Zinc in PDB 8b2g: SH3-Like Domain From Penicillium Virgatum Muramidase

The structure of SH3-Like Domain From Penicillium Virgatum Muramidase, PDB code: 8b2g was solved by O.V.Moroz, E.Blagova, A.A.Lebedev, L.K.Skov, R.A.Pache, K.M.Schnorr, L.Kiemer, S.Nymand-Grarup, L.Ming, L.Ye, M.Klausen, M.T.Cohn, E.G.W.Schmidt, G.J.Davies, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.48 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.142, 59.824, 36.109, 90, 112.13, 90
R / Rfree (%)	16.3 / 17.3

The binding sites of Zinc atom in the SH3-Like Domain From Penicillium Virgatum Muramidase (pdb code 8b2g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the SH3-Like Domain From Penicillium Virgatum Muramidase, PDB code: 8b2g:

Zinc binding site 1 out of 1 in the SH3-Like Domain From Penicillium Virgatum Muramidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SH3-Like Domain From Penicillium Virgatum Muramidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:14.2 occ:1.00 OD1 A:ASP29 1.9 16.6 1.0 OD1 B:ASP29 1.9 17.4 1.0 N B:TYR1 2.0 14.8 1.0 N A:TYR1 2.2 14.5 1.0 CG B:ASP29 2.7 14.5 1.0 CG A:ASP29 2.7 15.0 1.0 OD2 A:ASP29 2.9 17.0 1.0 OD2 B:ASP29 2.9 14.2 1.0 CA B:TYR1 3.0 14.2 1.0 CA A:TYR1 3.1 14.4 1.0 O B:VAL30 3.5 14.3 1.0 O A:VAL30 3.6 16.8 1.0 C B:TYR1 3.6 12.9 1.0 C A:TYR1 3.7 13.9 1.0 O B:TYR1 3.7 14.9 1.0 O A:TYR1 3.8 14.7 1.0 CB B:ASP29 4.1 15.4 1.0 CB A:ASP29 4.2 13.7 1.0 C A:VAL30 4.2 15.1 1.0 N B:VAL30 4.2 15.6 1.0 O A:HOH239 4.2 30.5 1.0 C B:VAL30 4.2 12.8 1.0 N A:VAL30 4.2 14.7 1.0 CB B:TYR1 4.4 13.4 1.0 CB A:TYR1 4.4 14.3 1.0 N B:PRO2 4.5 14.4 1.0 C B:ASP29 4.5 14.7 1.0 C A:ASP29 4.6 14.6 1.0 N A:PRO2 4.6 13.4 1.0 CA B:ASP29 4.7 15.1 1.0 CA A:ASP29 4.7 13.9 1.0 CG A:TYR1 4.8 12.6 1.0 CG B:TYR1 4.8 14.5 1.0 CA B:VAL30 4.9 14.3 1.0 CA A:VAL30 4.9 15.2 1.0 N A:ALA31 4.9 14.3 1.0 N B:ALA31 4.9 13.4 1.0 CD B:PRO2 5.0 18.0 1.0

O.V.Moroz, E.Blagova, A.A.Lebedev, L.K.Skov, R.A.Pache, K.M.Schnorr, L.Kiemer, E.P.Friis, S.Nymand-Grarup, L.Ming, L.Ye, M.Klausen, M.T.Cohn, E.G.W.Schmidt, G.J.Davies, K.S.Wilson. Module Walking Using An SH3-Like Cell-Wall-Binding Domain Leads to A New GH184 Family of Muramidases. Acta Crystallogr D Struct 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37428847
DOI: 10.1107/S2059798323005004