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Sodium in PDB 6uok: Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp

Enzymatic activity of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp

All present enzymatic activity of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp:
2.7.7.7;

Protein crystallography data

The structure of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp, PDB code: 6uok was solved by M.R.Smith, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.14 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.687, 79.957, 100.832, 90.00, 97.64, 90.00
R / Rfree (%) 22.4 / 27.9

Other elements in 6uok:

The structure of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Manganese (Mn) 6 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp (pdb code 6uok). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp, PDB code: 6uok:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6uok

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Sodium binding site 1 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na101

b:55.4
occ:1.00
 O F:LYS60 2.4 65.3 1.0
OP1 E:DC3 2.4 53.8 1.0
O F:VAL65 2.7 45.2 1.0
O F:LEU62 3.1 54.2 1.0
P E:DC3 3.3 45.1 1.0
OP2 E:DC3 3.3 38.6 1.0
C F:LYS60 3.6 58.7 1.0
C F:VAL65 3.7 47.4 1.0
C F:LEU62 4.1 56.1 1.0
CG F:LYS60 4.2 46.9 1.0
O5' E:DC3 4.2 37.6 1.0
N F:VAL65 4.2 44.2 1.0
CA F:LYS60 4.3 57.2 1.0
C F:LYS61 4.4 54.0 1.0
CA F:VAL65 4.5 42.2 1.0
N F:GLY66 4.6 44.6 1.0
N F:GLY64 4.6 47.6 1.0
O F:LYS61 4.6 56.1 1.0
O3' E:DT2 4.6 42.3 1.0
N F:LYS61 4.6 46.4 1.0
CA F:GLY66 4.7 44.2 1.0
N F:LEU62 4.7 47.2 1.0
CA F:PRO63 4.7 46.4 1.0
CA F:LYS61 4.7 49.2 1.0
CB F:LYS60 4.8 48.9 1.0
N F:PRO63 4.8 48.6 1.0

Sodium binding site 2 out of 6 in 6uok

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Sodium binding site 2 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na401

b:32.6
occ:1.00
 OP1 C:DG9 2.3 29.1 1.0
O F:THR101 2.4 34.3 1.0
O F:HOH513 2.6 28.3 1.0
O F:ILE106 2.9 26.6 1.0
O F:VAL103 3.1 30.5 1.0
P C:DG9 3.3 22.4 1.0
OP2 C:DG9 3.4 16.9 1.0
C F:THR101 3.5 29.9 1.0
C F:ILE106 3.8 24.0 1.0
C F:VAL103 4.0 27.2 1.0
O5' C:DG9 4.0 22.6 1.0
CA F:THR101 4.1 27.8 1.0
CA F:SER104 4.2 25.8 1.0
N F:ILE106 4.3 28.0 1.0
N F:GLY105 4.3 29.5 1.0
N F:SER104 4.4 33.6 1.0
CB F:THR101 4.5 25.8 1.0
C F:ARG102 4.5 28.9 1.0
N F:ARG102 4.6 26.3 1.0
O3' C:DC8 4.6 22.2 1.0
N F:GLY107 4.6 21.9 1.0
CA F:ILE106 4.6 23.6 1.0
N F:VAL103 4.7 26.9 1.0
CA F:GLY107 4.7 23.1 1.0
C F:SER104 4.7 27.3 1.0
O F:ARG102 4.8 32.6 1.0
C5' C:DG9 4.8 27.1 1.0
CA F:ARG102 4.8 27.1 1.0
CA F:VAL103 5.0 26.1 1.0

Sodium binding site 3 out of 6 in 6uok

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Sodium binding site 3 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na405

b:28.8
occ:1.00
 OD2 F:ASP256 2.5 35.7 1.0
OD2 F:ASP190 2.5 38.4 1.0
OD1 F:ASP192 2.6 37.1 1.0
O2A F:8GT406 2.7 34.6 1.0
O1A F:8GT406 3.3 48.3 1.0
PA F:8GT406 3.3 34.9 1.0
O5' F:8GT406 3.5 28.5 1.0
CG F:ASP190 3.5 35.2 1.0
CG F:ASP256 3.7 38.4 1.0
CG F:ASP192 3.7 38.4 1.0
OD1 F:ASP190 3.8 28.8 1.0
O5' C:DOC10 3.9 35.3 1.0
C5' F:8GT406 3.9 30.4 1.0
C4' C:DOC10 4.1 37.7 1.0
C5' C:DOC10 4.2 28.1 1.0
OD2 F:ASP192 4.2 33.3 1.0
MN F:MN402 4.3 41.4 1.0
CB F:ASP256 4.4 28.8 1.0
C3' C:DOC10 4.6 38.9 1.0
OD1 F:ASP256 4.6 38.8 1.0
CB F:ASP190 4.8 30.1 1.0
O3A F:8GT406 4.9 37.4 1.0
NH2 F:ARG254 4.9 30.7 1.0
CB F:ASP192 4.9 27.7 1.0

Sodium binding site 4 out of 6 in 6uok

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Sodium binding site 4 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:37.2
occ:1.00
 O A:HOH517 2.5 21.0 1.0
O A:LEU62 2.5 39.5 1.0
O A:VAL65 2.5 35.7 1.0
OP1 D:DC3 2.5 34.0 1.0
O A:LYS60 2.6 46.9 1.0
C A:VAL65 3.5 30.5 1.0
P D:DC3 3.5 37.5 1.0
OP2 D:DC3 3.6 27.0 1.0
C A:LEU62 3.6 34.6 1.0
N A:VAL65 3.6 26.4 1.0
C A:LYS60 3.8 38.9 1.0
N A:GLY64 4.0 32.1 1.0
CA A:VAL65 4.0 27.2 1.0
CA A:PRO63 4.1 35.9 1.0
N A:PRO63 4.3 33.3 1.0
O3' D:DT2 4.4 36.4 1.0
C A:PRO63 4.4 39.0 1.0
CB A:VAL65 4.4 32.9 1.0
C A:LYS61 4.4 37.6 1.0
CA A:LYS60 4.4 37.0 1.0
N A:LEU62 4.4 41.2 1.0
N A:GLY66 4.5 26.8 1.0
O A:LYS61 4.6 46.8 1.0
C A:GLY64 4.6 31.9 1.0
CG A:LYS60 4.7 36.9 1.0
CA A:LEU62 4.7 37.5 1.0
N A:LYS61 4.7 37.7 1.0
O5' D:DC3 4.8 25.2 1.0
CA A:GLY64 4.9 30.9 1.0
CA A:GLY66 4.9 31.9 1.0
CA A:LYS61 4.9 38.2 1.0

Sodium binding site 5 out of 6 in 6uok

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Sodium binding site 5 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:27.8
occ:1.00
 OP1 P:DG9 2.2 35.8 1.0
O A:THR101 2.3 24.0 1.0
O A:ILE106 2.7 29.6 1.0
O A:HOH519 3.0 17.6 1.0
O A:VAL103 3.1 19.2 1.0
P P:DG9 3.3 21.0 1.0
C A:THR101 3.5 18.4 1.0
OP2 P:DG9 3.6 27.7 1.0
C A:ILE106 3.8 23.8 1.0
C A:VAL103 3.9 17.7 1.0
O5' P:DG9 4.1 23.8 1.0
CA A:THR101 4.1 18.3 1.0
CA A:SER104 4.2 16.6 1.0
N A:ILE106 4.3 17.6 1.0
N A:SER104 4.4 19.7 1.0
C A:ARG102 4.4 22.8 1.0
N A:GLY105 4.5 22.6 1.0
CB A:THR101 4.5 20.1 1.0
N A:ARG102 4.5 19.5 1.0
N A:VAL103 4.6 19.2 1.0
CA A:ILE106 4.6 18.2 1.0
N A:GLY107 4.6 21.8 1.0
O3' P:DC8 4.6 23.2 1.0
CA A:ARG102 4.7 17.6 1.0
O A:ARG102 4.7 32.9 1.0
CA A:GLY107 4.7 21.8 1.0
C A:SER104 4.8 18.4 1.0
CA A:VAL103 4.9 16.1 1.0

Sodium binding site 6 out of 6 in 6uok

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Sodium binding site 6 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:54.1
occ:1.00
 OD1 A:ASP192 2.5 57.3 1.0
OD1 A:ASP190 2.6 53.5 1.0
O1A A:8GT405 2.6 58.4 0.8
C5' A:8GT405 2.8 61.1 0.8
OD2 A:ASP256 3.0 42.8 1.0
CG A:ASP190 3.1 51.5 1.0
CG A:ASP192 3.3 58.8 1.0
OD2 A:ASP190 3.3 54.4 1.0
OD2 A:ASP192 3.5 65.4 1.0
O5' A:8GT405 3.5 64.6 0.8
PA A:8GT405 3.7 67.6 0.8
C4' P:DOC10 4.0 50.1 1.0
MN A:MN404 4.1 52.2 0.6
CG A:ASP256 4.1 38.0 1.0
O5' P:DOC10 4.1 34.7 1.0
C4' A:8GT405 4.1 62.8 0.8
C5' P:DOC10 4.2 35.4 1.0
CB A:ASP190 4.3 44.0 1.0
C3' P:DOC10 4.4 49.5 1.0
CB A:ASP192 4.5 44.4 1.0
O3A A:8GT405 4.6 61.6 0.8
CB A:ASP256 4.7 36.4 1.0
O2A A:8GT405 4.8 62.7 0.8

Reference:

M.R.Smith, K.S.Alnajjar, N.M.Hoitsma, J.B.Sweasy, B.D.Freudenthal. Molecular Characterization of Oxidized Ribonucleotide Insertion By Human Dna Polymerase Beta J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Tue Oct 8 14:11:59 2024

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