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Sodium in PDB 7s9l: Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc

Enzymatic activity of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc

All present enzymatic activity of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc, PDB code: 7s9l was solved by B.D.Freudenthal, B.J.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.02 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.973, 79.218, 54.938, 90, 106.23, 90
R / Rfree (%) 19.6 / 26.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc (pdb code 7s9l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc, PDB code: 7s9l:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7s9l

Go back to Sodium Binding Sites List in 7s9l
Sodium binding site 1 out of 4 in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:15.9
occ:1.00
 O A:ILE106 2.3 18.1 1.0
O A:THR101 2.3 17.9 1.0
OP1 P:DG9 2.3 16.8 1.0
O A:VAL103 2.4 14.9 1.0
O P:HOH205 2.6 18.6 1.0
O P:HOH213 2.6 19.1 1.0
NA A:NA403 3.1 32.5 1.0
C A:VAL103 3.3 20.2 1.0
C A:THR101 3.3 17.6 1.0
C A:ILE106 3.4 17.2 1.0
P P:DG9 3.5 17.1 1.0
OP2 P:DG9 3.7 19.9 1.0
CA A:SER104 3.8 16.3 1.0
N A:ILE106 3.8 14.1 1.0
N A:SER104 3.9 17.1 1.0
N A:GLY105 3.9 18.7 1.0
CA A:THR101 4.0 16.2 1.0
N A:VAL103 4.1 20.2 1.0
CA A:ILE106 4.2 15.8 1.0
C A:ARG102 4.2 18.0 1.0
C A:SER104 4.3 17.2 1.0
N A:ARG102 4.3 20.8 1.0
CA A:VAL103 4.3 16.8 1.0
N A:GLY107 4.4 16.7 1.0
CB A:THR101 4.4 19.5 1.0
CA A:ARG102 4.5 17.7 1.0
O P:HOH201 4.5 30.0 1.0
O3' P:DC8 4.6 19.4 1.0
O5' P:DG9 4.6 20.9 1.0
CB A:ILE106 4.6 16.1 1.0
C A:GLY105 4.6 18.1 1.0
CA A:GLY107 4.7 16.5 1.0
O A:ARG102 4.7 17.6 1.0
CA A:GLY105 4.9 18.9 1.0
O A:HOH609 4.9 25.0 1.0
O A:LEU100 4.9 18.7 1.0

Sodium binding site 2 out of 4 in 7s9l

Go back to Sodium Binding Sites List in 7s9l
Sodium binding site 2 out of 4 in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:32.5
occ:1.00
 O A:LEU62 2.3 26.5 1.0
O A:VAL65 2.4 23.8 1.0
O A:LYS60 2.5 25.8 1.0
O D:HOH108 2.6 29.4 1.0
OP1 D:DC3 2.8 24.3 1.0
C A:LEU62 3.4 26.2 1.0
C A:VAL65 3.5 23.7 1.0
C A:LYS60 3.6 26.6 1.0
P D:DC3 3.7 21.4 1.0
OP2 D:DC3 3.8 22.9 1.0
N A:VAL65 4.0 21.4 1.0
N A:LEU62 4.0 23.5 1.0
C A:LYS61 4.1 26.5 1.0
N A:GLY64 4.2 28.6 1.0
CA A:PRO63 4.2 30.2 1.0
N A:PRO63 4.2 28.4 1.0
CA A:VAL65 4.3 21.1 1.0
CA A:LYS60 4.3 23.8 1.0
CA A:LEU62 4.4 25.1 1.0
O A:LYS61 4.5 24.4 1.0
CG A:LYS60 4.5 26.1 1.0
N A:LYS61 4.5 28.9 1.0
C A:PRO63 4.6 27.3 1.0
N A:GLY66 4.6 22.9 1.0
CA A:LYS61 4.6 29.3 1.0
O3' D:DT2 4.6 20.7 1.0
CB A:VAL65 4.6 24.1 1.0
CA A:GLY66 4.8 20.9 1.0
C A:GLY64 4.9 24.6 1.0
O A:ALA59 4.9 21.5 1.0
O5' D:DC3 5.0 19.8 1.0

Sodium binding site 3 out of 4 in 7s9l

Go back to Sodium Binding Sites List in 7s9l
Sodium binding site 3 out of 4 in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:32.5
occ:1.00
 O A:HOH609 2.3 25.0 1.0
O P:HOH205 2.6 18.6 1.0
O P:HOH213 2.6 19.1 1.0
O A:HOH588 2.6 24.7 1.0
O A:THR101 2.7 17.9 1.0
O A:HOH549 2.8 35.0 1.0
NA A:NA401 3.1 15.9 1.0
C A:THR101 3.8 17.6 1.0
O P:HOH201 3.8 30.0 1.0
NZ A:LYS27 3.9 33.0 1.0
CA A:ARG102 4.4 17.7 1.0
N A:ARG102 4.5 20.8 1.0
OP1 P:DG9 4.6 16.8 1.0
CB A:THR101 4.6 19.5 1.0
OP2 P:DG9 4.6 19.9 1.0
OG1 A:THR101 4.6 20.0 1.0
CA A:THR101 4.8 16.2 1.0
O A:ILE106 4.8 18.1 1.0
C A:ARG102 4.9 18.0 1.0

Sodium binding site 4 out of 4 in 7s9l

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Sodium binding site 4 out of 4 in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Dc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:27.9
occ:0.00
 OG A:SER171 2.5 33.2 1.0
O A:HOH539 2.6 33.7 1.0
CB A:SER171 3.8 29.8 1.0
N A:SER171 4.2 31.5 1.0
CA A:SER171 4.6 28.9 1.0
OD1 A:ASP170 4.7 30.9 1.0
O A:HOH575 4.8 32.1 1.0

Reference:

B.J.Ryan, H.Yang, J.H.T.Bacurio, M.R.Smith, A.K.Basu, M.M.Greenberg, B.D.Freudenthal. Structural Dynamics of A Common Mutagenic Oxidative Dna Lesion in Duplex Dna and During Dna Replication. J.Am.Chem.Soc. V. 144 8054 2022.
ISSN: ESSN 1520-5126
PubMed: 35499923
DOI: 10.1021/JACS.2C00193
Page generated: Wed Oct 9 08:54:51 2024

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