Vanadium in PDB 4zi4: Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site

All present enzymatic activity of Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site:
3.1.3.48;

The structure of Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site, PDB code: 4zi4 was solved by G.E.Moise, S.J.Johnson, A.C.Hengge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.26 / 1.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.888, 60.512, 89.358, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 15.9

The binding sites of Vanadium atom in the Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site (pdb code 4zi4). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 3 binding sites of Vanadium where determined in the Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site, PDB code: 4zi4:
Jump to Vanadium binding site number: 1; 2; 3;

Vanadium binding site 1 out of 3 in the Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:V501 b:16.9 occ:0.77 V02 A:DVG501 0.0 16.9 0.8 O01 A:DVG501 1.7 15.7 0.8 O03 A:DVG501 1.9 19.7 0.8 O09 A:DVG501 1.9 13.8 0.8 O3 A:DVG501 1.9 19.4 0.7 O2 A:DVG501 2.0 14.6 0.7 H011 A:DVG501 2.2 18.8 0.8 C3 A:DVG501 2.8 18.4 0.7 C2 A:DVG501 2.9 17.3 0.7 V06 A:DVG501 2.9 12.6 0.8 HE22 A:GLN450 3.1 18.5 1.0 HA3 A:GLY408 3.1 14.4 1.0 H32 A:DVG501 3.2 22.0 0.7 H2 A:DVG501 3.2 20.8 0.7 HE A:ARG409 3.4 18.1 0.5 H A:ARG409 3.4 13.6 0.5 H A:ARG409 3.4 13.6 0.5 HG3 A:ARG409 3.4 13.9 0.5 HE3 A:LYS447 3.5 36.8 1.0 HZ2 A:LYS447 3.6 43.3 1.0 HG3 A:ARG409 3.7 17.1 0.5 H31 A:DVG501 3.8 22.0 0.7 HE A:ARG409 3.8 19.1 0.5 NE2 A:GLN450 3.8 15.5 1.0 HE21 A:GLN450 3.9 18.5 1.0 HH21 A:ARG409 3.9 19.0 0.5 OE1 A:GLN446 3.9 20.2 1.0 O07 A:DVG501 3.9 12.3 0.8 NE A:ARG409 3.9 15.1 0.5 O08 A:DVG501 4.0 15.6 0.8 CA A:GLY408 4.1 12.0 1.0 O A:HOH702 4.1 30.4 1.0 N A:ARG409 4.1 11.3 1.0 HZ1 A:LYS447 4.2 43.3 1.0 NZ A:LYS447 4.2 36.1 1.0 C1 A:DVG501 4.2 21.5 0.7 CE A:LYS447 4.2 30.7 1.0 HD2 A:LYS447 4.4 32.7 1.0 NE A:ARG409 4.4 15.9 0.5 CG A:ARG409 4.4 11.6 0.5 NH2 A:ARG409 4.4 15.8 0.5 H A:GLY408 4.5 14.6 1.0 O1 A:DVG501 4.5 23.0 0.7 CG A:ARG409 4.5 14.3 0.5 CZ A:ARG409 4.5 15.4 0.5 O A:HOH872 4.6 21.4 1.0 H11 A:DVG501 4.6 25.8 0.7 C A:GLY408 4.6 11.6 1.0 HA2 A:GLY408 4.6 14.4 1.0 N A:GLY408 4.7 12.2 1.0 HB3 A:GLN446 4.7 17.9 1.0 CD A:ARG409 4.7 17.2 0.5 HH21 A:ARG409 4.8 26.1 0.5 CD A:ARG409 4.8 13.4 0.5 CD A:LYS447 4.8 27.3 1.0 HD2 A:ARG409 4.8 16.1 0.5 HG3 A:LYS447 4.8 24.7 1.0 HB2 A:ARG409 4.9 16.0 0.5 HD3 A:ARG409 4.9 20.6 0.5 HG2 A:ARG409 4.9 13.9 0.5 HZ3 A:LYS447 5.0 43.3 1.0 H12 A:DVG501 5.0 25.8 0.7

Vanadium binding site 2 out of 3 in the Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:V501 b:12.6 occ:0.77 V06 A:DVG501 0.0 12.6 0.8 O07 A:DVG501 1.8 12.3 0.8 O08 A:DVG501 1.8 15.6 0.8 O09 A:DVG501 1.8 13.8 0.8 O2 A:DVG501 2.0 14.6 0.7 SG A:CYS403 2.5 12.7 1.0 V02 A:DVG501 2.9 16.9 0.8 C2 A:DVG501 3.1 17.3 0.7 HH21 A:ARG409 3.1 19.0 0.5 HE A:ARG409 3.1 18.1 0.5 H A:GLY408 3.1 14.6 1.0 H A:ALA405 3.2 15.4 1.0 H2 A:DVG501 3.2 20.8 0.7 HB2 A:CYS403 3.3 13.9 1.0 H A:ARG409 3.3 13.6 0.5 H A:ARG409 3.3 13.6 0.5 H A:ARG404 3.4 14.8 0.5 H A:ARG404 3.4 14.8 0.5 H11 A:DVG501 3.4 25.8 0.7 CB A:CYS403 3.5 11.6 1.0 HA3 A:GLY408 3.6 14.4 1.0 H A:GLY406 3.6 15.5 1.0 H A:VAL407 3.7 13.8 1.0 HB3 A:ALA405 3.7 18.2 1.0 C1 A:DVG501 3.8 21.5 0.7 N A:GLY408 3.8 12.2 1.0 O01 A:DVG501 3.9 15.7 0.8 NH2 A:ARG409 3.9 15.8 0.5 NE A:ARG409 3.9 15.1 0.5 N A:ALA405 4.0 12.8 1.0 N A:ARG409 4.0 11.3 1.0 HB3 A:ARG404 4.1 18.4 0.5 N A:ARG404 4.1 12.4 1.0 HB3 A:CYS403 4.1 13.9 1.0 HB2 A:ARG409 4.1 16.0 0.5 HG3 A:ARG409 4.1 13.9 0.5 CA A:GLY408 4.1 12.0 1.0 HB2 A:ARG409 4.2 13.1 0.5 O3 A:DVG501 4.2 19.4 0.7 C3 A:DVG501 4.2 18.4 0.7 HB2 A:ARG404 4.3 17.6 0.5 N A:GLY406 4.3 13.0 1.0 O03 A:DVG501 4.3 19.7 0.8 O1 A:DVG501 4.4 23.0 0.7 HD2 A:ARG409 4.4 16.1 0.5 CZ A:ARG409 4.4 15.4 0.5 H A:THR410 4.4 13.0 1.0 CB A:ALA405 4.5 15.2 1.0 N A:VAL407 4.5 11.5 1.0 HG3 A:ARG409 4.5 17.1 0.5 HG22 A:VAL407 4.5 15.9 1.0 HH22 A:ARG409 4.6 19.0 0.5 C A:GLY408 4.6 11.6 1.0 CA A:ALA405 4.7 14.0 1.0 H32 A:DVG501 4.7 22.0 0.7 H12 A:DVG501 4.7 25.8 0.7 HG3 A:ARG404 4.7 21.5 0.5 OE1 A:GLN446 4.7 20.2 1.0 CA A:CYS403 4.7 11.7 1.0 HG23 A:VAL407 4.7 15.9 1.0 H011 A:DVG501 4.7 18.8 0.8 CG A:ARG409 4.8 11.6 0.5 HB2 A:ALA405 4.8 18.2 1.0 CB A:ARG409 4.8 11.0 0.5 CB A:ARG404 4.8 15.3 0.5 CB A:ARG409 4.8 13.3 0.5 CA A:ARG404 4.8 12.9 0.5 C A:CYS403 4.8 12.0 1.0 CA A:ARG404 4.9 13.1 0.5 HG1 A:THR410 4.9 14.8 1.0 C A:ALA405 4.9 13.4 1.0 C A:ARG404 4.9 12.4 1.0 CD A:ARG409 4.9 13.4 0.5 C A:VAL407 5.0 12.2 1.0 HE A:ARG409 5.0 19.1 0.5 CB A:ARG404 5.0 14.7 0.5 H A:CYS403 5.0 13.2 1.0 HA2 A:GLY408 5.0 14.4 1.0

Vanadium binding site 3 out of 3 in the Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of Yoph W354H Yersinia Enterocolitica Ptpase Bond with Divanadate Glycerol Ester in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:V502 b:30.8 occ:0.51 V A:VO4502 0.0 30.8 0.5 O3 A:VO4502 1.9 28.9 0.5 O1 A:VO4502 1.9 32.9 0.5 O2 A:VO4502 1.9 31.0 0.5 O4 A:VO4502 1.9 38.5 0.5 HZ2 A:LYS342 2.7 41.9 1.0 HH21 A:ARG278 2.9 23.5 1.0 HE A:ARG278 3.2 25.2 1.0 HG A:SER388 3.3 22.1 1.0 H A:SER389 3.4 24.7 1.0 NZ A:LYS342 3.5 34.9 1.0 O A:HOH609 3.6 48.6 1.0 HZ3 A:LYS342 3.6 41.9 1.0 HA A:SER388 3.7 21.8 1.0 OG A:SER388 3.7 18.4 1.0 O A:HOH613 3.7 51.5 1.0 NH2 A:ARG278 3.7 19.6 1.0 O A:HOH634 3.8 44.0 1.0 HD2 A:LYS342 3.9 32.2 1.0 HZ1 A:LYS342 4.0 41.9 1.0 NE A:ARG278 4.0 21.0 1.0 OG A:SER389 4.1 28.3 1.0 N A:SER389 4.1 20.6 1.0 H A:ALA390 4.2 23.1 1.0 HB2 A:SER388 4.3 22.3 1.0 HG A:SER389 4.3 34.0 1.0 CZ A:ARG278 4.4 18.1 1.0 HH22 A:ARG278 4.4 23.5 1.0 CA A:SER388 4.4 18.1 1.0 CB A:SER388 4.4 18.6 1.0 CE A:LYS342 4.5 29.0 1.0 CD A:LYS342 4.5 26.9 1.0 HD3 A:LYS342 4.7 32.2 1.0 HE3 A:LYS342 4.7 34.8 1.0 C A:SER388 4.7 19.2 1.0 HB2 A:ALA390 4.9 23.4 1.0 HG2 A:ARG278 4.9 19.7 1.0 N A:ALA390 4.9 19.2 1.0 CB A:SER389 4.9 26.1 1.0 HB3 A:SER389 5.0 31.3 1.0

G.Moise, N.M.Gallup, A.N.Alexandrova, A.C.Hengge, S.J.Johnson. Conservative Tryptophan Mutants of the Protein Tyrosine Phosphatase Yoph Exhibit Impaired Wpd-Loop Function and Crystallize with Divanadate Esters in Their Active Sites. Biochemistry V. 54 6490 2015.
ISSN: ISSN 0006-2960
PubMed: 26445170
DOI: 10.1021/ACS.BIOCHEM.5B00496