Vanadium in PDB 5z5a: Crystal Structure of Tk-Ptp in the Active Form

The structure of Crystal Structure of Tk-Ptp in the Active Form, PDB code: 5z5a was solved by B.Ku, H.Y.Yun, S.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.96 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	102.722, 102.722, 83.805, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.9

The binding sites of Vanadium atom in the Crystal Structure of Tk-Ptp in the Active Form (pdb code 5z5a). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 3 binding sites of Vanadium where determined in the Crystal Structure of Tk-Ptp in the Active Form, PDB code: 5z5a:
Jump to Vanadium binding site number: 1; 2; 3;

Vanadium binding site 1 out of 3 in the Crystal Structure of Tk-Ptp in the Active Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of Tk-Ptp in the Active Form within 5.0Å range: probe atom residue distance (Å) B Occ A:V201 b:22.0 occ:1.00 V A:VN3201 0.0 22.0 1.0 O1 A:VN3201 1.9 18.1 1.0 O2 A:VN3201 1.9 14.8 1.0 O3 A:VN3201 1.9 17.8 1.0 SG A:CYS93 2.6 13.4 1.0 CB A:CYS93 3.5 13.7 1.0 N A:GLY95 3.6 14.9 1.0 N A:GLY98 3.7 15.2 1.0 NE A:ARG99 3.8 16.5 1.0 N A:MET94 3.8 12.5 1.0 NH2 A:ARG99 3.9 13.5 1.0 N A:ARG99 3.9 14.0 1.0 O A:HOH308 4.0 18.2 1.0 OD1 A:ASP63 4.0 16.4 1.0 N A:LEU97 4.1 13.3 1.0 N A:GLY96 4.1 12.5 1.0 OE1 A:GLU132 4.2 21.7 1.0 CA A:GLY95 4.2 13.2 1.0 CZ A:ARG99 4.3 16.4 1.0 CA A:GLY98 4.4 14.4 1.0 CB A:ARG99 4.5 14.6 1.0 C A:MET94 4.5 12.4 1.0 C A:GLY95 4.6 15.3 1.0 CA A:MET94 4.6 14.7 1.0 C A:LEU97 4.6 14.6 1.0 C A:GLY98 4.6 14.1 1.0 C A:CYS93 4.7 14.6 1.0 CA A:CYS93 4.7 15.9 1.0 CA A:LEU97 4.7 16.8 1.0 CB A:MET94 4.8 16.0 1.0 CG A:ARG99 4.8 18.6 1.0 CA A:ARG99 4.8 14.1 1.0 CD A:ARG99 4.9 15.7 1.0 CG A:ASP63 4.9 17.6 1.0 CD A:GLU132 5.0 22.8 1.0 CB A:LEU97 5.0 17.1 1.0 CA A:GLY96 5.0 11.8 1.0 C A:GLY96 5.0 15.7 1.0

Vanadium binding site 2 out of 3 in the Crystal Structure of Tk-Ptp in the Active Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Crystal Structure of Tk-Ptp in the Active Form within 5.0Å range: probe atom residue distance (Å) B Occ B:V201 b:26.4 occ:1.00 V B:VN3201 0.0 26.4 1.0 O1 B:VN3201 1.9 18.6 1.0 O3 B:VN3201 1.9 19.9 1.0 O2 B:VN3201 1.9 17.8 1.0 SG B:CYS93 2.7 17.2 1.0 CB B:CYS93 3.5 15.9 1.0 N B:GLY95 3.6 20.1 1.0 N B:GLY98 3.7 16.7 1.0 N B:ARG99 3.8 12.0 1.0 NE B:ARG99 3.8 14.2 1.0 OD1 B:ASP63 3.8 14.5 1.0 N B:MET94 3.9 15.5 1.0 O B:HOH303 3.9 14.6 1.0 NH2 B:ARG99 3.9 14.1 1.0 N B:GLY96 4.0 16.7 1.0 OE1 B:GLU132 4.1 17.9 1.0 N B:LEU97 4.1 17.1 1.0 CA B:GLY95 4.2 16.3 1.0 CA B:GLY98 4.3 14.1 1.0 CZ B:ARG99 4.4 16.0 1.0 CB B:ARG99 4.5 15.5 1.0 C B:GLY95 4.5 23.4 1.0 C B:MET94 4.5 17.8 1.0 C B:GLY98 4.6 14.3 1.0 CA B:MET94 4.6 16.0 1.0 C B:LEU97 4.6 18.8 1.0 C B:CYS93 4.7 15.3 1.0 CA B:CYS93 4.7 16.4 1.0 CG B:ASP63 4.7 15.9 1.0 CA B:ARG99 4.8 13.7 1.0 CB B:MET94 4.8 18.3 1.0 CG B:ARG99 4.8 14.8 1.0 CA B:LEU97 4.8 16.1 1.0 CD B:ARG99 4.9 12.4 1.0 CD B:GLU132 4.9 19.8 1.0 CA B:GLY96 4.9 16.6 1.0 OD2 B:ASP63 5.0 16.1 1.0

Vanadium binding site 3 out of 3 in the Crystal Structure of Tk-Ptp in the Active Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of Crystal Structure of Tk-Ptp in the Active Form within 5.0Å range: probe atom residue distance (Å) B Occ C:V201 b:24.1 occ:1.00 V C:VN3201 0.0 24.1 1.0 O1 C:VN3201 1.9 20.1 1.0 O2 C:VN3201 1.9 19.7 1.0 O3 C:VN3201 1.9 22.3 1.0 SG C:CYS93 2.6 19.8 1.0 CB C:CYS93 3.5 24.0 1.0 N C:GLY95 3.6 20.7 1.0 N C:GLY98 3.7 20.4 1.0 NH2 C:ARG99 3.8 20.1 1.0 NE C:ARG99 3.8 17.1 1.0 N C:ARG99 3.8 19.5 1.0 N C:MET94 3.9 19.2 1.0 OD1 C:ASP63 3.9 18.6 1.0 N C:GLY96 4.0 17.3 1.0 OE1 C:GLU132 4.0 19.6 1.0 N C:LEU97 4.1 16.1 1.0 O C:HOH319 4.1 15.8 1.0 CA C:GLY95 4.2 21.1 1.0 CZ C:ARG99 4.3 22.0 1.0 CA C:GLY98 4.3 16.2 1.0 C C:GLY95 4.5 19.8 1.0 C C:GLY98 4.5 19.6 1.0 CB C:ARG99 4.6 17.3 1.0 C C:MET94 4.6 24.2 1.0 C C:LEU97 4.6 22.1 1.0 CA C:MET94 4.6 20.5 1.0 CA C:CYS93 4.7 21.6 1.0 C C:CYS93 4.7 24.5 1.0 CA C:LEU97 4.7 20.6 1.0 CA C:ARG99 4.8 20.0 1.0 CB C:MET94 4.8 21.2 1.0 CD C:GLU132 4.8 17.4 1.0 CG C:ASP63 4.9 18.2 1.0 CA C:GLY96 4.9 21.0 1.0 CG C:ARG99 4.9 20.1 1.0 CD C:ARG99 4.9 16.5 1.0 CB C:LEU97 5.0 17.3 1.0 C C:GLY96 5.0 21.6 1.0

H.Y.Yun, J.Lee, H.Kim, H.Ryu, H.C.Shin, B.H.Oh, B.Ku, S.J.Kim. Structural Study Reveals the Temperature-Dependent Conformational Flexibility of Tk-Ptp, A Protein Tyrosine Phosphatase From Thermococcus Kodakaraensis KOD1 Plos One V. 13 97635 2018.
ISSN: ESSN 1932-6203
PubMed: 29791483
DOI: 10.1371/JOURNAL.PONE.0197635