Sodium in PDB 5dy9: Y68T Hfq From Methanococcus Jannaschii in Complex with Amp

The structure of Y68T Hfq From Methanococcus Jannaschii in Complex with Amp, PDB code: 5dy9 was solved by A.D.Nikulin, A.O.Mikhailina, N.V.Lekontseva, V.A.Balobanov, E.Y.Nikonova, S.V.Tishchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.636, 67.635, 91.165, 90.00, 90.95, 90.00
R / Rfree (%)	16.9 / 20.1

The structure of Y68T Hfq From Methanococcus Jannaschii in Complex with Amp also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Y68T Hfq From Methanococcus Jannaschii in Complex with Amp (pdb code 5dy9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Y68T Hfq From Methanococcus Jannaschii in Complex with Amp, PDB code: 5dy9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Y68T Hfq From Methanococcus Jannaschii in Complex with Amp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Y68T Hfq From Methanococcus Jannaschii in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ F:Na102 b:35.2 occ:0.70 O F:HOH258 2.4 27.9 1.0 O F:HOH214 2.4 31.8 1.0 OD1 F:ASN16 2.6 41.2 1.0 O E:HOH273 2.7 37.0 1.0 NH2 I:ARG22 3.4 22.6 1.0 CG F:ASN16 3.4 38.5 1.0 N F:ASN16 3.5 30.9 1.0 CB F:ASN16 3.5 26.4 1.0 O E:LYS12 3.5 25.7 1.0 CZ I:ARG22 3.6 21.3 1.0 NE I:ARG22 3.9 16.1 1.0 N E:LYS12 4.0 38.2 1.0 CA F:ASN16 4.1 27.8 1.0 ND2 E:ASN47 4.2 27.0 1.0 C E:LYS12 4.2 29.3 1.0 NH1 I:ARG22 4.3 17.1 1.0 CB I:ARG22 4.3 15.6 1.0 O I:ARG22 4.4 18.0 1.0 C F:PRO15 4.5 32.8 1.0 CG I:ARG22 4.5 16.7 1.0 CA F:PRO15 4.6 32.5 1.0 ND2 F:ASN16 4.6 33.1 1.0 CA E:LYS12 4.7 36.6 1.0 N F:PHE17 4.7 19.5 1.0 CD I:ARG22 4.8 16.2 1.0 CA I:ARG22 4.9 13.5 1.0 C F:ASN16 5.0 26.6 1.0

Sodium binding site 2 out of 2 in the Y68T Hfq From Methanococcus Jannaschii in Complex with Amp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Y68T Hfq From Methanococcus Jannaschii in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ K:Na103 b:48.2 occ:1.00 O K:HOH268 2.3 33.8 1.0 O K:HOH214 2.3 32.1 1.0 O L:HOH257 3.3 39.6 1.0 CG K:TYR48 3.7 26.2 1.0 CB K:TYR48 3.9 19.1 1.0 CD1 K:TYR48 3.9 32.7 1.0 CD2 K:TYR48 4.2 30.0 1.0 O K:HOH238 4.3 17.3 1.0 ND1 K:HIS64 4.4 14.1 1.0 CE1 K:TYR48 4.4 33.6 1.0 O K:HOH261 4.5 25.7 1.0 CE1 K:HIS64 4.5 14.9 1.0 CE2 K:TYR48 4.7 33.5 1.0 CB L:LYS63 4.7 12.9 1.0 CD1 K:PHE62 4.7 15.3 1.0 CD L:LYS63 4.8 12.6 1.0 CE1 K:PHE62 4.8 17.0 1.0 CZ K:TYR48 4.8 39.5 1.0 O L:ASN47 4.9 16.4 1.0

A.Nikulin, A.Mikhailina, N.Lekontseva, V.Balobanov, E.Nikonova, S.Tishchenko. Characterization of Rna-Binding Properties of the Archaeal Hfq-Like Protein From Methanococcus Jannaschii. J. Biomol. Struct. Dyn. V. 35 1615 2017.
ISSN: ESSN 1538-0254
PubMed: 27187760
DOI: 10.1080/07391102.2016.1189849