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Cadmium in PDB 5wgx: Crystal Structure of Mala' H253A, Malbrancheamide B Complex

Protein crystallography data

The structure of Crystal Structure of Mala' H253A, Malbrancheamide B Complex, PDB code: 5wgx 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) 46.14 / 1.97
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 79.231, 120.435, 170.244, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.9

Other elements in 5wgx:

The structure of Crystal Structure of Mala' H253A, Malbrancheamide B Complex also contains other interesting chemical elements:

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

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Mala' H253A, Malbrancheamide B Complex (pdb code 5wgx). 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 Mala' H253A, Malbrancheamide B Complex, PDB code: 5wgx:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 5wgx

Go back to Cadmium Binding Sites List in 5wgx
Cadmium binding site 1 out of 4 in the Crystal Structure of Mala' H253A, 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 Mala' H253A, Malbrancheamide B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd702

b:40.3
occ:0.50
OE1 A:GLU11 2.6 49.4 1.0
OE2 A:GLU11 2.6 41.8 1.0
O A:HOH1233 2.6 22.6 1.0
CD A:GLU11 3.0 51.7 1.0
CG A:GLU11 4.4 44.2 1.0
O A:HOH844 4.5 33.6 1.0
CB A:TYR7 5.0 39.3 1.0

Cadmium binding site 2 out of 4 in 5wgx

Go back to Cadmium Binding Sites List in 5wgx
Cadmium binding site 2 out of 4 in the Crystal Structure of Mala' H253A, 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 Mala' H253A, Malbrancheamide B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd703

b:30.4
occ:0.40
OE2 A:GLU548 2.6 36.5 1.0
NE2 A:HIS531 2.6 36.1 1.0
OE1 A:GLU548 2.6 38.9 1.0
O A:HOH1271 2.7 33.1 0.5
CD A:GLU548 2.9 39.3 1.0
CD2 A:HIS531 3.3 38.6 1.0
CE1 A:HIS531 3.7 35.9 1.0
O A:HOH1110 4.1 45.3 1.0
CG A:GLU548 4.4 41.3 1.0
CG A:HIS531 4.6 35.4 1.0
ND1 A:HIS531 4.7 37.3 1.0

Cadmium binding site 3 out of 4 in 5wgx

Go back to Cadmium Binding Sites List in 5wgx
Cadmium binding site 3 out of 4 in the Crystal Structure of Mala' H253A, 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 Mala' H253A, Malbrancheamide B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd704

b:51.3
occ:0.80
OD2 A:ASP547 2.6 44.1 1.0
OD2 A:ASP543 2.6 58.1 1.0
OD1 A:ASP547 2.7 35.0 1.0
CG A:ASP547 3.0 40.7 1.0
OD1 A:ASP543 3.0 48.6 1.0
CG A:ASP543 3.2 51.1 1.0
NH2 A:ARG478 4.1 43.9 1.0
O A:ASP543 4.4 38.5 1.0
CB A:ASP547 4.5 34.0 1.0
NH1 A:ARG478 4.6 41.5 1.0
CB A:ASP543 4.7 42.4 1.0
O A:HOH1261 4.7 50.4 1.0
CZ A:ARG478 4.8 43.0 1.0
C A:ASP543 5.0 38.8 1.0

Cadmium binding site 4 out of 4 in 5wgx

Go back to Cadmium Binding Sites List in 5wgx
Cadmium binding site 4 out of 4 in the Crystal Structure of Mala' H253A, 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 Mala' H253A, Malbrancheamide B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd705

b:53.3
occ:0.80
SG A:CYS112 2.6 52.1 1.0
SG A:CYS128 2.7 47.8 1.0
CB A:CYS128 3.3 36.4 1.0
O A:HOH1243 3.3 0.7 1.0
CB A:CYS112 3.4 33.8 1.0
CA A:CYS128 3.7 29.5 1.0
O A:HOH905 3.8 32.6 1.0
O A:SER129 4.0 45.7 1.0
N A:SER129 4.1 37.0 1.0
C A:CYS128 4.3 38.2 1.0
OE1 A:GLU250 4.4 76.7 1.0
O A:HOH953 4.4 47.8 1.0
NH1 A:ARG590 4.4 59.9 1.0
O A:LEU248 4.5 49.5 1.0
CA A:CYS112 4.6 34.7 1.0
OH A:TYR114 4.8 43.2 1.0
C A:SER129 4.9 39.0 1.0
N A:CYS128 5.0 31.4 1.0

Reference:

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
Page generated: Sat Dec 12 08:27:54 2020

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