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Cadmium in PDB 5wgt: Crystal Structure of Mala' H253A, Premalbrancheamide Complex

Protein crystallography data

The structure of Crystal Structure of Mala' H253A, Premalbrancheamide Complex, PDB code: 5wgt 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 / 2.09
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 79.176, 120.451, 170.271, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.8

Other elements in 5wgt:

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

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

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 4 in 5wgt

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

b:49.9
occ:0.50
OE1 A:GLU11 2.7 63.9 1.0
O A:HOH1124 2.7 28.5 1.0
OE2 A:GLU11 2.7 63.3 1.0
CD A:GLU11 3.0 64.8 1.0
O A:HOH819 4.5 48.5 1.0
CG A:GLU11 4.5 56.2 1.0

Cadmium binding site 2 out of 4 in 5wgt

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

b:46.8
occ:0.50
OE2 A:GLU548 2.6 45.1 1.0
OE1 A:GLU548 2.6 47.6 1.0
NE2 A:HIS531 2.7 44.6 1.0
O A:HOH1158 2.7 35.9 0.5
CD A:GLU548 2.9 49.6 1.0
CD2 A:HIS531 3.2 47.6 1.0
CE1 A:HIS531 3.9 51.5 1.0
CG A:GLU548 4.4 50.1 1.0
CG A:HIS531 4.5 50.2 1.0
ND1 A:HIS531 4.8 50.5 1.0

Cadmium binding site 3 out of 4 in 5wgt

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

b:63.1
occ:0.80
OD2 A:ASP547 2.6 52.7 1.0
OD2 A:ASP543 2.7 73.0 1.0
OD1 A:ASP543 2.8 66.2 1.0
OD1 A:ASP547 2.8 44.5 1.0
CG A:ASP547 3.0 50.7 1.0
CG A:ASP543 3.1 67.5 1.0
NH2 A:ARG478 4.1 56.7 1.0
O A:ASP543 4.5 49.5 1.0
CB A:ASP547 4.5 43.0 1.0
NH1 A:ARG478 4.6 43.1 1.0
CB A:ASP543 4.6 54.2 1.0
CZ A:ARG478 4.7 53.2 1.0
C A:ASP543 5.0 51.8 1.0

Cadmium binding site 4 out of 4 in 5wgt

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

b:71.6
occ:1.00
SG A:CYS112 2.6 56.4 1.0
SG A:CYS128 2.7 59.3 1.0
OE1 A:GLU250 3.2 81.2 1.0
CB A:CYS128 3.3 46.0 1.0
CB A:CYS112 3.6 43.0 1.0
O A:HOH1180 3.6 45.2 1.0
CA A:CYS128 3.7 41.4 1.0
O A:HOH949 3.8 38.0 1.0
O A:SER129 4.1 53.2 1.0
N A:SER129 4.2 43.8 1.0
C A:CYS128 4.4 46.0 1.0
CD A:GLU250 4.4 81.1 1.0
O A:LEU248 4.5 57.9 1.0
O A:HOH870 4.6 52.4 1.0
CA A:CYS112 4.8 41.2 1.0
C A:SER129 4.9 46.8 1.0
OH A:TYR114 5.0 50.9 1.0
N A:CYS128 5.0 38.0 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 08:27:50 2020

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