Sodium in PDB 7f6t: Crystal Structure of Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State

The structure of Crystal Structure of Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State, PDB code: 7f6t was solved by S.P.Kanaujia, S.K.Mandal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.24 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.7, 108.37, 163.41, 90, 90, 90
R / Rfree (%)	17.3 / 20.7

The structure of Crystal Structure of Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State (pdb code 7f6t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State, PDB code: 7f6t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State


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 Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:35.7 occ:1.00 OD2 A:ASP265 2.7 22.2 1.0 O A:HOH554 2.9 29.7 1.0 O A:ALA6 2.9 45.3 1.0 CD2 A:LEU262 3.4 28.6 1.0 CB A:ASP265 3.5 21.2 1.0 CG A:ASP265 3.5 21.2 1.0 CA A:SER7 3.6 48.8 1.0 C A:ALA6 3.9 43.4 1.0 CA A:LEU262 4.1 25.2 1.0 CB A:SER7 4.1 51.6 1.0 N A:SER7 4.2 49.2 1.0 OH A:TYR43 4.3 35.8 1.0 O A:LYS261 4.5 23.1 1.0 OH A:TYR96 4.5 23.9 1.0 N A:ASP8 4.5 47.6 1.0 C A:SER7 4.6 48.8 1.0 O A:LEU262 4.6 24.5 1.0 CG A:LEU262 4.7 28.4 1.0 O A:HOH595 4.7 32.8 1.0 CB A:LEU262 4.7 26.9 1.0 N A:LEU262 4.7 24.5 1.0 OD1 A:ASP265 4.8 20.7 1.0 CB A:PRO5 4.9 35.8 1.0 C A:LEU262 4.9 23.9 1.0 C A:LYS261 4.9 24.4 1.0 CA A:ASP265 4.9 19.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State


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 Metal-Citrate-Binding Mutant (Y221F) Protein (Mcta) of Abc Transporter in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:21.1 occ:1.00 O A:HOH707 2.3 33.8 1.0 OG1 A:THR288 3.1 20.6 1.0 NE A:ARG286 3.1 19.4 1.0 NH1 A:ARG286 3.2 20.7 1.0 O A:HOH696 3.4 35.8 1.0 CZ A:ARG286 3.6 19.6 1.0 CB A:THR288 3.9 21.5 1.0 CG2 A:THR288 4.0 21.7 1.0 CD2 A:LEU270 4.1 26.8 1.0 CD A:ARG286 4.2 18.3 1.0 CB A:LEU270 4.2 24.0 1.0 CG A:LEU270 4.6 24.9 1.0 O A:HOH546 4.6 20.8 1.0 CG A:ARG286 4.7 17.1 1.0 O A:HOH699 4.8 25.9 1.0 CD1 A:LEU270 4.8 24.0 1.0 NH2 A:ARG286 4.9 18.2 1.0 O A:HOH532 4.9 36.5 1.0

S.K.Mandal, S.P.Kanaujia. Structural and Thermodynamic Insights Into A Novel MG2+-Citrate-Binding Protein From the Abc Transporter Superfamily Acta Crystallogr.,Sect.D V. 77 2021.
ISSN: ESSN 1399-0047
DOI: DOI.ORG/10.1107/S2059798321010457