Atomistry » Vanadium » PDB 4zi4-6raj » 5z5a
Atomistry »
  Vanadium »
    PDB 4zi4-6raj »
      5z5a »

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

Protein crystallography data

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

Vanadium Binding Sites:

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 5z5a

Go back to Vanadium Binding Sites List in 5z5a
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 5z5a

Go back to Vanadium Binding Sites List in 5z5a
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 5z5a

Go back to Vanadium Binding Sites List in 5z5a
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

Reference:

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
Page generated: Thu Oct 29 07:05:58 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy