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Sodium in PDB 5u2r: Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+, PDB code: 5u2r was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.96 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.910, 80.160, 55.640, 90.00, 107.68, 90.00
R / Rfree (%) 19.1 / 22.9

Other elements in 5u2r:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+ also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+ (pdb code 5u2r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+, PDB code: 5u2r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5u2r

Go back to Sodium Binding Sites List in 5u2r
Sodium binding site 1 out of 2 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:11.6
occ:1.00
O A:THR101 2.2 12.0 1.0
O P:HOH105 2.4 20.5 1.0
OP1 P:DG9 2.4 13.4 1.0
O A:HOH705 2.4 15.8 1.0
O A:ILE106 2.5 12.1 1.0
O A:VAL103 2.6 9.9 1.0
C A:THR101 3.3 12.2 1.0
C A:VAL103 3.4 10.7 1.0
C A:ILE106 3.5 11.7 1.0
P P:DG9 3.5 13.9 1.0
O A:HOH665 3.6 29.2 1.0
OP2 P:DG9 3.7 13.0 1.0
N A:ILE106 3.8 11.5 1.0
CA A:THR101 3.9 12.5 1.0
O P:HOH114 3.9 34.0 1.0
N A:GLY105 4.0 10.9 1.0
CA A:SER104 4.0 10.5 1.0
N A:VAL103 4.1 11.3 1.0
N A:SER104 4.1 10.3 1.0
CA A:ILE106 4.1 11.3 1.0
C A:ARG102 4.3 12.0 1.0
N A:ARG102 4.3 11.9 1.0
C A:SER104 4.4 10.8 1.0
CA A:VAL103 4.4 11.4 1.0
CB A:THR101 4.4 12.8 1.0
N A:GLY107 4.4 11.9 1.0
O3' P:DC8 4.5 14.0 1.0
CA A:ARG102 4.6 12.3 1.0
CB A:ILE106 4.6 11.4 1.0
O5' P:DG9 4.6 13.8 1.0
C A:GLY105 4.7 11.5 1.0
CA A:GLY107 4.7 12.3 1.0
O A:ARG102 4.7 12.2 1.0
O A:LEU100 4.8 12.5 1.0
CA A:GLY105 4.9 11.3 1.0

Sodium binding site 2 out of 2 in 5u2r

Go back to Sodium Binding Sites List in 5u2r
Sodium binding site 2 out of 2 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:22.9
occ:1.00
O A:LYS60 2.3 23.1 1.0
O A:VAL65 2.3 18.4 1.0
O A:HOH711 2.4 24.6 1.0
O A:LEU62 2.4 21.4 1.0
OP1 D:DC3 2.5 24.5 1.0
O D:HOH101 2.6 30.7 1.0
C A:LEU62 3.4 21.2 1.0
C A:LYS60 3.4 23.8 1.0
C A:VAL65 3.4 19.1 1.0
P D:DC3 3.6 25.4 1.0
OP2 D:DC3 3.7 22.6 1.0
N A:LEU62 3.9 21.3 1.0
N A:VAL65 3.9 19.6 1.0
C A:LYS61 4.0 24.0 1.0
CA A:PRO63 4.1 22.2 1.0
N A:PRO63 4.1 22.2 1.0
CA A:VAL65 4.1 19.2 1.0
CA A:LYS60 4.3 23.5 1.0
N A:GLY64 4.3 21.6 1.0
CA A:LEU62 4.3 21.0 1.0
N A:LYS61 4.3 24.2 1.0
CA A:LYS61 4.4 24.7 1.0
CB A:VAL65 4.4 19.3 1.0
O A:LYS61 4.5 24.7 1.0
N A:GLY66 4.5 19.1 1.0
O3' D:DT2 4.6 23.6 1.0
C A:PRO63 4.6 22.1 1.0
CD A:LYS60 4.8 28.1 1.0
O5' D:DC3 4.8 27.7 1.0
CA A:GLY66 4.8 19.6 1.0
O A:ALA59 4.8 19.6 1.0
CG A:LYS60 4.8 27.6 1.0
C A:GLY64 4.9 20.4 1.0

Reference:

R.Vyas, A.J.Reed, A.T.Raper, W.J.Zahurancik, P.C.Wallenmeyer, Z.Suo. Structural Basis For the D-Stereoselectivity of Human Dna Polymerase Beta. Nucleic Acids Res. V. 45 6228 2017.
ISSN: ESSN 1362-4962
PubMed: 28402499
DOI: 10.1093/NAR/GKX252
Page generated: Tue Oct 8 00:22:01 2024

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