Sodium in PDB 8cu0: 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd

All present enzymatic activity of 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd:
3.1.26.4;

The structure of 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd, PDB code: 8cu0 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.49 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.894, 89.403, 73.89, 90, 101.42, 90
R / Rfree (%)	20.2 / 24.6

The binding sites of Sodium atom in the 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd (pdb code 8cu0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd, PDB code: 8cu0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:33.4 occ:1.00 O A:VAL70 2.8 25.9 1.0 N A:ASN132 2.9 21.4 1.0 NA A:NA204 2.9 36.2 0.5 OD1 A:ASN132 3.0 29.0 1.0 OE1 A:GLU109 3.0 33.4 1.0 OD1 A:ASP71 3.3 30.8 1.0 CG A:ASN132 3.3 29.0 1.0 OG A:SER131 3.5 22.2 1.0 CA A:SER131 3.6 23.8 1.0 C A:SER131 3.7 22.5 1.0 CA A:ASP71 3.8 25.3 1.0 CD1 A:ILE189 3.8 27.4 1.0 CG A:ASP71 3.8 35.3 1.0 C A:VAL70 3.8 23.1 1.0 CD A:GLU109 3.9 33.1 1.0 CA A:ASN132 3.9 24.6 1.0 ND2 A:ASN132 3.9 33.9 1.0 CB A:SER131 3.9 24.5 1.0 OE2 A:GLU109 4.0 39.5 1.0 CB A:ASN132 4.0 27.4 1.0 CB A:ASP71 4.1 28.9 1.0 N A:SER133 4.2 25.6 1.0 N A:ASP71 4.3 23.1 1.0 C A:ASN132 4.4 27.4 1.0 CG2 A:ILE189 4.6 28.8 1.0 CG2 A:VAL70 4.6 22.3 1.0 OD2 A:ASP71 4.7 36.7 1.0 N A:SER131 4.9 19.9 1.0 O A:SER131 4.9 24.4 1.0 C A:ASP71 5.0 27.5 1.0 CG1 A:ILE189 5.0 29.5 1.0 O A:TYR130 5.0 20.2 1.0 N A:VAL72 5.0 30.6 1.0

Sodium binding site 2 out of 4 in the 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:36.2 occ:0.52 OE2 A:GLU109 2.1 39.5 1.0 OD1 A:ASN132 2.2 29.0 1.0 OD1 A:ASP71 2.2 30.8 1.0 CD A:GLU109 2.9 33.1 1.0 NA A:NA203 2.9 33.4 1.0 CG A:ASN132 3.0 29.0 1.0 OE1 A:GLU109 3.0 33.4 1.0 ND2 A:ASN132 3.1 33.9 1.0 CG A:ASP71 3.3 35.3 1.0 OD2 A:ASP71 3.8 36.7 1.0 CG A:GLU109 4.3 28.6 1.0 N A:VAL72 4.4 30.6 1.0 CB A:ASN132 4.4 27.4 1.0 CB A:ASP71 4.4 28.9 1.0 CG1 A:VAL72 4.4 32.2 1.0 CA A:ASP71 4.5 25.3 1.0 N A:ASN132 4.7 21.4 1.0 C A:ASN132 4.8 27.4 1.0 N A:SER133 4.8 25.6 1.0 CA A:ASN132 4.8 24.6 1.0 CB A:SER133 4.9 27.2 1.0 O A:VAL72 5.0 31.1 1.0

Sodium binding site 3 out of 4 in the 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:28.6 occ:1.00 N B:ASN106 2.9 19.0 1.0 ND2 B:ASN106 3.1 23.5 1.0 CG B:ASN106 3.3 22.7 1.0 N B:ASN105 3.4 21.2 1.0 ND2 B:ASN77 3.4 36.3 1.0 CB B:THR104 3.5 22.1 1.0 CB B:ASN106 3.5 18.9 1.0 CB B:ASN105 3.6 27.3 1.0 OD1 B:ASN77 3.7 34.1 1.0 OG1 B:THR104 3.8 20.4 1.0 CA B:ASN105 3.8 24.4 1.0 C B:ASN105 3.8 21.7 1.0 CA B:ASN106 3.8 19.2 1.0 OD1 B:ASN106 3.9 24.2 1.0 CG B:ASN77 3.9 31.9 1.0 C B:THR104 4.1 22.3 1.0 CG B:ASN105 4.3 33.6 1.0 CA B:THR104 4.3 22.8 1.0 ND2 B:ASN105 4.4 42.8 1.0 CG2 B:THR104 4.6 23.8 1.0 O B:THR104 4.9 19.8 1.0 C B:ASN106 5.0 19.1 1.0

Sodium binding site 4 out of 4 in the 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 12-Mer Dna Structure of Exbim Bound to Rnaseh -Modified Ddd within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:27.6 occ:1.00 O C:HOH334 2.8 29.3 1.0 N C:ASN106 2.9 22.5 1.0 O3' E:DT7 3.0 24.4 1.0 ND2 C:ASN77 3.2 25.8 1.0 N C:ASN105 3.3 25.1 1.0 ND2 C:ASN106 3.3 22.0 1.0 CG C:ASN106 3.4 26.8 1.0 CB C:ASN106 3.5 20.8 1.0 CB C:THR104 3.5 26.0 1.0 CB C:ASN105 3.5 23.1 1.0 C4' E:DT7 3.6 23.0 1.0 OD1 C:ASN77 3.6 28.7 1.0 CA C:ASN105 3.7 23.2 1.0 O4' E:DT7 3.7 21.2 1.0 C C:ASN105 3.7 26.2 1.0 CA C:ASN106 3.8 21.2 1.0 OG1 C:THR104 3.8 24.8 1.0 CG C:ASN77 3.8 30.1 1.0 C3' E:DT7 3.9 23.7 1.0 OD1 C:ASN106 4.0 24.7 1.0 C C:THR104 4.0 27.1 1.0 OP1 E:DG8 4.0 25.4 1.0 C1' E:DT7 4.1 22.4 1.0 P E:DG8 4.1 24.1 1.0 CA C:THR104 4.2 24.2 1.0 O5' E:DG8 4.3 23.8 1.0 CG2 C:THR104 4.6 27.9 1.0 C2' E:DT7 4.6 22.3 1.0 CG C:ASN105 4.8 36.3 1.0 O C:THR104 4.9 23.3 1.0 C C:ASN106 4.9 21.7 1.0 O C:ASN105 4.9 23.1 1.0 C5' E:DT7 4.9 26.8 1.0 N C:MET107 5.0 22.5 1.0

A.H.Kellum Jr., P.S.Pallan, A.Nilforoushan, S.J.Sturla, M.P.Stone, M.Egli. Conformation and Pairing Properties of An O 6 -Methyl-2'-Deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex Dna. Chem.Res.Toxicol. V. 35 1903 2022.
ISSN: ISSN 0893-228X
PubMed: 35973057
DOI: 10.1021/ACS.CHEMRESTOX.2C00165