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Sodium in PDB 6cr6: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue, PDB code: 6cr6 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) 20.85 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.141, 79.236, 55.539, 90.00, 106.69, 90.00
R / Rfree (%) 21.6 / 29.3

Other elements in 6cr6:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

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 Ch-CH3, Beta, Gamma Datp Analogue (pdb code 6cr6). 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 Ch-CH3, Beta, Gamma Datp Analogue, PDB code: 6cr6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6cr6

Go back to Sodium Binding Sites List in 6cr6
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue


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 Ch-CH3, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:37.0
occ:1.00
 O A:THR101 2.3 32.7 1.0
O A:ILE106 2.3 34.6 1.0
OP1 P:DG9 2.4 35.8 1.0
O A:VAL103 2.5 32.0 1.0
O P:HOH206 2.5 36.4 1.0
O P:HOH211 2.7 42.9 1.0
P P:DG9 3.3 37.2 1.0
C A:VAL103 3.3 36.7 1.0
OP2 P:DG9 3.4 40.7 1.0
C A:THR101 3.4 33.7 1.0
C A:ILE106 3.4 34.2 1.0
N A:ILE106 3.7 30.7 1.0
CA A:SER104 3.9 38.2 1.0
N A:GLY105 3.9 35.5 1.0
N A:SER104 4.0 34.9 1.0
CA A:THR101 4.1 35.6 1.0
N A:VAL103 4.1 35.1 1.0
CA A:ILE106 4.1 32.2 1.0
C A:ARG102 4.2 36.2 1.0
C A:SER104 4.3 34.8 1.0
O3' P:DC8 4.3 33.8 1.0
CA A:VAL103 4.4 33.6 1.0
N A:ARG102 4.4 33.3 1.0
N A:GLY107 4.4 33.0 1.0
O5' P:DG9 4.5 35.1 1.0
O A:ARG102 4.5 40.3 1.0
CA A:ARG102 4.5 35.1 1.0
C A:GLY105 4.6 34.9 1.0
CB A:ILE106 4.6 36.5 1.0
CB A:THR101 4.6 36.7 1.0
CA A:GLY107 4.7 34.5 1.0
CA A:GLY105 4.8 35.5 1.0
O A:LEU100 4.9 30.1 1.0

Sodium binding site 2 out of 3 in 6cr6

Go back to Sodium Binding Sites List in 6cr6
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue


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 Ch-CH3, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:52.3
occ:1.00
 OP1 D:DC3 2.3 47.1 1.0
O A:VAL65 2.4 51.5 1.0
O A:LYS60 2.5 52.7 1.0
O A:LEU62 2.7 49.5 1.0
C A:VAL65 3.4 49.2 1.0
P D:DC3 3.4 61.3 1.0
C A:LYS60 3.6 52.6 1.0
OP2 D:DC3 3.8 55.4 1.0
C A:LEU62 3.8 45.1 1.0
N A:VAL65 3.8 48.7 1.0
CA A:VAL65 4.1 48.1 1.0
CG A:LYS60 4.2 53.2 1.0
N A:GLY64 4.2 45.5 1.0
CA A:LYS60 4.2 48.2 1.0
C A:LYS61 4.4 55.0 1.0
CA A:PRO63 4.4 43.5 1.0
N A:GLY66 4.4 49.1 1.0
N A:LEU62 4.4 53.2 1.0
O A:LYS61 4.5 55.5 1.0
O3' D:DT2 4.5 54.2 1.0
O5' D:DC3 4.5 56.9 1.0
N A:PRO63 4.5 42.5 1.0
CB A:VAL65 4.5 49.3 1.0
N A:LYS61 4.6 48.6 1.0
C A:PRO63 4.7 46.0 1.0
CA A:GLY66 4.7 51.1 1.0
CA A:LEU62 4.8 46.6 1.0
CA A:LYS61 4.8 50.2 1.0
C A:GLY64 4.8 52.9 1.0
CB A:LYS60 4.8 52.5 1.0
NZ A:LYS60 4.9 55.7 1.0

Sodium binding site 3 out of 3 in 6cr6

Go back to Sodium Binding Sites List in 6cr6
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue


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 Ch-CH3, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:45.0
occ:1.00
 OD2 A:ASP256 2.2 42.2 1.0
OD2 A:ASP190 2.2 39.8 1.0
OD1 A:ASP192 2.2 28.7 1.0
O1A A:HGV401 2.9 27.2 1.0
CG A:ASP190 3.1 37.0 1.0
C3' P:DOC10 3.2 38.2 1.0
CG A:ASP256 3.3 37.8 1.0
CG A:ASP192 3.3 32.2 1.0
OD1 A:ASP190 3.4 32.0 1.0
C4' P:DOC10 3.5 40.4 1.0
C5' P:DOC10 3.5 40.7 1.0
OD2 A:ASP192 3.8 31.6 1.0
MG A:MG402 3.9 29.6 1.0
PA A:HGV401 3.9 31.0 1.0
CB A:ASP256 3.9 32.4 1.0
O5' A:HGV401 4.1 31.1 1.0
O5' P:DOC10 4.1 45.5 1.0
OD1 A:ASP256 4.2 36.3 1.0
O2A A:HGV401 4.3 26.7 1.0
CB A:ASP190 4.4 29.2 1.0
C2' P:DOC10 4.4 33.4 1.0
C5' A:HGV401 4.5 29.8 1.0
NH2 A:ARG254 4.6 35.5 1.0
CB A:ASP192 4.6 27.7 1.0
O A:MET191 4.8 30.1 1.0
OP1 P:DOC10 4.8 42.2 1.0
O4' P:DOC10 4.9 34.8 1.0
N A:ASP256 5.0 26.7 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 Oct 8 06:40:11 2024

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