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

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, 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 CCL2, Beta, Gamma Datp Analogue, PDB code: 6crc 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) 19.98 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.437, 78.939, 54.911, 90.00, 108.55, 90.00
R / Rfree (%) 20.7 / 28.5

Other elements in 6crc:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Datp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 2 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 Datp Analogue (pdb code 6crc). 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 Datp Analogue, PDB code: 6crc:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6crc

Go back to Sodium Binding Sites List in 6crc
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 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 CCL2, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:27.0
occ:1.00
 O A:THR101 2.3 31.8 1.0
OP1 P:DG9 2.3 22.7 1.0
O A:ILE106 2.4 27.2 1.0
O A:VAL103 2.6 32.7 1.0
C A:THR101 3.2 24.9 1.0
C A:ILE106 3.3 29.8 1.0
P P:DG9 3.4 32.8 1.0
C A:VAL103 3.5 28.3 1.0
OP2 P:DG9 3.7 33.7 1.0
N A:ILE106 3.7 32.1 1.0
CA A:THR101 3.8 22.0 1.0
N A:GLY105 3.9 30.5 1.0
CA A:ILE106 4.0 29.1 1.0
N A:VAL103 4.1 22.4 1.0
CA A:SER104 4.1 24.5 1.0
N A:SER104 4.1 24.3 1.0
N A:GLY107 4.1 28.4 1.0
N A:ARG102 4.3 25.0 1.0
C A:SER104 4.3 29.6 1.0
CA A:GLY107 4.3 27.5 1.0
C A:ARG102 4.3 28.4 1.0
CB A:THR101 4.4 24.9 1.0
C A:GLY105 4.4 30.9 1.0
CA A:VAL103 4.4 24.4 1.0
CB A:ILE106 4.5 25.4 1.0
O3' P:DC8 4.5 30.4 1.0
O5' P:DG9 4.6 30.6 1.0
CA A:ARG102 4.6 23.9 1.0
CA A:GLY105 4.7 33.2 1.0
O A:LEU100 4.7 22.6 1.0
O A:ARG102 4.9 32.4 1.0

Sodium binding site 2 out of 3 in 6crc

Go back to Sodium Binding Sites List in 6crc
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 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 CCL2, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:40.7
occ:1.00
 O D:HOH103 2.5 29.8 1.0
O A:HOH501 2.7 29.1 1.0
O A:LYS61 3.1 35.7 1.0
O A:LEU62 3.4 26.6 1.0
C A:LEU62 3.7 30.0 1.0
C A:LYS61 3.7 35.2 1.0
O A:LYS60 3.9 32.6 1.0
CA A:PRO63 3.9 25.5 1.0
N A:PRO63 3.9 27.6 1.0
OP1 D:DC3 3.9 30.9 1.0
O A:HOH548 4.0 28.1 1.0
N A:LEU62 4.4 34.8 1.0
CA A:LYS61 4.5 30.5 1.0
CB A:PRO63 4.5 26.6 1.0
CA A:LEU62 4.5 29.8 1.0
CD A:PRO63 4.8 30.1 1.0
C A:LYS60 4.9 34.8 1.0
P D:DC3 5.0 37.6 1.0

Sodium binding site 3 out of 3 in 6crc

Go back to Sodium Binding Sites List in 6crc
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 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 CCL2, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:36.5
occ:1.00
 OD1 A:ASP192 2.5 36.9 1.0
OD2 A:ASP190 2.6 41.2 1.0
OD1 A:ASP256 2.7 45.1 1.0
O1A A:VA7401 2.9 35.9 1.0
C5' P:DOC10 3.0 38.4 1.0
C3' P:DOC10 3.2 41.2 1.0
O5' P:DOC10 3.3 33.6 1.0
CG A:ASP190 3.4 33.9 1.0
C4' P:DOC10 3.4 42.4 1.0
CG A:ASP192 3.5 38.7 1.0
O5' A:VA7401 3.6 35.3 1.0
OD1 A:ASP190 3.6 30.7 1.0
PA A:VA7401 3.7 32.7 1.0
CG A:ASP256 3.7 38.8 1.0
OD2 A:ASP192 3.8 36.1 1.0
O2A A:VA7401 4.0 33.0 1.0
C5' A:VA7401 4.0 30.8 1.0
OD2 A:ASP256 4.4 36.8 1.0
C2' P:DOC10 4.6 40.9 1.0
CB A:ASP256 4.6 35.3 1.0
CB A:ASP190 4.7 31.3 1.0
P P:DOC10 4.8 40.2 1.0
O4' P:DOC10 4.8 40.8 1.0
CB A:ASP192 4.9 32.5 1.0
NH2 A:ARG254 4.9 37.2 1.0
MG A:MG402 5.0 41.7 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 06:41:47 2024

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