Sodium in PDB 2hzl: Crystal Structures of A Sodium-Alpha-Keto Acid Binding Subunit From A Trap Transporter in Its Closed Forms

The structure of Crystal Structures of A Sodium-Alpha-Keto Acid Binding Subunit From A Trap Transporter in Its Closed Forms, PDB code: 2hzl was solved by S.Gonin, P.Arnoux, B.Pierru, B.Alonso, M.Sabaty, D.Pignol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.01 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.021, 78.057, 95.139, 90.00, 124.98, 90.00
R / Rfree (%)	17.3 / 18.4

The binding sites of Sodium atom in the Crystal Structures of A Sodium-Alpha-Keto Acid Binding Subunit From A Trap Transporter in Its Closed Forms (pdb code 2hzl). 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 Structures of A Sodium-Alpha-Keto Acid Binding Subunit From A Trap Transporter in Its Closed Forms, PDB code: 2hzl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structures of A Sodium-Alpha-Keto Acid Binding Subunit From A Trap Transporter in Its Closed Forms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structures of A Sodium-Alpha-Keto Acid Binding Subunit From A Trap Transporter in Its Closed Forms within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:4.5 occ:1.00 O A:TRP215 2.3 6.6 1.0 OE1 A:GLU214 2.4 13.0 1.0 OE1 A:GLN156 2.4 6.5 1.0 O2 A:PYR601 2.4 9.3 1.0 OE2 A:GLU240 2.4 8.8 1.0 O3 A:PYR601 2.5 8.9 1.0 OE2 A:GLU214 2.8 18.1 1.0 CD A:GLU214 3.0 12.0 1.0 C1 A:PYR601 3.2 9.6 1.0 CD A:GLU240 3.2 9.5 1.0 C2 A:PYR601 3.3 9.7 1.0 CD A:GLN156 3.4 6.6 1.0 C A:TRP215 3.5 6.3 1.0 OE1 A:GLU240 3.5 9.8 1.0 NE2 A:GLN156 3.7 7.1 1.0 OH A:TYR99 3.9 10.9 1.0 O A:HOH634 4.1 11.3 1.0 CA A:TRP215 4.2 6.7 1.0 NH1 A:ARG177 4.4 8.7 1.0 NE1 A:TRP239 4.4 9.5 1.0 CD1 A:TRP239 4.4 9.2 1.0 CG A:GLU240 4.4 8.1 1.0 O A:HOH662 4.5 14.9 1.0 CG A:GLU214 4.5 9.8 1.0 O1 A:PYR601 4.5 8.9 1.0 N A:VAL216 4.5 6.0 1.0 N A:TRP215 4.6 7.1 1.0 C3 A:PYR601 4.7 10.1 1.0 CA A:VAL216 4.7 6.3 1.0 CG A:GLN156 4.7 6.4 1.0 C A:GLU214 4.8 8.2 1.0 O A:GLU214 4.9 8.7 1.0 CG2 A:VAL216 4.9 6.3 1.0 CZ A:TYR99 4.9 9.7 1.0 N A:GLY179 5.0 11.7 1.0 CB A:GLU240 5.0 7.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structures of A Sodium-Alpha-Keto Acid Binding Subunit From A Trap Transporter in Its Closed Forms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structures of A Sodium-Alpha-Keto Acid Binding Subunit From A Trap Transporter in Its Closed Forms within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:4.2 occ:1.00 O B:TRP215 2.3 6.0 1.0 OE1 B:GLU214 2.3 13.2 1.0 OE1 B:GLN156 2.4 6.1 1.0 O2 B:PYR602 2.4 9.3 1.0 OE2 B:GLU240 2.4 10.3 1.0 O3 B:PYR602 2.5 8.8 1.0 OE2 B:GLU214 3.0 17.9 1.0 CD B:GLU214 3.0 11.8 1.0 CD B:GLU240 3.2 9.2 1.0 C1 B:PYR602 3.2 9.2 1.0 C2 B:PYR602 3.3 8.6 1.0 CD B:GLN156 3.4 6.3 1.0 C B:TRP215 3.5 5.3 1.0 OE1 B:GLU240 3.5 9.3 1.0 NE2 B:GLN156 3.7 5.3 1.0 OH B:TYR99 3.9 11.0 1.0 O B:HOH656 4.1 10.2 1.0 CA B:TRP215 4.1 5.3 1.0 NH1 B:ARG177 4.4 7.4 1.0 O B:HOH702 4.4 17.4 1.0 CD1 B:TRP239 4.4 8.9 1.0 NE1 B:TRP239 4.4 8.9 1.0 CG B:GLU240 4.4 7.0 1.0 O1 B:PYR602 4.5 8.5 1.0 CG B:GLU214 4.5 8.7 1.0 N B:TRP215 4.5 5.6 1.0 N B:VAL216 4.5 4.7 1.0 C3 B:PYR602 4.7 10.4 1.0 CA B:VAL216 4.7 5.4 1.0 CG B:GLN156 4.7 5.6 1.0 C B:GLU214 4.8 6.1 1.0 CG2 B:VAL216 4.9 4.3 1.0 O B:GLU214 4.9 7.0 1.0 CZ B:TYR99 4.9 9.7 1.0 CB B:GLU240 5.0 6.5 1.0

S.Gonin, P.Arnoux, B.Pierru, J.Lavergne, B.Alonso, M.Sabaty, D.Pignol. Crystal Structures of An Extracytoplasmic Solute Receptor From A Trap Transporter in Its Open and Closed Forms Reveal A Helix-Swapped Dimer Requiring A Cation For Alpha-Keto Acid Binding. Bmc Struct.Biol. V. 7 11 2007.
ISSN: ESSN 1472-6807
PubMed: 17362499
DOI: 10.1186/1472-6807-7-11