Sodium in PDB 5zk0: Crystal Structure of Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae

All present enzymatic activity of Crystal Structure of Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae:
3.1.1.29;

The structure of Crystal Structure of Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae, PDB code: 5zk0 was solved by S.Shahid, A.Kabra, R.K.Pal, A.Arora, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.81 / 2.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.709, 117.491, 201.618, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 26.3

The binding sites of Sodium atom in the Crystal Structure of Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae (pdb code 5zk0). 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 Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae, PDB code: 5zk0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae


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 Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:17.0 occ:1.00 ND2 A:ASN25 3.2 28.4 1.0 N A:LYS21 3.2 39.1 1.0 NE1 A:TRP29 3.3 25.7 1.0 CB A:ASN25 3.8 29.0 1.0 CD1 A:TRP29 3.9 24.7 1.0 CA A:LYS21 3.9 38.1 1.0 CG A:ASN25 4.0 29.9 1.0 C A:ALA20 4.2 39.7 1.0 CA A:ALA20 4.2 39.4 1.0 CE2 A:TRP29 4.5 24.8 1.0 CD A:LYS21 4.5 41.9 1.0 O A:HOH313 4.7 21.5 1.0 O A:TYR19 4.8 36.9 1.0 N A:THR22 4.9 30.6 1.0 CG A:LYS21 4.9 42.5 1.0 C A:LYS21 4.9 35.8 1.0 CB A:ALA20 4.9 38.5 1.0 CB A:LYS21 5.0 40.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae


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 Peptidyl-Trna Hydrolase Mutant -M71A From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:29.1 occ:1.00 O B:HOH346 3.1 42.5 1.0 N B:LYS21 3.3 42.9 1.0 ND2 B:ASN25 3.3 32.5 1.0 NE1 B:TRP29 3.3 28.8 1.0 CB B:ASN25 3.9 28.9 1.0 CD1 B:TRP29 3.9 29.7 1.0 CA B:LYS21 4.1 43.5 1.0 CA B:ALA20 4.1 43.9 1.0 CG B:ASN25 4.1 30.4 1.0 C B:ALA20 4.2 41.7 1.0 CE2 B:TRP29 4.5 30.2 1.0 CB B:ALA20 4.5 42.5 1.0 OE2 B:GLU32 4.6 53.8 1.0 O B:HOH309 4.8 22.4 1.0 O B:TYR19 4.9 44.7 1.0 CG B:LYS21 5.0 43.8 1.0

S.Shahid, A.Kabra, S.Mundra, R.K.Pal, S.Tripathi, A.Jain, A.Arora. Role of Methionine 71 in Substrate Recognition and Structural Integrity of Bacterial Peptidyl-Trna Hydrolase. Biochim. Biophys. Acta V.1866 865 2018.
ISSN: ISSN 0006-3002
PubMed: 29733913
DOI: 10.1016/J.BBAPAP.2018.05.002