Sodium in PDB 5wph: Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440

The structure of Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440, PDB code: 5wph was solved by S.Venkadesh, D.S.Dheeman, M.Yoshinaga, P.Kandavelu, B.P.Rosen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.02 / 2.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	185.273, 141.735, 54.551, 90.00, 90.59, 90.00
R / Rfree (%)	18 / 23.2

The structure of Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440 (pdb code 5wph). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440, PDB code: 5wph:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440


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 Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:33.0 occ:1.00 NE2 A:HIS74 3.2 34.7 1.0 OH B:TYR160 3.3 25.3 1.0 CG B:PHE145 3.6 22.2 1.0 CD1 B:PHE145 3.7 20.0 1.0 CD A:ARG75 3.7 43.2 1.0 CE2 B:TYR160 3.8 23.5 1.0 CE1 A:TYR80 3.8 24.6 1.0 CD2 B:PHE145 3.9 22.8 1.0 CB B:PHE145 3.9 21.5 1.0 CZ B:TYR160 4.0 24.5 1.0 CE1 A:HIS74 4.0 26.3 1.0 OH A:TYR80 4.1 25.5 1.0 CD2 A:HIS74 4.1 24.8 1.0 CE1 B:PHE145 4.2 22.2 1.0 CG1 B:VAL148 4.2 20.1 1.0 CZ A:TYR80 4.3 25.4 1.0 CG2 B:VAL148 4.3 21.4 1.0 CE2 B:PHE145 4.4 24.6 1.0 CZ B:PHE145 4.5 19.1 1.0 CB B:VAL158 4.6 23.7 1.0 CD1 A:TYR80 4.6 21.6 1.0 NE A:ARG75 4.6 44.2 1.0 CG1 B:VAL158 4.8 25.3 1.0 CB B:VAL148 4.8 25.6 1.0 CG A:ARG75 4.8 32.3 1.0 CD2 B:TYR160 5.0 19.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440


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 Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:32.3 occ:1.00 NE2 B:HIS74 3.2 28.7 1.0 O B:HOH508 3.2 42.8 1.0 OH A:TYR160 3.4 30.4 1.0 CD B:ARG75 3.5 44.1 1.0 CG A:PHE145 3.7 24.7 1.0 CE1 B:TYR80 3.7 24.7 1.0 CE2 A:TYR160 3.7 24.2 1.0 CD1 A:PHE145 3.8 25.9 1.0 CD2 A:PHE145 4.0 24.5 1.0 CD2 B:HIS74 4.0 27.2 1.0 CZ A:TYR160 4.1 25.1 1.0 CB A:PHE145 4.1 22.7 1.0 OH B:TYR80 4.1 28.1 1.0 CE1 B:HIS74 4.2 30.5 1.0 CE1 A:PHE145 4.2 26.8 1.0 CZ B:TYR80 4.3 25.0 1.0 CG1 A:VAL148 4.4 16.0 1.0 CG2 A:VAL148 4.4 18.5 1.0 CE2 A:PHE145 4.4 27.7 1.0 CG B:ARG75 4.5 36.4 1.0 CZ A:PHE145 4.5 24.6 1.0 NE B:ARG75 4.5 46.6 1.0 CG1 A:VAL158 4.5 20.2 1.0 CD1 B:TYR80 4.5 24.6 1.0 CB A:VAL158 4.6 19.7 1.0 NH1 B:ARG75 4.7 51.6 1.0 CB A:VAL148 4.9 19.1 1.0 CD2 A:TYR160 5.0 22.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440


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 Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:35.2 occ:1.00 NE2 F:HIS74 3.2 23.3 1.0 OH C:TYR160 3.3 31.6 1.0 CE1 F:TYR80 3.5 25.0 1.0 CD F:ARG75 3.7 37.6 1.0 CE2 C:TYR160 3.8 25.9 1.0 CG C:PHE145 3.8 23.6 1.0 CD1 C:PHE145 4.0 24.4 1.0 CD2 F:HIS74 4.0 27.8 1.0 CZ C:TYR160 4.0 26.1 1.0 CG2 C:VAL148 4.0 25.3 1.0 OH F:TYR80 4.1 32.1 1.0 CB C:PHE145 4.1 22.2 1.0 CG1 C:VAL148 4.1 21.6 1.0 CZ F:TYR80 4.1 26.2 1.0 CD2 C:PHE145 4.2 23.1 1.0 CE1 F:HIS74 4.3 26.1 1.0 CD1 F:TYR80 4.3 24.4 1.0 CE1 C:PHE145 4.4 25.8 1.0 CB C:VAL158 4.5 23.7 1.0 CG1 C:VAL158 4.6 22.0 1.0 CE2 C:PHE145 4.6 23.6 1.0 CB C:VAL148 4.6 27.2 1.0 NE F:ARG75 4.7 39.2 1.0 CG F:ARG75 4.7 27.4 1.0 CZ C:PHE145 4.7 25.0 1.0 CG2 C:VAL158 4.8 25.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440


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 Arsn, N-Acetyltransferase with Substrate Ast From Pseudomonas Putida KT2440 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:35.3 occ:1.00 NE2 D:HIS74 3.2 25.9 1.0 OH E:TYR160 3.4 44.5 1.0 CD D:ARG75 3.6 43.1 1.0 CE1 D:TYR80 3.7 25.3 1.0 CE2 E:TYR160 3.8 30.7 1.0 CG E:PHE145 3.9 24.9 1.0 OH D:TYR80 4.0 30.0 1.0 CD1 E:PHE145 4.1 23.4 1.0 CD2 D:HIS74 4.1 28.3 1.0 CZ E:TYR160 4.1 31.3 1.0 CD2 E:PHE145 4.1 25.1 1.0 CE1 D:HIS74 4.1 30.3 1.0 CZ D:TYR80 4.2 26.5 1.0 CB E:PHE145 4.2 26.3 1.0 CG2 E:VAL148 4.4 20.9 1.0 CG1 E:VAL148 4.5 17.3 1.0 CE1 E:PHE145 4.5 26.2 1.0 CD1 D:TYR80 4.5 27.2 1.0 CG D:ARG75 4.5 34.2 1.0 CE2 E:PHE145 4.5 27.5 1.0 CB E:VAL158 4.7 22.1 1.0 NE D:ARG75 4.7 45.4 1.0 CG1 E:VAL158 4.7 21.6 1.0 CZ E:PHE145 4.7 22.9 1.0 CB E:VAL148 5.0 22.1 1.0

V.S.Nadar, J.Chen, D.S.Dheeman, A.E.Galvan, K.Yoshinaga-Sakurai, P.Kandavelu, B.Sankaran, M.Kuramata, S.Ishikawa, B.P.Rosen, M.Yoshinaga. Arsinothricin, An Arsenic-Containing Non-Proteinogenic Amino Acid Analog of Glutamate, Is A Broad-Spectrum Antibiotic. Commun Biol V. 2 131 2019.
ISSN: ESSN 2399-3642
PubMed: 30993215
DOI: 10.1038/S42003-019-0365-Y