Sodium in PDB 3kbc: Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury

The structure of Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury, PDB code: 3kbc was solved by N.Reyes, C.Ginter, O.Boudker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 3.51
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	113.142, 206.780, 205.971, 90.00, 90.00, 90.00
R / Rfree (%)	26.7 / 27

The structure of Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury also contains other interesting chemical elements:

Mercury

(Hg)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury (pdb code 3kbc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury, PDB code: 3kbc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury


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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range: probe atom residue distance (Å) B Occ A:Na454 b:86.1 occ:1.00 O A:GLY306 2.1 0.3 1.0 O A:ASN310 2.5 0.8 1.0 OD1 A:ASP405 2.7 0.1 1.0 O A:ASN401 3.0 0.4 1.0 OD2 A:ASP405 3.1 0.7 1.0 O A:ILE309 3.2 1.0 1.0 CG A:ASP405 3.3 1.0 1.0 C A:GLY306 3.3 0.3 1.0 C A:ASN310 3.4 0.7 1.0 C A:ASN401 3.6 0.4 1.0 CB A:ASN401 3.9 0.6 1.0 CG A:MET311 4.0 0.2 1.0 CA A:ASN401 4.0 0.5 1.0 CA A:MET311 4.1 0.0 1.0 N A:MET311 4.1 0.9 1.0 CA A:GLY306 4.2 0.2 1.0 CB A:ASN310 4.3 0.5 1.0 N A:ALA307 4.3 0.4 1.0 C A:ILE309 4.3 0.9 1.0 OG A:SER278 4.3 0.2 1.0 CA A:ASN310 4.4 0.5 1.0 CA A:ALA307 4.5 0.6 1.0 CG A:ASN310 4.5 0.3 1.0 N A:VAL402 4.5 0.3 1.0 C A:ALA307 4.6 0.7 1.0 CB A:MET311 4.6 0.2 1.0 O A:ALA307 4.7 0.8 1.0 CB A:ASP405 4.7 0.6 1.0 OD1 A:ASN310 4.8 0.8 1.0 N A:ASN310 4.8 0.2 1.0 CG A:ASN401 4.9 0.6 1.0 CA A:VAL402 5.0 0.2 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury


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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range: probe atom residue distance (Å) B Occ A:Na453 b:97.5 occ:1.00 O A:SER349 2.3 99.1 1.0 C A:ILE350 2.5 99.1 1.0 O A:THR352 2.6 100.0 1.0 O A:ILE350 2.7 99.1 1.0 O A:THR308 2.7 0.3 1.0 N A:GLY351 3.0 99.2 1.0 CA A:ILE350 3.0 99.0 1.0 N A:THR352 3.0 99.9 1.0 C A:SER349 3.2 99.0 1.0 C A:GLY351 3.2 99.7 1.0 C A:THR352 3.4 0.1 1.0 N A:ILE350 3.5 99.0 1.0 CA A:GLY351 3.6 99.5 1.0 CA A:THR352 3.6 0.1 1.0 SD A:MET311 3.6 0.8 1.0 C A:THR308 3.8 0.3 1.0 O A:GLY351 3.9 99.8 1.0 CB A:THR352 4.0 0.1 1.0 CG A:MET311 4.3 0.2 1.0 CB A:ILE350 4.4 99.0 1.0 CA A:ILE309 4.5 0.6 1.0 N A:ILE309 4.5 0.5 1.0 CA A:SER349 4.6 99.0 1.0 CG2 A:ILE350 4.6 99.0 1.0 N A:ALA353 4.7 0.3 1.0 CA A:THR308 4.7 0.2 1.0 OG1 A:THR352 4.8 0.1 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury


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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range: probe atom residue distance (Å) B Occ B:Na454 b:85.4 occ:1.00 O B:GLY306 2.1 0.5 1.0 O B:ASN310 2.5 0.6 1.0 OD1 B:ASP405 2.7 0.8 1.0 O B:ASN401 3.1 0.6 1.0 OD2 B:ASP405 3.1 0.0 1.0 O B:ILE309 3.2 0.9 1.0 CG B:ASP405 3.3 0.7 1.0 C B:GLY306 3.3 0.6 1.0 C B:ASN310 3.4 0.5 1.0 C B:ASN401 3.7 0.5 1.0 CB B:ASN401 3.9 0.5 1.0 CG B:MET311 4.0 0.1 1.0 CA B:ASN401 4.1 0.5 1.0 CA B:MET311 4.1 0.8 1.0 N B:MET311 4.1 0.7 1.0 CA B:GLY306 4.1 0.5 1.0 CB B:ASN310 4.2 0.3 1.0 C B:ILE309 4.3 0.9 1.0 N B:ALA307 4.3 0.7 1.0 CA B:ASN310 4.3 0.3 1.0 OG B:SER278 4.4 0.6 1.0 CA B:ALA307 4.5 0.8 1.0 CG B:ASN310 4.5 0.2 1.0 C B:ALA307 4.5 0.9 1.0 N B:VAL402 4.6 0.4 1.0 CB B:MET311 4.6 0.9 1.0 O B:ALA307 4.7 1.0 1.0 OD1 B:ASN310 4.8 0.8 1.0 CB B:ASP405 4.8 0.6 1.0 N B:ASN310 4.8 0.1 1.0 CG B:ASN401 4.9 0.6 1.0 ND2 B:ASN310 5.0 0.5 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury


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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range: probe atom residue distance (Å) B Occ B:Na453 b:98.1 occ:1.00 O B:SER349 2.2 98.9 1.0 C B:ILE350 2.5 99.4 1.0 O B:THR352 2.6 0.2 1.0 O B:ILE350 2.6 99.4 1.0 O B:THR308 2.7 0.5 1.0 N B:GLY351 2.9 99.5 1.0 CA B:ILE350 2.9 99.2 1.0 N B:THR352 3.0 0.1 1.0 C B:SER349 3.1 99.0 1.0 C B:GLY351 3.2 99.9 1.0 N B:ILE350 3.4 99.1 1.0 C B:THR352 3.5 0.2 1.0 CA B:GLY351 3.5 99.8 1.0 CA B:THR352 3.6 0.2 1.0 SD B:MET311 3.6 0.4 1.0 C B:THR308 3.8 0.5 1.0 O B:GLY351 3.9 0.0 1.0 CB B:THR352 3.9 0.1 1.0 CG B:MET311 4.3 0.1 1.0 CB B:ILE350 4.3 99.2 1.0 CA B:ILE309 4.5 0.7 1.0 CA B:SER349 4.5 98.9 1.0 N B:ILE309 4.6 0.6 1.0 CG2 B:ILE350 4.6 98.9 1.0 N B:ALA353 4.7 0.3 1.0 CA B:THR308 4.8 0.4 1.0 OG1 B:THR352 4.8 0.3 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range: probe atom residue distance (Å) B Occ C:Na454 b:86.8 occ:1.00 O C:GLY306 2.1 0.3 1.0 O C:ASN310 2.5 0.8 1.0 OD1 C:ASP405 2.6 0.2 1.0 O C:ASN401 3.0 0.5 1.0 OD2 C:ASP405 3.1 0.3 1.0 O C:ILE309 3.2 0.2 1.0 CG C:ASP405 3.2 0.0 1.0 C C:GLY306 3.3 0.4 1.0 C C:ASN310 3.5 0.8 1.0 C C:ASN401 3.7 0.5 1.0 CB C:ASN401 3.9 0.5 1.0 CG C:MET311 4.0 0.2 1.0 CA C:ASN401 4.1 0.5 1.0 CA C:GLY306 4.1 0.3 1.0 CA C:MET311 4.2 0.0 1.0 N C:MET311 4.2 0.9 1.0 CB C:ASN310 4.3 0.7 1.0 N C:ALA307 4.3 0.5 1.0 C C:ILE309 4.3 0.1 1.0 OG C:SER278 4.3 0.8 1.0 CA C:ASN310 4.4 0.6 1.0 CA C:ALA307 4.4 0.7 1.0 CG C:ASN310 4.5 0.7 1.0 C C:ALA307 4.5 0.9 1.0 N C:VAL402 4.5 0.5 1.0 O C:ALA307 4.7 0.9 1.0 CB C:MET311 4.7 0.1 1.0 CB C:ASP405 4.7 0.8 1.0 OD1 C:ASN310 4.8 0.6 1.0 N C:ASN310 4.8 0.3 1.0 CG C:ASN401 4.9 0.5 1.0 CA C:VAL402 5.0 0.5 1.0 ND2 C:ASN310 5.0 0.6 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range: probe atom residue distance (Å) B Occ C:Na453 b:98.6 occ:1.00 O C:SER349 2.2 99.1 1.0 C C:ILE350 2.5 99.2 1.0 O C:ILE350 2.6 99.2 1.0 O C:THR352 2.6 0.2 1.0 O C:THR308 2.7 0.5 1.0 CA C:ILE350 2.9 99.1 1.0 N C:GLY351 2.9 99.3 1.0 N C:THR352 3.0 99.8 1.0 C C:SER349 3.1 99.1 1.0 C C:GLY351 3.2 99.7 1.0 N C:ILE350 3.4 99.1 1.0 C C:THR352 3.5 0.2 1.0 CA C:GLY351 3.5 99.5 1.0 CA C:THR352 3.6 0.1 1.0 SD C:MET311 3.6 0.3 1.0 C C:THR308 3.8 0.5 1.0 O C:GLY351 3.9 99.7 1.0 CB C:THR352 4.0 0.1 1.0 CB C:ILE350 4.3 99.1 1.0 CG C:MET311 4.3 0.2 1.0 CA C:ILE309 4.5 0.9 1.0 CA C:SER349 4.5 99.0 1.0 N C:ILE309 4.6 0.7 1.0 CG2 C:ILE350 4.6 99.0 1.0 CA C:THR308 4.8 0.4 1.0 N C:ALA353 4.8 0.3 1.0 OG1 C:THR352 4.8 0.1 1.0

N.Reyes, C.Ginter, O.Boudker. Transport Mechanism of A Bacterial Homologue of Glutamate Transporters. Nature V. 462 880 2009.
ISSN: ISSN 0028-0836
PubMed: 19924125
DOI: 10.1038/NATURE08616