Zinc in PDB 5vjw: Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate

All present enzymatic activity of Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate:
3.1.3.48;

The structure of Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate, PDB code: 5vjw was solved by K.K.S.Ng, A.Labandera, G.Moorhead, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	102.660, 102.660, 60.210, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 19.9

The structure of Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate also contains other interesting chemical elements:

Tungsten

(W)

2 atoms

The binding sites of Zinc atom in the Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate (pdb code 5vjw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate, PDB code: 5vjw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:16.4 occ:1.00 O1 A:WO4403 2.0 22.9 1.0 OD1 A:ASN80 2.1 11.3 1.0 O A:HOH505 2.2 11.3 1.0 NE2 A:HIS213 2.2 9.2 1.0 ND1 A:HIS266 2.2 10.8 1.0 OD2 A:ASP47 2.3 10.7 1.0 CE1 A:HIS266 3.1 11.7 1.0 CD2 A:HIS213 3.1 9.2 1.0 CG A:ASN80 3.2 12.3 1.0 CG A:ASP47 3.2 10.2 1.0 CE1 A:HIS213 3.2 8.8 1.0 CG A:HIS266 3.3 11.4 1.0 ZN A:ZN402 3.4 16.5 1.0 W A:WO4403 3.4 38.8 1.0 OD1 A:ASP47 3.5 10.4 1.0 ND2 A:ASN80 3.6 12.5 1.0 CB A:HIS266 3.7 10.8 1.0 CA A:HIS266 3.8 11.9 1.0 OD2 A:ASP13 3.9 10.7 1.0 O2 A:WO4403 3.9 22.5 1.0 CD2 A:HIS81 4.1 10.9 1.0 O A:LEU242 4.2 12.3 1.0 O A:HIS266 4.2 12.4 1.0 NE2 A:HIS266 4.3 11.6 1.0 ND1 A:HIS213 4.3 9.1 1.0 CG A:HIS213 4.3 9.4 1.0 O4 A:WO4403 4.3 28.5 1.0 CD2 A:HIS266 4.4 11.1 1.0 N A:ASN80 4.4 12.1 1.0 CB A:ASP47 4.5 10.2 1.0 CB A:ASN80 4.5 11.2 1.0 C A:HIS266 4.5 12.4 1.0 NE2 A:HIS81 4.7 10.8 1.0 N A:HIS266 4.8 11.9 1.0 O A:HOH525 5.0 14.4 1.0 CA A:ASN80 5.0 12.0 1.0

Zinc binding site 2 out of 2 in the Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Arabidopsis Thaliana Rhizobiales-Like Phosphatase 2 Complexed with Tungstate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:16.5 occ:1.00 O2 A:WO4403 2.0 22.5 1.0 OD2 A:ASP13 2.1 10.7 1.0 O A:HOH505 2.1 11.3 1.0 O A:HOH525 2.1 14.4 1.0 NE2 A:HIS15 2.2 9.2 1.0 OD2 A:ASP47 2.2 10.7 1.0 CE1 A:HIS15 3.1 9.8 1.0 CG A:ASP13 3.2 11.0 1.0 CG A:ASP47 3.2 10.2 1.0 CD2 A:HIS15 3.2 10.4 1.0 ZN A:ZN401 3.4 16.4 1.0 W A:WO4403 3.4 38.8 1.0 CB A:ASP47 3.5 10.2 1.0 CB A:ASP13 3.7 11.1 1.0 O1 A:WO4403 3.9 22.9 1.0 OD2 A:ASP280 4.1 15.1 1.0 OD1 A:ASP13 4.2 12.0 1.0 ND1 A:HIS15 4.3 9.8 1.0 O A:HIS266 4.3 12.4 1.0 CG A:HIS15 4.3 9.7 1.0 OD1 A:ASP47 4.4 10.4 1.0 NH1 A:ARG51 4.4 23.0 1.0 O4 A:WO4403 4.4 28.5 1.0 O A:HOH509 4.4 29.5 1.0 CA A:HIS266 4.4 11.9 1.0 NE2 A:HIS213 4.4 9.2 1.0 CE1 A:HIS213 4.4 8.8 1.0 CD2 A:HIS81 4.5 10.9 1.0 NE2 A:HIS81 4.7 10.8 1.0 C A:HIS266 4.8 12.4 1.0 CG A:ASP280 4.9 14.2 1.0 OD1 A:ASP280 4.9 13.8 1.0 N A:HIS266 4.9 11.9 1.0 ND1 A:HIS266 5.0 10.8 1.0

A.M.Labandera, R.G.Uhrig, K.Colville, G.B.Moorhead, K.K.S.Ng. Structural Basis For the Preference of the Arabidopsis Thalianaphosphatase RLPH2 For Tyrosine-Phosphorylated Substrates. Sci Signal V. 11 2018.
ISSN: ESSN 1937-9145
PubMed: 29615518
DOI: 10.1126/SCISIGNAL.AAN8804