Cadmium in PDB 8b2e: Muramidase From Kionochaeta Sp Natural Catalytic Core

The structure of Muramidase From Kionochaeta Sp Natural Catalytic Core, PDB code: 8b2e 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)	53.28 / 1.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.521, 61.521, 85.188, 90, 90, 120
R / Rfree (%)	11.3 / 12.4

The binding sites of Cadmium atom in the Muramidase From Kionochaeta Sp Natural Catalytic Core (pdb code 8b2e). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Muramidase From Kionochaeta Sp Natural Catalytic Core, PDB code: 8b2e:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Muramidase From Kionochaeta Sp Natural Catalytic Core


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Muramidase From Kionochaeta Sp Natural Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:13.5 occ:1.00 ND1 A:HIS29 2.3 12.5 1.0 O A:HOH362 2.3 17.6 1.0 O A:HOH451 2.4 15.6 1.0 O A:HOH339 2.4 15.0 1.0 CE1 A:HIS29 3.1 12.1 1.0 CG A:HIS29 3.4 12.0 1.0 CB A:HIS29 3.7 12.2 1.0 O A:HOH421 4.2 30.9 1.0 NE2 A:HIS29 4.3 12.6 1.0 O A:GLN107 4.4 13.1 1.0 CA A:HIS29 4.4 11.5 1.0 CD2 A:HIS29 4.5 12.2 1.0 OE1 A:GLN32 4.5 15.6 1.0

Cadmium binding site 2 out of 2 in the Muramidase From Kionochaeta Sp Natural Catalytic Core


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Muramidase From Kionochaeta Sp Natural Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:15.7 occ:0.25 O A:HOH397 1.5 16.4 0.8 O A:HOH502 2.4 17.9 0.2 NE2 A:HIS60 2.4 15.0 1.0 O A:HOH453 2.5 10.3 0.2 O A:HOH470 2.5 28.0 1.0 O A:HOH475 2.5 37.3 1.0 O A:HOH435 2.6 21.6 1.0 O A:HOH485 2.6 22.2 0.8 CE1 A:HIS60 3.1 14.2 1.0 CD2 A:HIS60 3.5 13.5 1.0 ND1 A:HIS60 4.3 13.1 1.0 CG A:HIS60 4.5 12.1 1.0 CD2 A:LEU56 4.7 18.1 1.0 CD2 A:LEU63 4.9 21.3 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