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

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

All present enzymatic activity of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc 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 (-)Ftc and Ppi., PDB code: 5tbb 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) 44.52 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.170, 79.330, 55.460, 90.00, 107.20, 90.00
R / Rfree (%) 21.3 / 26.9

Other elements in 5tbb:

The structure of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi. also contains other interesting chemical elements:

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

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 5tbb

Go back to Sodium Binding Sites List in 5tbb
Sodium binding site 1 out of 4 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc 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 (-)Ftc and Ppi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:16.9
occ:1.00
 O A:THR101 2.2 20.9 1.0
OP1 P:DG9 2.3 18.8 1.0
O P:HOH201 2.4 16.6 1.0
O A:ILE106 2.4 14.9 1.0
O A:VAL103 2.5 20.5 1.0
O A:ACT405 2.7 37.8 1.0
C A:ILE106 3.3 16.6 1.0
P P:DG9 3.3 21.0 1.0
C A:THR101 3.3 20.1 1.0
C A:VAL103 3.4 20.0 1.0
N A:ILE106 3.5 19.3 1.0
OP2 P:DG9 3.5 23.9 1.0
O A:HOH506 3.6 27.8 1.0
C A:ACT405 3.7 49.5 1.0
N A:GLY105 3.8 18.7 1.0
CA A:ILE106 3.9 16.8 1.0
CA A:SER104 3.9 18.6 1.0
CA A:THR101 4.0 17.8 1.0
N A:SER104 4.1 20.1 1.0
N A:GLY107 4.2 17.8 1.0
N A:VAL103 4.2 21.2 1.0
O3' P:DC8 4.3 21.2 1.0
C A:SER104 4.3 18.6 1.0
CB A:ILE106 4.3 16.4 1.0
C A:ARG102 4.4 20.9 1.0
N A:ARG102 4.4 20.8 1.0
C A:GLY105 4.4 18.3 1.0
CB A:THR101 4.4 17.5 1.0
CH3 A:ACT405 4.5 50.6 1.0
CA A:VAL103 4.5 20.4 1.0
O5' P:DG9 4.5 21.3 1.0
CA A:GLY107 4.5 20.7 1.0
OXT A:ACT405 4.6 55.1 1.0
CA A:ARG102 4.7 19.7 1.0
CA A:GLY105 4.7 18.9 1.0
O A:ARG102 4.8 20.9 1.0
O A:LEU100 5.0 18.4 1.0

Sodium binding site 2 out of 4 in 5tbb

Go back to Sodium Binding Sites List in 5tbb
Sodium binding site 2 out of 4 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc 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 (-)Ftc and Ppi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:38.5
occ:1.00
 O A:LYS60 2.4 39.5 1.0
O A:VAL65 2.4 27.1 1.0
O A:LEU62 2.6 30.3 1.0
OP1 D:DC3 2.9 29.5 1.0
C A:LEU62 3.5 29.8 1.0
C A:LYS60 3.5 34.9 1.0
C A:VAL65 3.6 27.4 1.0
C A:LYS61 3.9 32.0 1.0
P D:DC3 3.9 28.2 1.0
N A:LEU62 3.9 30.3 1.0
OP2 D:DC3 4.0 23.3 1.0
N A:VAL65 4.0 27.0 1.0
O A:LYS61 4.1 30.3 1.0
N A:PRO63 4.2 29.9 1.0
CA A:PRO63 4.3 31.9 1.0
CA A:VAL65 4.3 25.6 1.0
CA A:LEU62 4.3 30.8 1.0
CA A:LYS60 4.4 36.9 1.0
N A:GLY64 4.4 33.8 1.0
N A:LYS61 4.4 34.0 1.0
CA A:LYS61 4.4 35.4 1.0
CB A:VAL65 4.6 24.7 1.0
CG A:LYS60 4.6 43.5 1.0
N A:GLY66 4.7 26.1 1.0
C A:PRO63 4.8 32.7 1.0
O3' D:DT2 4.8 26.7 1.0
CA A:GLY66 4.9 25.0 1.0
O A:ALA59 5.0 36.7 1.0

Sodium binding site 3 out of 4 in 5tbb

Go back to Sodium Binding Sites List in 5tbb
Sodium binding site 3 out of 4 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc 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 (-)Ftc and Ppi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:47.0
occ:1.00
 OD2 A:ASP190 2.2 49.2 1.0
OD1 A:ASP192 2.2 52.1 1.0
O3A P:43X101 2.2 60.5 1.0
OD2 A:ASP256 2.2 47.4 1.0
O3' P:DC10 2.9 46.7 1.0
CG A:ASP192 3.0 45.9 1.0
OD2 A:ASP192 3.0 57.4 1.0
PA P:43X101 3.1 59.3 1.0
CG A:ASP190 3.2 45.5 1.0
MN A:MN401 3.2 72.5 1.0
OD1 A:ASP190 3.4 57.2 1.0
CG A:ASP256 3.5 40.1 1.0
C3' P:DC10 3.8 39.5 1.0
C4' P:DC10 4.1 36.7 1.0
O5' P:43X101 4.3 50.1 1.0
C5' P:43X101 4.3 49.5 1.0
NH2 A:ARG258 4.3 78.3 1.0
OD1 A:ASP256 4.3 45.0 1.0
O2A P:43X101 4.3 48.4 1.0
C5' P:DC10 4.4 33.1 1.0
CB A:ASP256 4.4 32.4 1.0
CB A:ASP192 4.5 39.9 1.0
CB A:ASP190 4.5 43.3 1.0
O11 A:PPV407 4.9 86.7 1.0
O5' P:DC10 5.0 27.1 1.0
S3' P:43X101 5.0 53.8 1.0

Sodium binding site 4 out of 4 in 5tbb

Go back to Sodium Binding Sites List in 5tbb
Sodium binding site 4 out of 4 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc 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 (-)Ftc and Ppi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:30.5
occ:1.00
 NH1 A:ARG112 2.6 46.1 1.0
O A:ASN28 2.6 19.1 1.0
OE1 A:GLN31 2.6 29.5 1.0
O A:PRO108 2.7 22.6 1.0
CZ A:ARG112 3.4 44.5 1.0
C A:PRO108 3.4 22.4 1.0
CD A:GLN31 3.6 28.7 1.0
O A:VAL29 3.7 18.9 1.0
CB A:ARG112 3.7 35.3 1.0
CG2 A:ILE97 3.7 19.6 1.0
C A:ASN28 3.7 19.7 1.0
CB A:PRO108 3.7 22.6 1.0
CA A:PRO108 3.8 22.5 1.0
NH2 A:ARG112 3.8 40.4 1.0
CA A:VAL29 4.0 19.4 1.0
CG A:GLN31 4.0 26.9 1.0
C A:VAL29 4.1 19.5 1.0
N A:VAL29 4.3 19.6 1.0
NE A:ARG112 4.3 47.6 1.0
N A:ARG112 4.5 29.4 1.0
N A:SER109 4.5 22.1 1.0
CA A:ARG112 4.6 33.3 1.0
CD A:ARG112 4.7 43.8 1.0
CG A:ARG112 4.8 38.5 1.0
CD1 A:ILE97 4.8 18.3 1.0
NE2 A:GLN31 4.8 31.7 1.0
CA A:SER109 4.9 21.9 1.0
CA A:ASN28 4.9 19.4 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 00:06:43 2024

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