103 3.5 21.0 1.0
N A:ILE106 3.9 20.3 1.0
CA A:THR101 4.0 19.5 1.0
CA A:SER104 4.1 21.4 1.0
N A:GLY105 4.1 20.8 1.0
O3' P:DC8 4.2 25.3 1.0
CA A:ILE106 4.2 19.9 1.0
N A:SER104 4.2 21.3 1.0
N A:VAL103 4.2 21.8 1.0
N A:GLY107 4.4 18.7 1.0
N A:ARG102 4.4 21.1 1.0
O5' P:DG9 4.4 26.8 1.0
C A:ARG102 4.4 22.5 1.0
C A:SER104 4.5 21.3 1.0
CA A:VAL103 4.6 21.2 1.0
CB A:THR101 4.6 18.8 1.0
CA A:ARG102 4.6 22.4 1.0
CA A:GLY107 4.6 18.5 1.0
CB A:ILE106 4.6 20.1 1.0
C A:GLY105 4.8 20.9 1.0
O A:LEU100 4.9 18.2 1.0
O A:ARG102 5.0 23.4 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 00:06:03 2024

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