Cadmium in PDB 5wgr: Crystal Structure of Wild-Type Mala', Premalbrancheamide Complex

The structure of Crystal Structure of Wild-Type Mala', Premalbrancheamide Complex, PDB code: 5wgr 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)	39.64 / 2.36
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	79.284, 120.619, 170.388, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 20.5

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

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

The binding sites of Cadmium atom in the Crystal Structure of Wild-Type Mala', Premalbrancheamide Complex (pdb code 5wgr). 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', Premalbrancheamide Complex, PDB code: 5wgr:
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', Premalbrancheamide 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', Premalbrancheamide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd702 b:60.8 occ:0.50 O A:HOH1116 2.6 23.0 1.0 OE1 A:GLU11 2.6 79.7 1.0 OE2 A:GLU11 2.7 81.4 1.0 CD A:GLU11 3.0 73.5 1.0 O A:HOH1153 3.7 76.5 1.0 O A:HOH1029 3.8 49.2 1.0 CG A:GLU11 4.5 59.3 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Wild-Type Mala', Premalbrancheamide 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', Premalbrancheamide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd703 b:52.3 occ:0.50 OE2 A:GLU548 2.4 53.4 1.0 OE1 A:GLU548 2.5 48.0 1.0 NE2 A:HIS531 2.6 56.4 1.0 CD A:GLU548 2.7 47.2 1.0 CD2 A:HIS531 3.2 49.4 1.0 CE1 A:HIS531 3.8 52.1 1.0 CG A:GLU548 4.2 42.1 1.0 CG A:HIS531 4.5 56.8 1.0 ND1 A:HIS531 4.7 57.8 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Wild-Type Mala', Premalbrancheamide 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', Premalbrancheamide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd704 b:73.9 occ:0.80 OD2 A:ASP547 2.6 67.5 1.0 OD2 A:ASP543 2.7 82.3 1.0 OD1 A:ASP547 2.9 58.1 1.0 OD1 A:ASP543 2.9 75.8 1.0 CG A:ASP547 3.1 63.4 1.0 CG A:ASP543 3.2 75.9 1.0 NH2 A:ARG478 4.1 45.1 1.0 O A:ASP543 4.5 48.5 1.0 CB A:ASP547 4.6 57.8 1.0 CB A:ASP543 4.7 65.3 1.0 NH1 A:ARG478 4.8 50.9 1.0 O A:HOH1084 4.8 62.9 1.0 CZ A:ARG478 4.8 50.9 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Wild-Type Mala', Premalbrancheamide 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', Premalbrancheamide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd705 b:0.7 occ:0.50 SG A:CYS128 1.6 0.6 1.0 SG A:CYS112 2.8 77.9 1.0 O A:HOH1119 2.8 86.6 1.0 CB A:CYS128 3.0 89.7 1.0 NE2 A:HIS253 3.4 64.4 1.0 O A:HOH866 3.5 61.4 1.0 O A:HOH977 3.7 38.2 1.0 CB A:CYS112 3.8 48.4 1.0 CE1 A:HIS253 4.0 64.4 1.0 CD2 A:HIS253 4.0 61.0 1.0 CA A:CYS128 4.0 57.1 1.0 O A:LEU248 4.0 60.5 1.0 OE1 A:GLU250 4.1 89.6 1.0 NH2 A:ARG575 4.3 90.0 1.0 OH A:TYR114 4.5 59.8 1.0 NE A:ARG575 4.6 91.4 1.0 ND1 A:HIS253 4.7 59.7 1.0 CG A:HIS253 4.7 52.2 1.0 O A:SER129 4.8 52.7 1.0 C A:CYS128 4.8 56.2 1.0 N A:SER129 4.9 48.9 1.0 CZ A:ARG575 5.0 92.1 1.0 CA A:CYS112 5.0 47.4 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