Sodium in PDB 5w1z: Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)

The structure of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4), PDB code: 5w1z 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)	32.24 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	24.884, 32.798, 34.034, 90.25, 107.32, 111.04
R / Rfree (%)	20.7 / 23.4

The structure of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Magnesium	(Mg)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) (pdb code 5w1z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4), PDB code: 5w1z:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:30.6 occ:1.00 O2 A:DC6 2.8 20.7 1.0 O2 B:DC16 2.8 18.7 1.0 O B:HOH127 2.8 18.4 0.5 O B:HOH128 2.9 21.0 0.5 O4' B:DC17 3.1 21.2 1.0 O4' A:DC7 3.4 19.7 1.0 C4' B:DC17 3.7 22.6 1.0 C2 A:DC6 3.9 16.1 1.0 C2 B:DC16 3.9 15.1 1.0 C4' A:DC7 4.0 21.3 1.0 C5' B:DC17 4.0 20.6 1.0 C2 A:DI5 4.1 17.5 1.0 C1' A:DC6 4.1 19.8 1.0 C1' B:DC17 4.3 20.1 1.0 C1' B:DC16 4.3 18.3 1.0 C5' A:DC7 4.3 20.5 1.0 C2 B:DI15 4.3 15.5 1.0 N1 A:DC6 4.5 19.2 1.0 C1' A:DC7 4.5 17.3 1.0 O4' A:DC6 4.6 21.4 1.0 N1 B:DC16 4.6 17.7 1.0 N1 B:DC17 4.7 19.1 1.0 O B:HOH115 4.8 20.4 1.0 O4' B:DC16 4.8 19.3 1.0 N3 A:DC6 4.8 15.8 1.0 N3 A:DI5 4.8 17.8 1.0 N1 A:DI5 4.8 17.1 1.0 N3 B:DC16 4.9 15.0 1.0 N1 A:DC7 4.9 16.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:32.2 occ:0.70 O C:HOH230 2.2 34.0 1.0 O B:HOH118 2.6 24.0 1.0 OP1 C:DC6 2.8 26.9 1.0 O3' C:DI5 3.3 21.1 1.0 O5' B:DC11 3.3 25.2 1.0 O D:HOH236 3.5 32.9 1.0 P C:DC6 3.7 24.9 1.0 C6 B:DC11 3.9 20.5 1.0 C5 B:DC12 4.1 19.9 1.0 C5 B:DC11 4.2 17.3 1.0 C3' C:DI5 4.4 23.2 1.0 C4' C:DI5 4.4 24.2 1.0 N4 B:DC12 4.5 19.4 1.0 O B:HOH133 4.5 31.3 1.0 OP2 C:DC6 4.7 23.2 1.0 NA D:NA102 4.7 33.6 1.0 C5' C:DC6 4.7 21.3 1.0 O5' C:DC6 4.7 21.1 1.0 C5' B:DC11 4.7 25.1 1.0 O D:HOH237 4.7 31.1 1.0 O A:HOH218 4.8 23.0 1.0 C4 B:DC12 4.8 19.1 1.0 N1 B:DC11 4.9 20.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:33.6 occ:1.00 O A:HOH218 2.7 23.0 1.0 O D:HOH214 2.8 26.2 1.0 O B:HOH123 3.1 28.6 1.0 O3' D:DI19 4.0 22.4 1.0 C3' D:DI19 4.0 23.7 1.0 C5' D:DI19 4.2 26.6 1.0 C5 B:DC12 4.2 19.9 1.0 C4' D:DI19 4.2 23.2 1.0 N4 A:DC7 4.3 16.2 1.0 O4 A:BRU8 4.3 19.3 1.0 O B:HOH118 4.4 24.0 1.0 N6 B:DA13 4.4 18.4 1.0 O C:HOH230 4.5 34.0 1.0 OP2 D:DI20 4.5 28.3 1.0 P D:DI20 4.6 25.5 1.0 NA C:NA102 4.7 32.2 0.7 C6 B:DC12 4.7 18.5 1.0 OP1 D:DI20 4.7 24.2 1.0 O5' D:DI19 4.9 27.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na103 b:32.0 occ:1.00 O D:HOH237 2.5 31.1 1.0 O C:HOH221 2.5 28.4 1.0 O2 D:BRU18 2.7 19.7 1.0 O4' D:DI19 2.8 23.4 1.0 O4' D:BRU18 3.4 24.7 1.0 C1' D:BRU18 3.4 20.9 1.0 C4' D:DI19 3.6 23.2 1.0 C4' D:BRU18 3.7 24.9 1.0 C2 D:BRU18 3.8 18.4 1.0 C5' D:DI19 3.9 26.6 1.0 C1' D:DI19 3.9 21.1 1.0 O D:HOH236 3.9 32.9 1.0 O3' D:BRU18 4.0 27.8 1.0 N9 D:DI19 4.0 20.2 1.0 C2 C:DI4 4.1 20.1 1.0 O C:HOH230 4.1 34.0 1.0 N1 D:BRU18 4.1 19.2 1.0 C4 D:DI19 4.2 18.1 1.0 O D:HOH216 4.2 23.2 1.0 O D:HOH226 4.3 33.4 1.0 N3 C:DI4 4.3 17.4 1.0 N3 D:DI19 4.4 18.7 1.0 C3' D:BRU18 4.4 22.2 1.0 O2 D:DC17 4.4 16.6 1.0 C2' D:BRU18 4.6 22.3 1.0 C8 D:DI19 4.6 20.1 1.0 O5' D:DI19 4.7 27.6 1.0 O4' C:DI5 4.8 23.0 1.0 C5 D:DI19 4.8 19.5 1.0 N3 D:BRU18 4.9 20.9 1.0 C3' D:DI19 5.0 23.7 1.0

J.P.Peters, E.A.Kowal, P.S.Pallan, M.Egli, L.J.Maher 3Rd.. Comparative Analysis of Inosine-Substituted Duplex Dna By Circular Dichroism and X-Ray Crystallography. J. Biomol. Struct. Dyn. V. 36 2753 2018.
ISSN: ESSN 1538-0254
PubMed: 28818035
DOI: 10.1080/07391102.2017.1369164