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

The structure of Crystal Structure of Wild-Type Mala', Isomalbrancheamide B Complex, PDB code: 5wgz 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)	46.18 / 2.04
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	79.093, 120.651, 170.849, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 21

The structure of Crystal Structure of Wild-Type Mala', Isomalbrancheamide 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', Isomalbrancheamide B Complex (pdb code 5wgz). 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', Isomalbrancheamide B Complex, PDB code: 5wgz:
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', Isomalbrancheamide 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', Isomalbrancheamide B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd702 b:42.0 occ:0.40 OE1 A:GLU11 2.6 62.2 1.0 OE2 A:GLU11 2.6 70.8 1.0 O A:HOH1154 2.6 27.9 1.0 CD A:GLU11 2.9 65.6 1.0 CG A:GLU11 4.4 57.2 1.0 O A:HOH821 4.6 44.4 1.0 CB A:TYR7 5.0 42.1 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Wild-Type Mala', Isomalbrancheamide 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', Isomalbrancheamide B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd703 b:45.2 occ:0.50 OE2 A:GLU548 2.5 41.3 1.0 OE1 A:GLU548 2.5 44.3 1.0 NE2 A:HIS531 2.6 39.8 1.0 CD A:GLU548 2.8 44.6 1.0 O A:HOH1118 2.8 61.1 1.0 CD2 A:HIS531 3.1 41.8 1.0 CE1 A:HIS531 3.8 39.0 1.0 CG A:GLU548 4.2 43.6 1.0 O A:HOH1162 4.4 67.9 1.0 CG A:HIS531 4.4 47.5 1.0 ND1 A:HIS531 4.7 39.0 1.0 O A:HOH885 4.8 65.9 1.0 CB A:GLU548 5.0 40.0 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Wild-Type Mala', Isomalbrancheamide 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', Isomalbrancheamide B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd704 b:67.1 occ:0.80 OD2 A:ASP547 2.6 55.6 1.0 OD2 A:ASP543 2.7 72.9 1.0 OD1 A:ASP547 2.8 50.5 1.0 OD1 A:ASP543 2.9 68.6 1.0 CG A:ASP547 3.0 53.4 1.0 CG A:ASP543 3.1 68.8 1.0 O A:HOH887 4.0 60.0 1.0 NH2 A:ARG478 4.1 50.5 1.0 O A:ASP543 4.4 45.4 1.0 CB A:ASP547 4.5 43.8 1.0 CB A:ASP543 4.6 58.7 1.0 NH1 A:ARG478 4.7 49.7 1.0 O A:HOH1159 4.8 54.9 1.0 CZ A:ARG478 4.8 46.9 1.0 C A:ASP543 4.9 52.0 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Wild-Type Mala', Isomalbrancheamide 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', Isomalbrancheamide B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd705 b:0.2 occ:1.00 SG A:CYS112 2.6 78.5 1.0 O A:HOH1125 2.7 36.3 1.0 SG A:CYS128 2.7 0.8 1.0 CB A:CYS128 3.3 75.3 1.0 O A:HOH829 3.3 58.0 1.0 O A:HOH1012 3.7 41.8 1.0 NE2 A:HIS253 3.7 56.9 1.0 O A:LEU248 3.9 55.9 1.0 CB A:CYS112 3.9 49.7 1.0 CD2 A:HIS253 4.1 59.1 1.0 CA A:CYS128 4.1 48.2 1.0 NH1 A:ARG590 4.2 86.9 1.0 OH A:TYR114 4.3 59.4 1.0 NH1 A:ARG575 4.4 88.2 1.0 CE1 A:HIS253 4.4 57.8 1.0 NE A:ARG575 4.7 87.8 1.0 CG A:HIS253 4.9 52.8 1.0 OE1 A:GLU250 4.9 61.6 1.0 C A:LEU248 5.0 52.8 1.0 OD2 A:ASP126 5.0 79.7 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