Zinc in PDB 8b2h: Muramidase From Thermothielavioides Terrestris, Catalytic Domain

The structure of Muramidase From Thermothielavioides Terrestris, Catalytic Domain, PDB code: 8b2h 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)	36.64 / 2.36
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	84.616, 84.616, 62.882, 90, 90, 120
R / Rfree (%)	19.7 / 22.1

The binding sites of Zinc atom in the Muramidase From Thermothielavioides Terrestris, Catalytic Domain (pdb code 8b2h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Muramidase From Thermothielavioides Terrestris, Catalytic Domain, PDB code: 8b2h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Muramidase From Thermothielavioides Terrestris, Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Muramidase From Thermothielavioides Terrestris, Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:83.2 occ:1.00 O A:HOH424 2.0 69.8 1.0 O A:HOH429 2.0 64.6 1.0 OE1 A:GLU116 2.0 73.5 1.0 ND1 A:HIS113 2.3 69.0 1.0 CE1 A:HIS113 3.2 70.7 1.0 CD A:GLU116 3.2 71.4 1.0 CG A:HIS113 3.3 64.0 1.0 CB A:HIS113 3.7 60.9 1.0 CA A:HIS113 3.7 64.2 1.0 OE2 A:GLU116 3.9 76.0 1.0 CG2 A:VAL195 4.0 74.1 1.0 NE2 A:HIS113 4.3 68.5 1.0 CD2 A:HIS113 4.4 64.0 1.0 CG A:GLU116 4.4 70.0 1.0 N A:HIS113 4.5 64.2 1.0 CB A:GLU116 4.8 66.6 1.0 C A:HIS113 4.8 61.5 1.0 O A:HIS113 4.8 56.6 1.0

Zinc binding site 2 out of 2 in the Muramidase From Thermothielavioides Terrestris, Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Muramidase From Thermothielavioides Terrestris, Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:97.5 occ:0.33 NE2 A:HIS151 2.0 83.2 1.0 O A:HOH438 2.6 53.6 0.3 CD2 A:HIS151 2.9 80.7 1.0 CE1 A:HIS151 3.0 92.6 1.0 CG A:HIS151 4.1 85.0 1.0 ND1 A:HIS151 4.1 88.6 1.0 NH1 A:ARG160 4.6 79.8 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