Zinc in PDB 5vn5: Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6

The structure of Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6, PDB code: 5vn5 was solved by E.Kuatsjah, A.C.K.Chan, M.J.Kobylarz, M.E.P.Murphy, L.D.Eltis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.61 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.020, 195.361, 178.249, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.9

The structure of Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6 (pdb code 5vn5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6, PDB code: 5vn5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:22.7 occ:1.00 NE2 A:HIS179 2.0 15.9 1.0 NE2 A:HIS8 2.1 14.6 1.0 NE2 A:HIS6 2.1 16.1 1.0 OE2 A:GLU282 2.2 17.4 0.6 O A:HOH519 2.5 19.8 0.6 HG3 A:GLU282 2.9 22.5 0.4 CE1 A:HIS8 2.9 13.2 1.0 CD2 A:HIS179 3.0 14.8 1.0 HE1 A:HIS8 3.0 15.9 1.0 CE1 A:HIS179 3.0 15.9 1.0 CE1 A:HIS6 3.1 14.5 1.0 CD2 A:HIS6 3.1 16.1 1.0 CD A:GLU282 3.1 19.0 0.6 CD2 A:HIS8 3.1 15.6 1.0 HD2 A:HIS179 3.2 17.7 1.0 HG3 A:GLU282 3.2 23.4 0.6 HG2 A:GLU282 3.2 23.4 0.6 HE1 A:HIS6 3.2 17.4 1.0 HE1 A:HIS179 3.3 19.0 1.0 HD2 A:HIS6 3.3 19.3 1.0 CG A:GLU282 3.4 19.5 0.6 HD2 A:HIS8 3.4 18.7 1.0 HG2 A:GLU282 3.6 22.5 0.4 HG2 A:PRO73 3.6 20.8 1.0 CG A:GLU282 3.6 18.8 0.4 HE1 A:HIS223 3.8 22.8 1.0 ND1 A:HIS8 4.1 16.5 1.0 HD2 A:PRO73 4.1 21.4 1.0 ND1 A:HIS179 4.1 15.1 1.0 CG A:HIS179 4.1 15.3 1.0 ND1 A:HIS6 4.2 15.8 1.0 CG A:HIS8 4.2 14.9 1.0 CE1 A:HIS223 4.3 19.0 1.0 CG A:HIS6 4.3 16.4 1.0 OE1 A:GLU282 4.3 19.3 0.6 NE2 A:HIS223 4.4 19.1 1.0 CD A:GLU282 4.4 17.7 0.4 CG A:PRO73 4.4 17.3 1.0 HD3 A:PRO73 4.5 21.4 1.0 CD A:PRO73 4.5 17.8 1.0 HB2 A:GLU282 4.6 22.8 0.4 CB A:GLU282 4.8 19.0 0.4 OE2 A:GLU282 4.8 15.2 0.4 HD1 A:HIS8 4.8 19.9 1.0 HE2 A:PHE194 4.9 21.9 1.0 HG3 A:PRO73 4.9 20.8 1.0 HD1 A:HIS179 4.9 18.1 1.0 HD1 A:HIS6 5.0 18.9 1.0 CB A:GLU282 5.0 19.1 0.6

Zinc binding site 2 out of 3 in the Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:22.5 occ:1.00 NE2 B:HIS8 2.0 30.5 1.0 NE2 B:HIS179 2.1 20.2 1.0 NE2 B:HIS6 2.1 25.7 1.0 OE2 B:GLU282 2.2 21.0 0.3 CE1 B:HIS8 2.8 26.2 1.0 HE1 B:HIS8 3.0 31.5 1.0 CD2 B:HIS179 3.0 22.2 1.0 HG3 B:GLU282 3.0 29.6 0.3 CE1 B:HIS179 3.1 19.3 1.0 CE1 B:HIS6 3.1 25.1 1.0 CD B:GLU282 3.1 22.3 0.3 CD2 B:HIS6 3.1 26.3 1.0 CD2 B:HIS8 3.1 26.2 1.0 HD2 B:HIS179 3.2 26.6 1.0 HG3 B:GLU282 3.2 32.1 0.7 HE1 B:HIS6 3.2 30.1 1.0 HD2 B:HIS6 3.3 31.5 1.0 HE1 B:HIS179 3.3 23.1 1.0 HG2 B:GLU282 3.4 29.6 0.3 CG B:GLU282 3.4 24.7 0.3 HD2 B:HIS8 3.4 31.5 1.0 HG2 B:GLU282 3.4 32.1 0.7 HG2 B:PRO73 3.7 26.1 1.0 HE1 B:HIS223 3.7 26.0 1.0 CG B:GLU282 3.7 26.8 0.7 ND1 B:HIS8 4.0 24.9 1.0 ND1 B:HIS179 4.1 18.1 1.0 CG B:HIS179 4.1 19.6 1.0 CG B:HIS8 4.2 25.0 1.0 ND1 B:HIS6 4.2 25.4 1.0 HD2 B:PRO73 4.2 27.1 1.0 CE1 B:HIS223 4.2 21.6 1.0 CG B:HIS6 4.2 27.3 1.0 OE1 B:GLU282 4.2 21.1 0.3 NE2 B:HIS223 4.2 22.2 1.0 CG B:PRO73 4.5 21.7 1.0 CD B:GLU282 4.5 30.3 0.7 HD3 B:PRO73 4.6 27.1 1.0 CD B:PRO73 4.6 22.6 1.0 HD1 B:HIS8 4.8 29.9 1.0 HE2 B:PHE194 4.8 26.3 1.0 HB2 B:GLU282 4.8 30.0 0.7 CB B:GLU282 4.9 24.9 0.3 HD1 B:HIS179 4.9 21.7 1.0 CB B:GLU282 4.9 25.0 0.7 OE2 B:GLU282 4.9 32.8 0.7 HG3 B:PRO73 4.9 26.1 1.0 HD1 B:HIS6 4.9 30.5 1.0 CE2 B:PHE194 5.0 21.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ligy From Sphingobium Sp. Strain Syk-6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn400 b:24.4 occ:1.00 CL C:CL410 1.9 30.0 1.0 NE2 C:HIS8 2.0 24.1 1.0 NE2 C:HIS179 2.1 19.8 1.0 NE2 C:HIS6 2.1 24.8 1.0 CE1 C:HIS8 2.9 23.9 1.0 HE1 C:HIS8 3.0 28.7 1.0 CD2 C:HIS179 3.0 20.0 1.0 CE1 C:HIS179 3.1 19.3 1.0 HG3 C:GLU282 3.1 40.4 1.0 CE1 C:HIS6 3.1 24.2 1.0 CD2 C:HIS6 3.1 24.9 1.0 CD2 C:HIS8 3.1 24.9 1.0 HD2 C:HIS179 3.1 24.0 1.0 HE1 C:HIS6 3.3 29.1 1.0 HD2 C:HIS6 3.3 29.9 1.0 HE1 C:HIS179 3.3 23.2 1.0 HD2 C:HIS8 3.4 29.9 1.0 HE1 C:HIS223 3.5 29.4 1.0 HG2 C:PRO73 3.6 23.1 1.0 HG2 C:GLU282 3.7 40.4 1.0 CG C:GLU282 3.8 33.7 1.0 ND1 C:HIS8 4.0 24.1 1.0 CE1 C:HIS223 4.1 24.5 1.0 CG C:HIS179 4.1 19.0 1.0 ND1 C:HIS179 4.2 17.9 1.0 NE2 C:HIS223 4.2 23.8 1.0 CG C:HIS8 4.2 24.4 1.0 HD2 C:PRO73 4.2 24.3 1.0 ND1 C:HIS6 4.2 24.6 1.0 CG C:HIS6 4.3 24.3 1.0 CG C:PRO73 4.5 19.3 1.0 CD C:GLU282 4.5 37.3 1.0 HD3 C:PRO73 4.6 24.3 1.0 CD C:PRO73 4.6 20.2 1.0 HE2 C:PHE194 4.8 27.1 1.0 HD1 C:HIS8 4.8 29.0 1.0 OE1 C:GLU282 4.8 38.9 1.0 HB2 C:GLU282 4.8 36.1 1.0 HD1 C:HIS179 4.9 21.5 1.0 HG3 C:PRO73 4.9 23.1 1.0 CE2 C:PHE194 5.0 22.6 1.0 HD1 C:HIS6 5.0 29.5 1.0 CB C:GLU282 5.0 30.1 1.0 HB3 C:SER222 5.0 26.4 1.0

E.Kuatsjah, A.C.K.Chan, M.J.Kobylarz, M.E.P.Murphy, L.D.Eltis. The Bacterialmeta-Cleavage Hydrolase Ligy Belongs to the Amidohydrolase Superfamily, Not to the Alpha / Beta-Hydrolase Superfamily. J. Biol. Chem. V. 292 18290 2017.
ISSN: ESSN 1083-351X
PubMed: 28935670
DOI: 10.1074/JBC.M117.797696