Sodium in PDB 4uhv: The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System

The structure of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System, PDB code: 4uhv was solved by M.Spinola-Amilibia, I.Davo-Siguero, F.M.Ruiz, E.Santillana, F.J.Medrano, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.73 / 1.88
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	78.620, 78.620, 430.320, 90.00, 90.00, 120.00
R / Rfree (%)	22.332 / 24.845

The structure of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System also contains other interesting chemical elements:

Chlorine

(Cl)

38 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System (pdb code 4uhv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System, PDB code: 4uhv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1652 b:34.9 occ:1.00 OD2 A:ASP609 2.3 31.9 1.0 O A:HOH2240 2.6 20.6 1.0 CG A:ASP609 3.5 37.4 1.0 OD1 A:ASP609 4.4 35.9 1.0 CB A:ASP609 4.4 37.3 1.0 O A:ASP609 4.6 38.2 1.0 NH2 A:ARG607 4.9 35.2 1.0 OG A:SER612 5.0 47.3 1.0

Sodium binding site 2 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1653 b:35.2 occ:1.00 NE2 A:GLN632 3.2 20.4 1.0 O A:HOH2250 3.3 25.1 1.0 O A:GLY622 3.7 30.2 1.0 CD A:GLN632 4.1 19.9 1.0 CD A:LYS623 4.1 28.1 1.0 O A:HOH2266 4.3 29.2 1.0 CE A:LYS623 4.4 28.1 1.0 OE1 A:GLN632 4.5 20.0 1.0 CG2 A:THR628 4.6 30.9 1.0 C A:GLY622 4.9 27.9 1.0

Sodium binding site 3 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1654 b:41.8 occ:1.00 O A:HOH2126 2.2 46.0 1.0 O A:GLU261 2.5 40.0 1.0 OE1 A:GLU261 3.5 40.8 1.0 C A:GLU261 3.5 42.1 1.0 CA A:TYR262 4.2 42.9 1.0 N A:TYR262 4.2 41.7 1.0 O A:HOH2075 4.4 27.5 1.0 CB A:GLU261 4.5 41.9 1.0 CA A:GLU261 4.6 41.6 1.0 CD A:GLU261 4.6 42.9 1.0

Sodium binding site 4 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1655 b:34.9 occ:1.00 O A:HIS397 3.0 36.9 1.0 O A:HOH2181 3.5 35.9 1.0 O A:HOH2182 3.7 23.6 1.0 C A:HIS397 3.8 36.2 1.0 CB A:HIS397 3.9 33.6 1.0 CA A:HIS397 4.4 35.4 1.0 OE1 A:GLN399 4.4 35.4 1.0 N A:ASP398 4.6 35.7 1.0 CA A:ASP398 4.8 34.2 1.0 CG A:HIS397 4.9 32.0 1.0

Sodium binding site 5 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1710 b:36.5 occ:1.00 O A:HOH2267 3.6 27.1 1.0 OG A:SER188 4.1 39.8 1.0 CB A:SER188 4.8 44.7 1.0 N A:SER188 5.0 45.4 1.0

Sodium binding site 6 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1711 b:33.4 occ:1.00 O A:ASP603 3.7 38.6 1.0 O A:HOH2238 4.3 26.1 1.0 OD1 A:ASN601 4.3 34.4 1.0 O A:HOH2268 4.3 33.7 1.0 O A:ILE602 4.5 45.0 1.0 C A:ASP603 4.7 42.9 1.0

Sodium binding site 7 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1662 b:20.5 occ:1.00 OG B:SER553 2.9 18.4 1.0 CB B:SER553 3.9 19.5 1.0 O B:HOH2274 4.2 21.9 1.0 CA B:SER553 5.0 19.5 1.0

Sodium binding site 8 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1663 b:61.0 occ:1.00 O B:HOH2275 2.9 24.8 1.0 OG1 B:THR201 3.0 63.7 1.0 CD2 B:LEU202 3.8 50.7 1.0 CG2 B:THR201 4.1 56.8 1.0 CB B:THR201 4.1 58.5 1.0 O B:THR201 4.9 58.1 1.0

Sodium binding site 9 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1710 b:32.6 occ:1.00 O B:HOH2276 3.4 36.8 1.0 O B:HOH2227 4.7 18.8 1.0 O B:HOH2277 4.7 24.0 1.0

Sodium binding site 10 out of 13 in the The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Structure of VGRG1, the Needle Tip of the Bacterial Type VI Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1711 b:48.7 occ:1.00 O B:HOH2070 2.6 24.2 1.0 CE3 B:TRP96 3.8 34.6 1.0 CB B:TRP96 4.1 36.1 1.0 O B:TRP96 4.1 31.4 1.0 CD2 B:TRP96 4.5 37.3 1.0 O B:LEU125 4.5 39.5 1.0 CD1 B:LEU100 4.6 25.6 1.0 CG B:TRP96 4.6 36.0 1.0 CZ3 B:TRP96 4.7 35.5 1.0 C B:TRP96 4.7 33.4 1.0 CA B:GLY126 4.8 40.3 1.0 CA B:TRP96 4.9 33.6 1.0 CB B:LEU99 4.9 26.4 1.0 CD1 B:LEU99 4.9 25.1 1.0 CE2 B:PHE127 4.9 34.4 1.0 CD2 B:PHE127 5.0 33.8 1.0

M.Spinola-Amilibia, I.Davo-Siguero, F.M.Ruiz, E.Santillana, F.J.Medrano, A.Romero. The Structure of VGRG1 From Pseudomonas Aeruginosa, the Needle Tip of the Bacterial Type VI Secretion System Acta Crystallogr.,Sect.D V. 72 34 2016.
ISSN: ESSN 1399-0047
PubMed: 26894532
DOI: 10.1107/S205979831502149X