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Sodium in PDB 6cti: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp 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 CCL2, Beta, Gamma Dttp Analogue, PDB code: 6cti 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) 26.49 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.618, 79.117, 55.407, 90.00, 107.00, 90.00
R / Rfree (%) 17.7 / 22.7

Other elements in 6cti:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp Analogue 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 CCL2, Beta, Gamma Dttp Analogue (pdb code 6cti). 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 CCL2, Beta, Gamma Dttp Analogue, PDB code: 6cti:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6cti

Go back to Sodium Binding Sites List in 6cti
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp 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 CCL2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:24.0
occ:1.00
 O A:THR101 2.4 24.5 1.0
OP1 P:DG9 2.4 25.0 1.0
O A:VAL103 2.4 22.4 1.0
O A:ILE106 2.4 22.6 1.0
O P:HOH204 2.4 29.4 1.0
O A:HOH710 2.5 24.0 1.0
C A:THR101 3.3 22.0 1.0
C A:VAL103 3.4 22.9 1.0
C A:ILE106 3.4 19.2 1.0
P P:DG9 3.4 28.3 1.0
OP2 P:DG9 3.6 22.1 1.0
N A:ILE106 3.7 18.0 1.0
O A:HOH664 3.7 38.3 1.0
CA A:THR101 3.9 22.7 1.0
N A:GLY105 3.9 23.9 1.0
CA A:SER104 4.0 22.0 1.0
CA A:ILE106 4.1 24.7 1.0
N A:SER104 4.1 21.6 1.0
N A:VAL103 4.1 21.9 1.0
C A:SER104 4.3 21.7 1.0
C A:ARG102 4.3 26.0 1.0
N A:ARG102 4.4 23.1 1.0
N A:GLY107 4.4 22.4 1.0
CB A:THR101 4.4 24.2 1.0
CA A:VAL103 4.4 23.4 1.0
O3' P:DC8 4.4 23.5 1.0
CB A:ILE106 4.5 20.4 1.0
C A:GLY105 4.5 26.2 1.0
CA A:ARG102 4.6 24.9 1.0
O5' P:DG9 4.6 27.8 1.0
CA A:GLY107 4.7 24.0 1.0
CA A:GLY105 4.8 26.9 1.0
O A:LEU100 4.8 20.4 1.0
O A:ARG102 4.8 24.2 1.0

Sodium binding site 2 out of 3 in 6cti

Go back to Sodium Binding Sites List in 6cti
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp 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 CCL2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:33.2
occ:1.00
 O A:LEU62 2.2 32.0 1.0
O A:VAL65 2.4 33.8 1.0
O A:HOH623 2.5 37.5 1.0
O A:LYS60 2.5 38.1 1.0
OP1 D:DC3 2.5 30.0 1.0
O D:HOH204 2.7 37.4 1.0
C A:LEU62 3.4 34.8 1.0
C A:VAL65 3.4 33.5 1.0
P D:DC3 3.6 33.5 1.0
C A:LYS60 3.6 37.8 1.0
OP2 D:DC3 3.7 30.0 1.0
N A:VAL65 3.8 31.7 1.0
N A:GLY64 4.0 30.8 1.0
CA A:PRO63 4.0 28.6 1.0
CA A:VAL65 4.1 31.4 1.0
N A:LEU62 4.1 32.0 1.0
N A:PRO63 4.1 34.8 1.0
C A:LYS61 4.2 37.1 1.0
CA A:LYS60 4.3 32.7 1.0
CA A:LEU62 4.4 27.7 1.0
CB A:VAL65 4.4 29.4 1.0
C A:PRO63 4.4 32.9 1.0
O A:LYS61 4.4 35.2 1.0
O3' D:DT2 4.5 35.1 1.0
N A:GLY66 4.5 31.9 1.0
CG A:LYS60 4.5 36.6 1.0
N A:LYS61 4.6 32.2 1.0
CA A:LYS61 4.7 33.1 1.0
C A:GLY64 4.7 32.1 1.0
O5' D:DC3 4.8 37.1 1.0
CA A:GLY66 4.8 31.2 1.0
O A:ALA59 4.9 27.8 1.0
CA A:GLY64 4.9 31.2 1.0

Sodium binding site 3 out of 3 in 6cti

Go back to Sodium Binding Sites List in 6cti
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp 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 CCL2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:28.8
occ:1.00
 OD1 A:ASP192 2.2 22.4 1.0
OD2 A:ASP190 2.3 26.8 1.0
OD2 A:ASP256 2.4 32.9 1.0
O1A A:VT8404 2.5 24.7 1.0
C5' P:DOC10 2.9 46.6 1.0
CG A:ASP190 3.1 27.4 1.0
CG A:ASP192 3.2 23.3 1.0
OD1 A:ASP190 3.3 24.4 1.0
C4' P:DOC10 3.4 51.6 1.0
C3' P:DOC10 3.4 39.7 1.0
PA A:VT8404 3.5 27.4 1.0
OD2 A:ASP192 3.5 21.2 1.0
CG A:ASP256 3.5 34.2 1.0
MG A:MG401 3.7 20.6 1.0
O5' A:VT8404 3.7 23.6 1.0
O2A A:VT8404 4.0 23.2 1.0
CB A:ASP256 4.1 28.8 1.0
C5' A:VT8404 4.1 25.5 1.0
O5' P:DOC10 4.2 52.9 1.0
OD1 A:ASP256 4.5 30.2 1.0
CB A:ASP190 4.5 19.0 1.0
NH1 A:ARG254 4.5 23.8 0.4
CB A:ASP192 4.5 20.4 1.0
O A:HOH672 4.5 37.7 1.0
O A:HOH728 4.7 39.3 1.0
OP1 P:DOC10 4.7 53.0 1.0
O1G A:VT8404 4.7 26.8 1.0
O4' P:DOC10 4.8 49.6 1.0
C2' P:DOC10 4.8 35.5 1.0
NH2 A:ARG254 4.9 27.3 0.6
O3A A:VT8404 4.9 24.7 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 06:43:18 2024

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