Copper in PDB 5imt: Toxin Receptor Complex

The structure of Toxin Receptor Complex, PDB code: 5imt was solved by C.J.Morton, S.L.Lawrence, S.C.Feil, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.21 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	93.730, 166.560, 118.250, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.7

The structure of Toxin Receptor Complex also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Copper atom in the Toxin Receptor Complex (pdb code 5imt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Toxin Receptor Complex, PDB code: 5imt:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu609 b:52.0 occ:1.00 HD22 A:ASN297 2.4 26.2 1.0 HG2 A:LYS117 2.9 47.8 1.0 HA A:TYR389 3.0 21.3 1.0 OG A:SER388 3.0 24.7 1.0 HG A:SER388 3.2 29.6 1.0 ND2 A:ASN297 3.2 21.9 1.0 OG A:SER299 3.2 16.5 1.0 HG A:SER299 3.3 19.8 1.0 OG1 A:THR390 3.3 32.7 1.0 HD21 A:ASN297 3.3 26.2 1.0 H A:SER299 3.4 19.8 1.0 CA A:TYR389 3.5 17.8 1.0 HG1 A:THR390 3.5 39.2 1.0 HE3 A:LYS117 3.5 52.5 1.0 C A:TYR389 3.5 16.5 1.0 N A:TYR389 3.6 20.4 1.0 HB2 A:SER299 3.6 19.8 1.0 C A:SER388 3.7 20.4 1.0 O A:SER388 3.8 16.5 1.0 CG A:LYS117 3.8 39.8 1.0 N A:THR390 3.8 16.5 1.0 N A:SER299 3.8 16.5 1.0 HA A:VAL298 3.9 31.9 1.0 CB A:SER299 3.9 16.5 1.0 O A:ASN297 3.9 22.2 1.0 O A:TYR389 3.9 16.5 1.0 H A:THR390 4.0 19.8 1.0 H A:TYR389 4.0 24.5 1.0 HB2 A:SER388 4.0 19.9 1.0 HZ2 A:LYS117 4.0 54.9 1.0 HB3 A:ASN297 4.0 32.3 1.0 CB A:SER388 4.0 16.6 1.0 HA A:LYS117 4.2 41.7 1.0 HB3 A:LYS117 4.2 40.3 1.0 HB A:THR390 4.2 19.8 1.0 CE A:LYS117 4.3 43.7 1.0 CB A:THR390 4.3 16.5 1.0 HG3 A:LYS117 4.3 47.8 1.0 CG A:ASN297 4.3 29.8 1.0 C A:ASN297 4.4 22.4 1.0 C A:VAL298 4.4 21.7 1.0 CA A:VAL298 4.5 26.6 1.0 CD A:LYS117 4.5 54.7 1.0 CA A:SER299 4.5 20.6 1.0 CB A:LYS117 4.5 33.6 1.0 CA A:SER388 4.5 23.1 1.0 NZ A:LYS117 4.6 45.8 1.0 HD3 A:LYS117 4.6 65.7 1.0 CA A:THR390 4.6 17.7 1.0 CB A:ASN297 4.6 26.9 1.0 N A:VAL298 4.7 16.5 1.0 HZ1 A:LYS117 4.8 54.9 1.0 HB3 A:SER299 4.8 19.8 1.0 CA A:LYS117 4.8 34.8 1.0 HB3 A:SER388 4.9 19.9 1.0 HA A:THR390 4.9 21.3 1.0 CB A:TYR389 5.0 16.5 1.0 HA A:SER299 5.0 24.7 1.0

Copper binding site 2 out of 2 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu610 b:0.7 occ:1.00 O A:HOH731 2.3 41.3 1.0 O A:HOH737 2.3 38.2 1.0 OE1 A:GLU100 2.4 67.1 1.0 O A:HOH708 2.4 57.5 1.0 OE2 A:GLU100 2.8 62.3 1.0 CD A:GLU100 2.9 61.2 1.0 HH21 A:ARG97 3.0 89.8 1.0 HZ1 A:LYS417 3.1 59.2 1.0 HZ3 A:LYS417 3.1 59.2 1.0 HE2 A:LYS313 3.1 66.1 1.0 HG A:SER415 3.5 58.0 1.0 NZ A:LYS417 3.5 49.3 1.0 HB2 A:SER415 3.6 47.0 1.0 NH2 A:ARG97 3.7 74.8 1.0 HZ3 A:LYS313 3.9 75.5 1.0 HZ2 A:LYS417 3.9 59.2 1.0 HH22 A:ARG97 3.9 89.8 1.0 HG2 A:LYS313 3.9 66.8 1.0 CE A:LYS313 4.0 55.1 1.0 HD3 A:LYS313 4.1 72.9 1.0 OG A:SER415 4.1 48.3 1.0 CB A:SER415 4.2 39.1 1.0 NZ A:LYS313 4.3 62.9 1.0 HB3 A:SER415 4.3 47.0 1.0 HZ1 A:LYS313 4.3 75.5 1.0 CG A:GLU100 4.3 38.0 1.0 HE A:ARG97 4.4 71.5 1.0 CD A:LYS313 4.4 60.8 1.0 CG A:LYS313 4.6 55.7 1.0 CZ A:ARG97 4.6 69.3 1.0 HG2 A:GLU100 4.7 45.6 1.0 HE3 A:LYS313 4.7 66.1 1.0 HE2 A:LYS417 4.7 64.2 1.0 CE A:LYS417 4.8 53.5 1.0 HB3 A:GLU100 4.8 36.9 1.0 NE A:ARG97 4.9 59.6 1.0 HB2 A:GLU100 4.9 36.9 1.0 HG3 A:GLU100 4.9 45.6 1.0 HB2 A:LYS313 4.9 63.1 1.0 CB A:GLU100 5.0 30.7 1.0

S.L.Lawrence, M.A.Gorman, S.C.Feil, T.D.Mulhern, M.J.Kuiper, A.J.Ratner, R.K.Tweten, C.J.Morton, M.W.Parker. Structural Basis For Receptor Recognition By the Human CD59-Responsive Cholesterol-Dependent Cytolysins. Structure V. 24 1488 2016.
ISSN: ISSN 0969-2126
PubMed: 27499440
DOI: 10.1016/J.STR.2016.06.017