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Sodium in PDB 6cr4: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp, PDB code: 6cr4 was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.62 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.847, 79.564, 55.647, 90.00, 107.69, 90.00
R / Rfree (%) 17.3 / 21.4

Other elements in 6cr4:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp (pdb code 6cr4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp, PDB code: 6cr4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6cr4

Go back to Sodium Binding Sites List in 6cr4
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:14.5
occ:1.00
O A:THR101 2.3 14.8 1.0
O A:ILE106 2.3 13.8 1.0
OP1 P:DG9 2.4 13.9 1.0
O A:VAL103 2.5 12.7 1.0
O P:HOH108 2.5 16.4 1.0
O A:HOH785 2.6 17.7 1.0
C A:THR101 3.3 15.0 1.0
C A:ILE106 3.4 13.8 1.0
C A:VAL103 3.4 12.3 1.0
P P:DG9 3.4 15.2 1.0
O A:HOH547 3.6 23.1 1.0
OP2 P:DG9 3.6 15.2 1.0
N A:ILE106 3.8 13.1 1.0
CA A:THR101 3.8 13.9 1.0
CA A:SER104 4.0 12.5 1.0
N A:GLY105 4.0 13.0 1.0
N A:SER104 4.1 12.2 1.0
CA A:ILE106 4.1 13.6 1.0
N A:VAL103 4.1 13.6 1.0
C A:ARG102 4.3 16.4 1.0
C A:SER104 4.3 13.2 1.0
CB A:THR101 4.3 15.5 1.0
N A:GLY107 4.3 14.6 1.0
N A:ARG102 4.4 14.4 1.0
O P:HOH127 4.4 31.0 1.0
CA A:VAL103 4.4 13.6 1.0
O3' P:DC8 4.4 16.2 1.0
CB A:ILE106 4.5 12.9 1.0
O5' P:DG9 4.5 14.9 1.0
C A:GLY105 4.6 15.5 1.0
CA A:ARG102 4.6 16.0 1.0
CA A:GLY107 4.6 14.1 1.0
O A:ARG102 4.8 15.6 1.0
O A:LEU100 4.8 12.5 1.0
CA A:GLY105 4.9 13.1 1.0

Sodium binding site 2 out of 3 in 6cr4

Go back to Sodium Binding Sites List in 6cr4
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:22.5
occ:1.00
O A:VAL65 2.3 18.2 1.0
O A:LEU62 2.4 18.4 1.0
O A:LYS60 2.4 19.0 1.0
O A:HOH754 2.5 24.7 1.0
OP1 D:DC3 2.6 19.7 1.0
O D:HOH102 2.7 25.7 1.0
C A:LEU62 3.4 17.6 1.0
C A:VAL65 3.4 19.2 1.0
C A:LYS60 3.5 21.2 1.0
P D:DC3 3.6 20.8 1.0
OP2 D:DC3 3.7 15.7 1.0
N A:VAL65 3.9 15.8 1.0
O D:HOH110 3.9 27.5 1.0
N A:LEU62 3.9 15.9 1.0
CA A:PRO63 4.0 21.3 1.0
N A:PRO63 4.1 19.9 1.0
CA A:VAL65 4.1 16.4 1.0
C A:LYS61 4.1 21.2 1.0
N A:GLY64 4.2 19.5 1.0
CA A:LYS60 4.2 16.6 1.0
CA A:LEU62 4.3 17.7 1.0
CG A:LYS60 4.4 21.1 1.0
CB A:VAL65 4.4 16.0 1.0
O A:LYS61 4.4 21.7 1.0
N A:LYS61 4.5 18.2 1.0
N A:GLY66 4.5 17.4 1.0
C A:PRO63 4.5 18.2 1.0
O3' D:DT2 4.5 20.4 1.0
CA A:LYS61 4.6 20.9 1.0
CA A:GLY66 4.7 21.2 1.0
C A:GLY64 4.8 18.3 1.0
O5' D:DC3 4.8 23.6 1.0
O A:ALA59 4.9 18.5 1.0
CB A:LYS60 4.9 20.3 1.0

Sodium binding site 3 out of 3 in 6cr4

Go back to Sodium Binding Sites List in 6cr4
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:17.6
occ:1.00
OD2 A:ASP190 2.1 19.9 1.0
OD1 A:ASP192 2.1 12.3 1.0
O P:HOH107 2.3 25.9 1.0
OD2 A:ASP256 2.4 20.7 1.0
O2A A:DTP401 2.4 13.0 1.0
CG A:ASP190 2.9 14.1 1.0
OD1 A:ASP190 3.1 13.4 1.0
CG A:ASP192 3.2 11.0 1.0
MG A:MG402 3.5 12.7 1.0
PA A:DTP401 3.5 15.0 1.0
CG A:ASP256 3.5 16.0 1.0
OD2 A:ASP192 3.5 11.3 1.0
C3' P:DOC10 3.8 27.2 1.0
O5' A:DTP401 3.8 12.9 1.0
O1A A:DTP401 4.0 13.6 1.0
C5' A:DTP401 4.2 12.4 1.0
CB A:ASP256 4.2 13.6 1.0
CB A:ASP190 4.3 13.4 1.0
C4' P:DOC10 4.3 30.5 1.0
O P:HOH106 4.3 21.9 1.0
C5' P:DOC10 4.3 28.4 1.0
OD1 A:ASP256 4.5 14.2 1.0
CB A:ASP192 4.5 10.4 1.0
O A:HOH691 4.5 22.2 1.0
O5' P:DOC10 4.5 32.5 1.0
O3G A:DTP401 4.7 14.0 1.0
O A:MET191 4.7 11.1 1.0
O3A A:DTP401 4.9 13.1 1.0
NH2 A:ARG254 4.9 17.6 1.0
C2' P:DOC10 5.0 28.7 1.0

Reference:

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418
Page generated: Tue Dec 15 12:05:15 2020

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