Sodium in PDB 4x9d: High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump

The structure of High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump, PDB code: 4x9d was solved by A.D.Nikulin, S.V.Tishchenko, E.Y.Nikonova, V.N.Murina, A.O.Mihailina, N.V.Lekontseva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.70 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.741, 66.874, 109.310, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.3

The structure of High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump (pdb code 4x9d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump, PDB code: 4x9d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:22.6 occ:1.00 O A:TYR48 2.9 11.7 1.0 N A:HIS64 2.9 10.9 1.0 ND1 A:HIS64 3.0 13.2 1.0 O3' B:U5P104 3.2 37.1 1.0 O2' B:U5P104 3.2 36.5 1.0 N A:LYS63 3.2 9.4 1.0 O4' A:U5P104 3.5 34.0 0.7 CG A:HIS64 3.6 13.6 1.0 CB A:HIS64 3.7 12.5 1.0 C2' B:U5P104 3.7 34.2 1.0 CA A:LYS63 3.7 9.5 1.0 CB A:LYS63 3.7 10.9 1.0 C A:LYS63 3.8 10.0 1.0 C A:TYR48 3.8 11.5 1.0 CB A:TYR48 3.8 17.4 1.0 C4' A:U5P104 3.8 33.2 0.8 C5' A:U5P104 3.9 33.3 1.0 CA A:HIS64 3.9 11.6 1.0 CE1 A:HIS64 3.9 10.8 1.0 C A:PHE62 3.9 9.6 1.0 C3' B:U5P104 4.0 41.4 1.0 CA A:TYR48 4.0 12.9 1.0 CB A:PHE62 4.0 11.4 1.0 CD1 A:TYR48 4.1 30.1 1.0 CD1 A:PHE62 4.2 13.2 1.0 CA A:PHE62 4.3 9.5 1.0 CG A:TYR48 4.5 24.9 1.0 O5' A:U5P104 4.6 38.4 0.2 CD2 A:HIS64 4.6 12.1 1.0 CG A:PHE62 4.6 10.8 1.0 O B:HOH237 4.6 35.6 1.0 C1' A:U5P104 4.7 29.2 0.9 CG A:LYS63 4.7 10.9 1.0 NE2 A:HIS64 4.7 11.7 1.0 O A:PHE62 4.8 11.9 1.0 O A:LYS63 4.9 11.2 1.0

Sodium binding site 2 out of 5 in the High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:29.2 occ:1.00 O3P C:U5P104 2.4 41.6 0.5 O C:HOH240 2.5 32.4 1.0 O C:HOH213 2.7 18.0 1.0 O B:HOH235 2.8 23.9 1.0 O C:HOH241 2.9 22.2 1.0 P C:U5P104 3.5 48.2 0.5 O5' C:U5P104 3.7 38.0 0.5 CB B:HIS64 3.8 12.7 1.0 O2P C:U5P104 4.0 31.7 0.5 O1P B:U5P104 4.0 43.2 0.5 O B:HOH208 4.0 19.2 1.0 CB C:HIS64 4.1 10.1 1.0 CG B:HIS64 4.2 11.9 1.0 O2P D:U5P101 4.3 42.2 0.7 O3P B:U5P104 4.4 45.1 0.5 O5' B:U5P104 4.4 40.7 0.5 O B:HOH237 4.4 35.6 1.0 O D:HOH221 4.4 17.9 1.0 ND1 B:HIS64 4.5 12.6 1.0 O B:HOH239 4.5 46.1 1.0 P B:U5P104 4.6 51.8 0.5 O1P C:U5P104 4.7 43.6 0.5 O3' C:U5P104 4.7 28.3 0.5 CA C:HIS64 4.7 11.2 1.0 CD2 B:HIS64 4.8 12.6 1.0 O F:HOH226 4.9 22.8 1.0 O C:HIS64 4.9 13.1 1.0 C5' C:U5P104 4.9 30.1 0.5 O D:HOH235 5.0 24.7 1.0

Sodium binding site 3 out of 5 in the High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:21.6 occ:1.00 O B:TYR48 2.9 12.2 1.0 N B:HIS64 2.9 10.1 1.0 O3' C:U5P104 3.0 28.3 0.5 ND1 B:HIS64 3.0 12.6 1.0 N B:LYS63 3.2 10.4 1.0 CG B:HIS64 3.5 11.9 1.0 O2' C:U5P104 3.5 27.7 0.5 C5' B:U5P104 3.6 37.2 1.0 CB B:HIS64 3.6 12.7 1.0 O4' B:U5P104 3.6 42.7 1.0 CB B:LYS63 3.7 10.5 1.0 CA B:LYS63 3.7 11.0 1.0 C B:LYS63 3.8 9.3 1.0 C4' B:U5P104 3.8 34.3 1.0 CA B:HIS64 3.8 9.3 1.0 C B:TYR48 3.8 11.1 1.0 CE1 B:HIS64 3.9 11.8 1.0 CB B:TYR48 3.9 15.1 1.0 C B:PHE62 3.9 10.0 1.0 C2' C:U5P104 3.9 28.6 0.5 CB B:PHE62 3.9 11.5 1.0 C3' C:U5P104 4.0 34.0 0.5 CA B:TYR48 4.0 14.5 1.0 CA B:PHE62 4.2 8.8 1.0 CD1 B:TYR48 4.2 33.3 1.0 CD1 B:PHE62 4.3 12.5 1.0 O C:HOH240 4.5 32.4 1.0 CD2 B:HIS64 4.5 12.6 1.0 CG B:TYR48 4.6 23.1 1.0 O5' B:U5P104 4.6 40.7 0.5 CG B:PHE62 4.6 10.8 1.0 NE2 B:HIS64 4.7 12.2 1.0 O B:PHE62 4.7 11.6 1.0 CG B:LYS63 4.8 11.7 1.0 C1' B:U5P104 4.9 32.4 1.0 O B:LYS63 4.9 11.4 1.0

Sodium binding site 4 out of 5 in the High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:24.5 occ:1.00 O C:TYR48 2.8 13.5 1.0 O3' D:U5P101 2.9 30.2 0.7 N C:HIS64 2.9 11.9 1.0 ND1 C:HIS64 3.0 12.9 1.0 N C:LYS63 3.2 11.3 1.0 O2' D:U5P101 3.4 28.8 0.5 CG C:HIS64 3.5 12.5 1.0 O4' C:U5P104 3.5 34.3 0.5 CB C:HIS64 3.6 10.1 1.0 CB C:LYS63 3.7 12.3 1.0 CA C:LYS63 3.7 10.2 1.0 C C:LYS63 3.7 11.6 1.0 C2' D:U5P101 3.8 37.8 1.0 C5' C:U5P104 3.8 30.1 0.5 C C:TYR48 3.8 13.2 1.0 CE1 C:HIS64 3.8 12.4 1.0 CA C:HIS64 3.8 11.2 1.0 C4' C:U5P104 3.8 33.5 0.5 C3' D:U5P101 3.8 36.3 0.9 C C:PHE62 3.9 10.8 1.0 CB C:PHE62 4.0 10.9 1.0 CB C:TYR48 4.0 20.2 1.0 O5' C:U5P104 4.0 38.0 0.5 CA C:TYR48 4.1 16.4 1.0 CA C:PHE62 4.2 10.6 1.0 CD1 C:TYR48 4.3 37.0 1.0 CD1 C:PHE62 4.3 14.1 1.0 CD2 C:HIS64 4.5 11.3 1.0 CG C:PHE62 4.6 12.4 1.0 NE2 C:HIS64 4.6 11.8 1.0 CG C:TYR48 4.6 29.3 1.0 CG C:LYS63 4.7 11.7 1.0 O C:PHE62 4.7 10.6 1.0 O2P C:U5P104 4.7 31.7 0.5 C1' C:U5P104 4.8 27.4 0.5 O C:LYS63 4.9 11.4 1.0

Sodium binding site 5 out of 5 in the High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High-Resolution Structure of Hfq From Methanococcus Jannaschii in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ F:Na103 b:21.5 occ:1.00 O F:TYR48 2.8 12.2 1.0 O3' A:U5P104 2.9 32.3 0.8 N F:HIS64 2.9 9.5 1.0 ND1 F:HIS64 3.0 13.1 1.0 N F:LYS63 3.3 8.7 1.0 O2' A:U5P104 3.3 25.6 0.4 C5' F:U5P104 3.4 33.4 0.7 O5' F:U5P104 3.4 40.3 0.7 CG F:HIS64 3.6 9.8 1.0 CB F:HIS64 3.6 12.1 1.0 C2' A:U5P104 3.7 30.7 1.0 O4' F:U5P104 3.7 29.3 0.7 CA F:LYS63 3.7 8.1 1.0 CB F:LYS63 3.8 9.4 1.0 C F:LYS63 3.8 9.4 1.0 C4' F:U5P104 3.8 28.5 0.7 C F:TYR48 3.8 11.4 1.0 C3' A:U5P104 3.8 34.9 0.7 CB F:TYR48 3.8 17.9 1.0 CA F:HIS64 3.8 9.8 1.0 CE1 F:HIS64 3.9 11.8 1.0 C F:PHE62 3.9 8.9 1.0 CA F:TYR48 4.0 14.4 1.0 CB F:PHE62 4.0 10.1 1.0 CD1 F:TYR48 4.1 32.0 1.0 CA F:PHE62 4.2 10.7 1.0 CD1 F:PHE62 4.3 12.8 1.0 CG F:TYR48 4.5 22.8 1.0 CD2 F:HIS64 4.6 10.7 1.0 CG F:PHE62 4.6 10.6 1.0 NE2 F:HIS64 4.7 10.1 1.0 CG F:LYS63 4.7 10.2 1.0 O F:PHE62 4.8 11.0 1.0 O F:LYS63 4.9 10.6 1.0 P F:U5P104 4.9 58.9 0.7

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