Zinc in PDB 5vjv: Rhizobiales-Like Phosphatase 2

All present enzymatic activity of Rhizobiales-Like Phosphatase 2:
3.1.3.48;

The structure of Rhizobiales-Like Phosphatase 2, PDB code: 5vjv 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 / 1.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	102.600, 102.600, 61.040, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 21.9

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

Zinc binding site 1 out of 2 in the Rhizobiales-Like Phosphatase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rhizobiales-Like Phosphatase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:21.8 occ:1.00 OD1 A:ASN80 2.1 18.0 1.0 O A:HOH510 2.1 24.8 1.0 ND1 A:HIS266 2.2 17.6 1.0 NE2 A:HIS213 2.2 16.4 1.0 O4 A:PO4401 2.3 27.1 1.0 OD2 A:ASP47 2.4 15.0 1.0 CE1 A:HIS266 3.0 19.4 1.0 CG A:ASN80 3.1 18.5 1.0 CD2 A:HIS213 3.1 15.4 1.0 CG A:ASP47 3.2 17.1 1.0 CE1 A:HIS213 3.3 17.0 1.0 CG A:HIS266 3.3 20.2 1.0 P A:PO4401 3.4 31.0 1.0 ZN A:ZN403 3.4 24.3 1.0 ND2 A:ASN80 3.5 16.9 1.0 OD1 A:ASP47 3.5 15.5 1.0 CB A:HIS266 3.7 19.8 1.0 O2 A:PO4401 3.7 33.5 1.0 CA A:HIS266 3.8 19.0 1.0 OD2 A:ASP13 3.9 19.0 1.0 O1 A:PO4401 3.9 29.5 1.0 O A:LEU242 4.1 16.8 1.0 CD2 A:HIS81 4.2 19.9 1.0 NE2 A:HIS266 4.2 19.5 1.0 O A:HIS266 4.2 17.2 1.0 CG A:HIS213 4.3 16.0 1.0 ND1 A:HIS213 4.3 16.4 1.0 CD2 A:HIS266 4.3 20.1 1.0 N A:ASN80 4.4 16.7 1.0 CB A:ASN80 4.4 16.7 1.0 CB A:ASP47 4.5 15.6 1.0 C A:HIS266 4.5 21.1 1.0 O3 A:PO4401 4.6 40.2 1.0 N A:HIS266 4.8 17.6 1.0 NE2 A:HIS81 4.8 21.4 1.0 CA A:ASN80 4.9 18.0 1.0 O A:HOH522 5.0 17.6 1.0

Zinc binding site 2 out of 2 in the Rhizobiales-Like Phosphatase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rhizobiales-Like Phosphatase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:24.3 occ:1.00 O A:HOH522 2.1 17.6 1.0 O A:HOH510 2.1 24.8 1.0 NE2 A:HIS15 2.1 19.0 1.0 OD2 A:ASP13 2.2 19.0 1.0 OD2 A:ASP47 2.2 15.0 1.0 O2 A:PO4401 2.3 33.5 1.0 CE1 A:HIS15 3.0 18.3 1.0 CD2 A:HIS15 3.2 18.4 1.0 CG A:ASP13 3.2 20.0 1.0 CG A:ASP47 3.2 17.1 1.0 P A:PO4401 3.4 31.0 1.0 ZN A:ZN402 3.4 21.8 1.0 CB A:ASP47 3.5 15.6 1.0 CB A:ASP13 3.6 17.7 1.0 O4 A:PO4401 3.7 27.1 1.0 O1 A:PO4401 4.0 29.5 1.0 OD2 A:ASP280 4.2 22.3 1.0 ND1 A:HIS15 4.2 18.9 1.0 O A:HOH563 4.3 31.2 1.0 CG A:HIS15 4.3 19.3 1.0 NH1 A:ARG51 4.3 45.3 1.0 OD1 A:ASP13 4.3 20.8 1.0 O A:HIS266 4.3 17.2 1.0 OD1 A:ASP47 4.4 15.5 1.0 NE2 A:HIS213 4.4 16.4 1.0 CA A:HIS266 4.4 19.0 1.0 CD2 A:HIS81 4.5 19.9 1.0 CE1 A:HIS213 4.5 17.0 1.0 O3 A:PO4401 4.6 40.2 1.0 NE2 A:HIS81 4.7 21.4 1.0 C A:HIS266 4.8 21.1 1.0 CG A:ASP280 4.8 18.8 1.0 OD1 A:ASP280 4.9 19.8 1.0 N A:HIS266 4.9 17.6 1.0 OD1 A:ASN80 5.0 18.0 1.0 ND1 A:HIS266 5.0 17.6 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