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Sodium in PDB 6bel: Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp, PDB code: 6bel 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) 23.70 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.709, 79.533, 55.458, 90.00, 107.66, 90.00
R / Rfree (%) 16.8 / 20.2

Other elements in 6bel:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp (pdb code 6bel). 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 R-Isomer of Beta-Gamma-Chf-Dctp, PDB code: 6bel:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6bel

Go back to Sodium Binding Sites List in 6bel
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp


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 R-Isomer of Beta-Gamma-Chf-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:18.2
occ:1.00
 OD1 A:ASP192 2.1 17.1 1.0
OD2 A:ASP256 2.2 20.6 1.0
OD2 A:ASP190 2.3 22.4 1.0
O1A A:F3C406 2.5 15.0 1.0
O A:HOH557 2.6 28.6 1.0
CG A:ASP190 3.0 18.3 1.0
OD1 A:ASP190 3.0 18.3 1.0
CG A:ASP192 3.1 16.6 1.0
CG A:ASP256 3.4 19.2 1.0
OD2 A:ASP192 3.5 16.4 1.0
MG A:MG402 3.5 14.9 1.0
PA A:F3C406 3.6 17.3 1.0
O5' A:F3C406 3.8 17.4 1.0
C3' P:2DA10 3.9 17.9 1.0
CB A:ASP256 4.0 17.7 1.0
C5' A:F3C406 4.1 16.4 1.0
O2A A:F3C406 4.1 18.0 1.0
O A:HOH535 4.3 27.5 1.0
CB A:ASP190 4.3 16.8 1.0
C5' P:2DA10 4.4 21.5 1.0
OD1 A:ASP256 4.4 18.6 1.0
O A:HOH613 4.4 25.9 1.0
CB A:ASP192 4.5 15.6 1.0
C4' P:2DA10 4.5 20.8 1.0
O A:MET191 4.7 16.0 1.0
OP1 P:2DA10 4.7 18.8 1.0
O1G A:F3C406 4.7 17.0 1.0
O5' P:2DA10 4.8 22.5 1.0
NH2 A:ARG254 4.8 20.2 1.0
CA A:ASP192 5.0 16.0 1.0
C A:MET191 5.0 15.1 1.0

Sodium binding site 2 out of 3 in 6bel

Go back to Sodium Binding Sites List in 6bel
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp


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 R-Isomer of Beta-Gamma-Chf-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:22.6
occ:1.00
 O A:THR101 2.3 23.3 1.0
O A:ILE106 2.4 20.5 1.0
O A:VAL103 2.5 18.8 1.0
O P:HOH104 2.5 27.0 1.0
O A:HOH810 2.6 25.1 1.0
OP1 P:DG9 2.6 26.0 1.0
C A:THR101 3.3 21.3 1.0
C A:VAL103 3.4 17.9 1.0
C A:ILE106 3.4 22.8 1.0
O A:HOH652 3.5 35.4 1.0
P P:DG9 3.6 24.9 1.0
OP2 P:DG9 3.8 23.3 1.0
N A:ILE106 3.8 20.4 1.0
CA A:THR101 3.9 21.1 1.0
CA A:SER104 4.0 17.9 1.0
N A:GLY105 4.1 20.6 1.0
N A:VAL103 4.1 20.8 1.0
N A:SER104 4.1 17.6 1.0
CA A:ILE106 4.1 19.1 1.0
N A:ARG102 4.3 18.8 1.0
C A:ARG102 4.3 22.8 1.0
CA A:VAL103 4.4 20.5 1.0
C A:SER104 4.4 19.7 1.0
N A:GLY107 4.4 19.4 1.0
CB A:THR101 4.4 22.4 1.0
CB A:ILE106 4.5 20.3 1.0
O3' P:DC8 4.5 24.9 1.0
CA A:ARG102 4.6 20.2 1.0
O P:HOH122 4.7 46.2 1.0
C A:GLY105 4.7 21.9 1.0
CA A:GLY107 4.7 20.0 1.0
O A:HOH554 4.8 37.5 1.0
O A:LEU100 4.8 19.9 1.0
O A:ARG102 4.8 21.8 1.0
O A:HOH815 4.9 34.5 1.0
O5' P:DG9 4.9 24.1 1.0
CA A:GLY105 4.9 20.9 1.0

Sodium binding site 3 out of 3 in 6bel

Go back to Sodium Binding Sites List in 6bel
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp


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 R-Isomer of Beta-Gamma-Chf-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:27.0
occ:1.00
 O A:LEU62 2.3 24.4 1.0
O A:HOH782 2.4 30.3 1.0
O A:LYS60 2.4 24.2 1.0
O A:VAL65 2.4 23.6 1.0
O D:HOH105 2.6 30.4 1.0
OP1 D:DC3 2.7 25.8 1.0
C A:LEU62 3.3 23.4 1.0
C A:LYS60 3.5 26.3 1.0
C A:VAL65 3.6 21.7 1.0
P D:DC3 3.8 27.0 1.0
O D:HOH108 3.8 32.5 1.0
N A:LEU62 3.9 25.2 1.0
N A:VAL65 3.9 22.0 1.0
OP2 D:DC3 3.9 24.4 1.0
C A:LYS61 4.0 29.0 1.0
N A:PRO63 4.1 28.7 1.0
CA A:PRO63 4.1 28.7 1.0
CA A:VAL65 4.2 20.1 1.0
CA A:LEU62 4.2 24.1 1.0
N A:GLY64 4.2 25.4 1.0
O A:LYS61 4.2 28.5 1.0
CA A:LYS60 4.2 22.3 1.0
N A:LYS61 4.4 27.4 1.0
CB A:VAL65 4.4 22.4 1.0
CA A:LYS61 4.4 26.8 1.0
CG A:LYS60 4.5 30.7 1.0
C A:PRO63 4.6 25.1 1.0
N A:GLY66 4.6 24.6 1.0
O3' D:DT2 4.7 27.2 1.0
O A:ALA59 4.9 24.0 1.0
C A:GLY64 4.9 23.5 1.0
CA A:GLY66 5.0 26.6 1.0
O5' D:DC3 5.0 31.9 1.0
CB A:LYS60 5.0 27.2 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 02:03:48 2024

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