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Sodium in PDB 6bem: Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp

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

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp, PDB code: 6bem 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) 24.64 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.806, 79.995, 55.521, 90.00, 107.68, 90.00
R / Rfree (%) 18.7 / 22.6

Other elements in 6bem:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 6bem

Go back to Sodium Binding Sites List in 6bem
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-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 S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:22.2
occ:1.00
 O A:THR101 2.3 20.6 1.0
O A:HOH793 2.5 25.1 1.0
O P:HOH105 2.5 25.0 1.0
O A:VAL103 2.5 15.3 1.0
O A:ILE106 2.6 18.7 1.0
OP1 P:DG9 2.7 23.8 1.0
C A:THR101 3.3 19.6 1.0
C A:VAL103 3.5 17.8 1.0
C A:ILE106 3.5 18.0 1.0
P P:DG9 3.7 25.8 1.0
O A:HOH713 3.8 47.0 1.0
N A:ILE106 3.8 16.3 1.0
OP2 P:DG9 3.8 22.7 1.0
CA A:THR101 3.9 17.5 1.0
CA A:SER104 4.0 17.2 1.0
N A:GLY105 4.1 18.6 1.0
N A:SER104 4.1 15.9 1.0
N A:VAL103 4.2 21.2 1.0
CA A:ILE106 4.2 16.7 1.0
O P:HOH120 4.3 30.4 1.0
C A:ARG102 4.3 21.6 1.0
N A:ARG102 4.3 17.3 1.0
O P:HOH124 4.3 44.8 1.0
C A:SER104 4.4 15.2 1.0
CB A:THR101 4.4 22.4 1.0
CA A:VAL103 4.5 18.9 1.0
N A:GLY107 4.5 16.6 1.0
CA A:ARG102 4.6 20.6 1.0
O3' P:DC8 4.6 22.4 1.0
CB A:ILE106 4.6 18.1 1.0
C A:GLY105 4.7 20.0 1.0
CA A:GLY107 4.8 17.3 1.0
O A:ARG102 4.8 21.8 1.0
O A:LEU100 4.8 16.9 1.0
O5' P:DG9 5.0 26.0 1.0
CA A:GLY105 5.0 21.0 1.0

Sodium binding site 2 out of 3 in 6bem

Go back to Sodium Binding Sites List in 6bem
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-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 S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:28.0
occ:1.00
 O A:VAL65 2.4 23.1 1.0
O A:LEU62 2.4 25.2 1.0
O A:LYS60 2.5 27.1 1.0
O A:HOH784 2.5 27.5 1.0
OP1 D:DC3 2.6 21.4 1.0
O D:HOH206 2.7 28.8 1.0
C A:LEU62 3.4 24.9 1.0
C A:VAL65 3.5 22.3 1.0
C A:LYS60 3.5 24.5 1.0
P D:DC3 3.7 23.3 1.0
N A:VAL65 3.8 21.2 1.0
O D:HOH210 3.9 35.1 1.0
OP2 D:DC3 3.9 22.0 1.0
N A:LEU62 4.0 24.2 1.0
C A:LYS61 4.0 27.9 1.0
CA A:VAL65 4.1 24.1 1.0
CA A:PRO63 4.1 28.9 1.0
N A:PRO63 4.1 28.8 1.0
CA A:LYS60 4.2 25.3 1.0
N A:GLY64 4.2 24.2 1.0
O A:LYS61 4.3 28.0 1.0
CA A:LEU62 4.3 23.2 1.0
CB A:VAL65 4.3 21.5 1.0
N A:LYS61 4.4 25.1 1.0
CG A:LYS60 4.4 29.6 1.0
N A:GLY66 4.5 22.4 1.0
CA A:LYS61 4.5 25.2 1.0
C A:PRO63 4.5 27.4 1.0
O3' D:DT2 4.6 26.5 1.0
O A:ALA59 4.8 24.2 1.0
C A:GLY64 4.8 22.9 1.0
CA A:GLY66 4.8 25.7 1.0
CB A:LYS60 5.0 27.5 1.0
O5' D:DC3 5.0 30.9 1.0
NZ A:LYS60 5.0 35.6 1.0

Sodium binding site 3 out of 3 in 6bem

Go back to Sodium Binding Sites List in 6bem
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-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 S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:15.6
occ:1.00
 OD1 A:ASP192 2.2 15.5 1.0
OD2 A:ASP256 2.2 20.9 1.0
OD2 A:ASP190 2.3 17.9 1.0
O A:HOH580 2.4 24.4 1.0
O1A A:DJJ408 2.5 13.5 1.0
CG A:ASP190 3.0 17.1 1.0
OD1 A:ASP190 3.1 14.0 1.0
CG A:ASP192 3.2 13.3 1.0
CG A:ASP256 3.4 16.7 1.0
OD2 A:ASP192 3.5 14.4 1.0
MG A:MG401 3.5 14.1 1.0
PA A:DJJ408 3.6 13.6 1.0
O5' A:DJJ408 3.8 15.6 1.0
C3' P:2DA10 3.8 17.2 1.0
O2A A:DJJ408 4.0 17.0 1.0
C5' A:DJJ408 4.1 17.1 1.0
CB A:ASP256 4.1 17.4 1.0
C5' P:2DA10 4.2 20.5 1.0
O A:HOH573 4.2 24.4 1.0
O A:HOH578 4.3 23.6 1.0
CB A:ASP190 4.4 15.0 1.0
OD1 A:ASP256 4.4 17.0 1.0
C4' P:2DA10 4.4 22.8 1.0
CB A:ASP192 4.5 12.6 1.0
OP1 P:2DA10 4.6 14.9 1.0
O5' P:2DA10 4.7 22.6 1.0
NH2 A:ARG254 4.7 18.0 1.0
O1G A:DJJ408 4.7 13.7 1.0
O A:MET191 4.8 14.2 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 02:03:50 2024

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