Cadmium in PDB 5wgw: Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex

The structure of Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex, PDB code: 5wgw was solved by A.E.Fraley, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.29 / 2.09
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	79.387, 120.880, 170.919, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 20.4

The structure of Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Cadmium atom in the Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex (pdb code 5wgw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex, PDB code: 5wgw:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd702 b:36.3 occ:0.40 O A:HOH1185 2.6 25.1 1.0 OE1 A:GLU11 2.7 50.9 1.0 OE2 A:GLU11 2.7 58.1 1.0 CD A:GLU11 3.1 55.6 1.0 O A:HOH811 4.6 46.8 1.0 CG A:GLU11 4.6 52.9 1.0 O A:HOH1095 4.8 47.9 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd703 b:36.8 occ:0.50 OE2 A:GLU548 2.7 44.8 1.0 OE1 A:GLU548 2.7 37.1 1.0 NE2 A:HIS531 2.7 38.7 1.0 O A:HOH1228 2.7 38.1 0.5 CD A:GLU548 3.0 43.3 1.0 CD2 A:HIS531 3.2 34.7 1.0 CE1 A:HIS531 3.9 38.8 1.0 O A:HOH947 4.1 48.6 1.0 CG A:GLU548 4.4 45.8 1.0 CG A:HIS531 4.5 41.2 1.0 O A:HOH891 4.8 55.2 1.0 ND1 A:HIS531 4.8 40.5 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd704 b:65.0 occ:0.80 OD2 A:ASP547 2.7 57.5 1.0 OD2 A:ASP543 2.7 74.9 1.0 OD1 A:ASP547 2.8 47.0 1.0 CG A:ASP547 3.1 52.9 1.0 OD1 A:ASP543 3.2 70.5 1.0 CG A:ASP543 3.3 66.5 1.0 NH2 A:ARG478 4.1 49.1 1.0 O A:ASP543 4.5 37.5 1.0 CB A:ASP547 4.6 45.8 1.0 NH1 A:ARG478 4.6 47.2 1.0 CZ A:ARG478 4.8 47.8 1.0 CB A:ASP543 4.8 53.7 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Wild-Type Mala', Malbrancheamide B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd705 b:0.9 occ:0.50 O A:HOH1244 2.8 0.8 1.0 O A:HOH1049 2.8 64.0 1.0 SG A:CYS112 2.9 61.8 1.0 SG A:CYS128 3.0 58.6 1.0 O A:LEU248 3.3 45.9 1.0 O A:HOH883 3.3 46.0 1.0 CB A:CYS128 3.6 50.4 1.0 NE2 A:HIS253 3.6 51.7 1.0 OH A:TYR114 4.0 46.1 1.0 CD2 A:HIS253 4.0 48.3 1.0 OE1 A:GLU250 4.2 60.8 1.0 CB A:CYS112 4.3 33.9 1.0 CE1 A:HIS253 4.3 52.4 1.0 C A:LEU248 4.4 44.0 1.0 N A:GLU250 4.7 31.2 1.0 CD A:GLU250 4.8 61.3 1.0 CA A:CYS128 4.8 34.0 1.0 CB A:LEU248 4.9 49.3 1.0 CB A:GLU250 4.9 37.9 1.0 CA A:TYR249 4.9 34.9 1.0 CG A:HIS253 4.9 42.9 1.0 CG A:GLU250 4.9 49.5 1.0

A.E.Fraley, M.Garcia-Borras, A.Tripathi, D.Khare, E.V.Mercado-Marin, H.Tran, Q.Dan, G.P.Webb, K.R.Watts, P.Crews, R.Sarpong, R.M.Williams, J.L.Smith, K.N.Houk, D.H.Sherman. Function and Structure of Mala/Mala', Iterative Halogenases For Late-Stage C-H Functionalization of Indole Alkaloids. J. Am. Chem. Soc. V. 139 12060 2017.
ISSN: ESSN 1520-5126
PubMed: 28777910
DOI: 10.1021/JACS.7B06773