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Sodium in PDB 5tb8: Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and MN2+., PDB code: 5tb8 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) 46.41 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.480, 81.400, 53.570, 90.00, 110.28, 90.00
R / Rfree (%) 18.2 / 23

Other elements in 5tb8:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+. also contains other interesting chemical elements:

Manganese (Mn) 6 atoms
Chlorine (Cl) 2 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 (-)3TC-Tp and MN2+. (pdb code 5tb8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+., PDB code: 5tb8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5tb8

Go back to Sodium Binding Sites List in 5tb8
Sodium binding site 1 out of 5 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:22.2
occ:1.00
 O A:HOH644 2.2 31.5 1.0
O A:HOH520 2.2 24.7 1.0
O A:HOH564 2.2 21.8 0.5
OD2 A:ASP130 2.3 36.4 1.0
OD1 A:ASP130 2.3 35.4 1.0
CG A:ASP130 2.6 36.9 1.0
OD1 A:ASN128 4.0 20.5 1.0
CB A:ASP130 4.2 34.2 1.0
O A:LYS127 4.4 19.5 1.0
CA A:ASN128 4.7 20.0 1.0
CG A:ASN128 4.8 18.1 1.0

Sodium binding site 2 out of 5 in 5tb8

Go back to Sodium Binding Sites List in 5tb8
Sodium binding site 2 out of 5 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:17.5
occ:1.00
 O A:HOH590 2.0 29.4 1.0
OD2 A:ASP145 2.2 16.6 1.0
ND1 A:HIS252 2.7 20.8 1.0
CG A:ASP145 3.2 17.9 1.0
CE1 A:HIS252 3.4 20.3 1.0
OD1 A:ASP145 3.6 18.2 1.0
CG A:HIS252 3.8 18.6 1.0
N A:HIS252 3.8 17.1 1.0
CB A:HIS252 4.2 17.4 1.0
OE2 A:GLU249 4.3 54.5 1.0
CA A:PRO251 4.4 18.1 1.0
O A:TYR250 4.5 20.1 1.0
CB A:ASP145 4.6 16.8 1.0
NE2 A:GLN240 4.6 20.7 1.0
C A:PRO251 4.6 17.1 1.0
NE2 A:HIS252 4.6 19.2 1.0
CA A:HIS252 4.7 16.1 1.0
CD1 A:TYR142 4.7 17.7 1.0
CE1 A:TYR142 4.8 18.3 1.0
CD2 A:HIS252 4.9 19.1 1.0
CD A:GLU249 4.9 53.0 1.0
O A:HOH566 4.9 27.4 1.0

Sodium binding site 3 out of 5 in 5tb8

Go back to Sodium Binding Sites List in 5tb8
Sodium binding site 3 out of 5 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:23.8
occ:1.00
 O D:HOH112 2.3 19.1 1.0
O A:VAL65 2.4 22.2 1.0
O A:LEU62 2.4 24.8 1.0
O A:LYS60 2.5 24.5 1.0
OP1 D:DC3 2.5 23.5 1.0
C A:VAL65 3.5 21.5 1.0
C A:LEU62 3.5 23.0 1.0
P D:DC3 3.5 20.4 1.0
C A:LYS60 3.6 25.9 1.0
OP2 D:DC3 3.7 19.6 1.0
N A:VAL65 3.8 19.8 1.0
N A:GLY64 4.0 21.2 1.0
CA A:PRO63 4.1 23.5 1.0
CA A:VAL65 4.2 20.3 1.0
N A:LEU62 4.2 23.8 1.0
N A:PRO63 4.2 23.6 1.0
CA A:LYS60 4.3 25.9 1.0
C A:LYS61 4.3 26.5 1.0
C A:PRO63 4.5 22.4 1.0
CA A:LEU62 4.5 24.0 1.0
O3' D:DT2 4.5 22.4 1.0
N A:GLY66 4.5 20.2 1.0
CG A:LYS60 4.5 33.8 1.0
CB A:VAL65 4.5 20.5 1.0
N A:LYS61 4.6 25.9 1.0
O A:LYS61 4.6 22.8 1.0
CA A:GLY66 4.7 20.9 1.0
C A:GLY64 4.7 19.4 1.0
O5' D:DC3 4.8 20.4 1.0
CA A:LYS61 4.8 28.1 1.0
CA A:GLY64 4.9 21.4 1.0

Sodium binding site 4 out of 5 in 5tb8

Go back to Sodium Binding Sites List in 5tb8
Sodium binding site 4 out of 5 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:15.5
occ:1.00
 O A:THR101 2.2 12.5 1.0
OP1 P:DG9 2.4 17.7 1.0
O A:VAL103 2.4 11.6 1.0
O A:ILE106 2.5 11.1 1.0
O A:HOH650 2.5 24.9 1.0
O P:HOH106 2.6 15.1 1.0
C A:THR101 3.2 13.5 1.0
C A:VAL103 3.4 14.3 1.0
P P:DG9 3.4 18.0 1.0
C A:ILE106 3.6 13.2 1.0
OP2 P:DG9 3.7 18.3 1.0
N A:ILE106 3.9 13.8 1.0
CA A:THR101 3.9 12.9 1.0
CA A:SER104 4.0 14.8 1.0
N A:VAL103 4.0 15.2 1.0
N A:GLY105 4.0 13.6 1.0
N A:SER104 4.0 13.7 1.0
C A:ARG102 4.1 16.4 1.0
O A:HOH605 4.2 42.6 1.0
N A:ARG102 4.2 14.3 1.0
CA A:ILE106 4.3 13.5 1.0
CA A:VAL103 4.3 14.5 1.0
C A:SER104 4.4 13.5 1.0
O3' P:DC8 4.4 18.3 1.0
O A:ARG102 4.4 18.5 1.0
CB A:THR101 4.5 13.5 1.0
CA A:ARG102 4.5 15.3 1.0
N A:GLY107 4.6 12.9 1.0
O5' P:DG9 4.6 17.4 1.0
CB A:ILE106 4.7 14.4 1.0
C A:GLY105 4.8 14.9 1.0
CA A:GLY107 4.8 12.9 1.0
O A:LEU100 4.9 11.0 1.0
CA A:GLY105 5.0 14.1 1.0
O A:HOH501 5.0 27.9 1.0

Sodium binding site 5 out of 5 in 5tb8

Go back to Sodium Binding Sites List in 5tb8
Sodium binding site 5 out of 5 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.


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 in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:11.5
occ:1.00
 OXT A:ACT416 2.1 32.6 1.0
O A:HOH542 2.2 15.7 1.0
OD2 A:ASP91 2.3 31.1 1.0
O A:HOH613 2.4 31.0 1.0
CG A:ASP91 3.3 27.9 1.0
C A:ACT416 3.3 38.5 1.0
OD1 A:ASP91 3.5 28.3 1.0
CH3 A:ACT416 4.1 37.0 1.0
OG A:SER94 4.1 20.7 1.0
O A:HOH582 4.2 23.5 1.0
O A:ACT416 4.3 39.5 1.0
CB A:THR93 4.5 20.7 1.0
CB A:ASP91 4.6 25.1 1.0
CG2 A:THR93 4.8 21.4 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 00:05:58 2024

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