Zinc 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:

Copper

(Cu)

2 atoms

The binding sites of Zinc atom in the Toxin Receptor Complex (pdb code 5imt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Toxin Receptor Complex, PDB code: 5imt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:60.2 occ:1.00 OE2 A:GLU445 2.1 48.9 1.0 OE1 A:GLU445 2.2 68.8 1.0 CD A:GLU445 2.3 57.3 1.0 O A:HOH701 2.3 50.2 1.0 HZ2 D:LYS66 3.1 76.2 1.0 HZ1 D:LYS66 3.5 76.2 1.0 CG A:GLU445 3.5 46.9 1.0 HG2 A:GLU445 3.6 56.3 1.0 NZ D:LYS66 3.7 63.5 1.0 HG3 A:GLU445 3.9 56.3 1.0 HZ3 D:LYS66 4.1 76.2 1.0 HB3 A:ALA444 4.3 61.9 1.0 O D:HOH201 4.7 41.2 1.0 CB A:GLU445 4.8 43.2 1.0 HA A:GLU445 4.8 49.0 1.0 HE3 D:LYS66 4.8 72.3 1.0 HB1 A:ALA444 4.8 61.9 1.0 CE D:LYS66 4.9 60.2 1.0 HB3 A:GLU445 4.9 51.9 1.0 H A:GLU445 5.0 44.4 1.0

Zinc binding site 2 out of 7 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:38.5 occ:1.00 OD2 A:ASP418 2.0 23.9 1.0 O A:HOH796 2.2 16.5 1.0 O A:HOH757 2.2 16.5 1.0 O A:HOH800 2.3 16.5 1.0 CG A:ASP418 3.0 28.4 1.0 H A:GLY99 3.2 33.3 1.0 HB3 A:ASP418 3.2 20.0 1.0 HB2 A:ASP418 3.2 20.0 1.0 HA2 A:GLY99 3.3 33.4 1.0 HH12 A:ARG471 3.3 62.1 1.0 CB A:ASP418 3.4 16.6 1.0 HE2 A:HIS96 3.6 39.6 1.0 N A:GLY99 3.9 27.8 1.0 NH1 A:ARG471 4.0 51.8 1.0 CA A:GLY99 4.0 27.8 1.0 HH22 A:ARG471 4.0 50.8 1.0 OD1 A:ASP418 4.1 32.0 1.0 HE1 A:HIS96 4.2 53.2 1.0 NE2 A:HIS96 4.3 33.0 1.0 HH11 A:ARG471 4.4 62.1 1.0 NH2 A:ARG471 4.5 42.4 1.0 C A:GLY99 4.6 24.4 1.0 CE1 A:HIS96 4.6 44.4 1.0 CZ A:ARG471 4.6 55.6 1.0 HA A:LYS473 4.7 19.8 1.0 HA A:PRO98 4.7 40.6 1.0 HA3 A:GLY99 4.8 33.4 1.0 CA A:ASP418 4.9 24.7 1.0 O A:GLY99 4.9 21.1 1.0

Zinc binding site 3 out of 7 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:50.4 occ:1.00 NE2 A:HIS81 2.1 43.3 1.0 O A:HOH748 2.1 34.1 1.0 O A:HOH798 2.2 26.4 1.0 OE1 A:GLU142 2.4 41.3 1.0 CE1 A:HIS81 2.8 43.5 1.0 HE1 A:HIS81 2.9 52.3 1.0 CD A:GLU142 3.1 40.8 1.0 OE2 A:GLU142 3.2 36.7 1.0 CD2 A:HIS81 3.2 41.1 1.0 HD2 A:HIS81 3.5 49.3 1.0 HE22 A:GLN138 3.8 27.2 1.0 HB1 A:ALA225 3.8 38.8 1.0 HB2 A:ALA225 3.8 38.8 1.0 HE21 A:GLN138 4.0 27.2 1.0 ND1 A:HIS81 4.0 47.2 1.0 CB A:ALA225 4.2 32.4 1.0 NE2 A:GLN138 4.2 22.7 1.0 CG A:HIS81 4.2 30.6 1.0 HB3 A:ALA225 4.6 38.8 1.0 CG A:GLU142 4.6 41.4 1.0 O A:HOH767 4.7 26.1 1.0 HD1 A:HIS81 4.8 56.7 1.0 HG3 A:GLU142 4.8 49.7 1.0 HA A:GLU142 4.8 27.1 1.0 HE22 A:GLN220 5.0 54.1 1.0

Zinc binding site 4 out of 7 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn607 b:53.6 occ:1.00 NE2 A:HIS442 2.1 49.8 1.0 O A:HOH765 2.2 33.0 1.0 OE2 A:GLU448 2.3 60.5 1.0 O A:HOH787 2.5 57.5 1.0 OE1 A:GLU448 2.7 46.9 1.0 CD A:GLU448 2.7 58.8 1.0 CE1 A:HIS442 2.9 44.7 1.0 HE1 A:HIS442 2.9 53.6 1.0 CD2 A:HIS442 3.3 43.6 1.0 HH21 A:ARG92 3.4 81.0 1.0 HE A:ARG92 3.4 74.4 1.0 HD2 A:HIS442 3.6 52.3 1.0 HB2 A:ALA94 3.6 36.4 1.0 HB3 A:ARG92 3.7 62.1 1.0 HB3 A:ALA94 3.7 36.4 1.0 HB2 A:ARG92 3.8 62.1 1.0 ND1 A:HIS442 4.1 53.5 1.0 CG A:GLU448 4.1 42.8 1.0 NH2 A:ARG92 4.1 67.5 1.0 CB A:ALA94 4.1 30.3 1.0 NE A:ARG92 4.1 62.0 1.0 HG2 A:GLU448 4.2 51.4 1.0 CB A:ARG92 4.2 51.8 1.0 CG A:HIS442 4.3 39.6 1.0 O A:ARG92 4.5 49.7 1.0 HG3 A:GLU448 4.5 51.4 1.0 CZ A:ARG92 4.6 71.3 1.0 HB1 A:ALA94 4.6 36.4 1.0 HH22 A:ARG92 4.7 81.0 1.0 HD1 A:HIS442 4.8 64.2 1.0 HH A:TYR101 4.8 64.3 1.0 C A:ARG92 4.9 36.1 1.0 HA A:GLU448 4.9 46.8 1.0

Zinc binding site 5 out of 7 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn608 b:0.9 occ:1.00 NE2 A:HIS465 2.7 67.7 1.0 HD2 A:HIS465 2.9 52.5 1.0 CD2 A:HIS465 3.1 43.7 1.0 CE1 A:HIS465 3.9 42.9 1.0 HE1 A:HIS465 4.3 51.5 1.0 CG A:HIS465 4.4 49.5 1.0 ND1 A:HIS465 4.8 40.9 1.0

Zinc binding site 6 out of 7 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:52.5 occ:1.00 OE2 D:GLU73 2.0 40.0 1.0 O D:HOH213 2.2 21.4 1.0 CD D:GLU73 3.1 48.0 1.0 OE1 D:GLU73 3.5 54.4 1.0 HD21 D:ASN77 4.0 61.8 1.0 HZ1 D:LYS30 4.3 47.1 1.0 ND2 D:ASN77 4.3 51.5 1.0 CG D:GLU73 4.4 34.6 1.0 HG2 D:GLU73 4.4 41.5 1.0 OD1 D:ASN77 4.5 46.6 1.0 HZ3 D:LYS30 4.6 47.1 1.0 CG D:ASN77 4.6 53.9 1.0 HD22 D:ASN77 4.7 61.8 1.0 HG3 D:GLU73 4.7 41.5 1.0 NZ D:LYS30 4.8 39.3 1.0 HA D:GLU73 4.9 41.4 1.0

Zinc binding site 7 out of 7 in the Toxin Receptor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Toxin Receptor Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn103 b:0.7 occ:1.00 HH22 D:ARG53 1.7 86.6 1.0 HH12 D:ARG53 1.8 94.0 1.0 NH2 D:ARG53 2.1 72.2 1.0 ND1 D:HIS44 2.2 71.8 1.0 NH1 D:ARG53 2.2 78.3 1.0 CZ D:ARG53 2.4 83.8 1.0 O D:HOH204 2.5 40.8 1.0 HH21 D:ARG53 2.8 86.6 1.0 HH11 D:ARG53 3.0 94.0 1.0 O D:HOH203 3.0 45.3 1.0 HB2 D:HIS44 3.1 54.1 1.0 CG D:HIS44 3.1 61.5 1.0 O D:HOH205 3.1 57.6 1.0 HD2 D:LYS41 3.1 84.6 1.0 CE1 D:HIS44 3.2 71.7 1.0 HB3 D:HIS44 3.3 54.1 1.0 HE1 D:HIS44 3.4 86.1 1.0 CB D:HIS44 3.4 45.1 1.0 NE D:ARG53 3.6 70.1 1.0 HB2 D:LYS41 3.7 59.8 1.0 HE D:ARG53 4.0 84.1 1.0 CD D:LYS41 4.1 70.5 1.0 NE2 D:HIS44 4.3 72.9 1.0 CD2 D:HIS44 4.3 54.4 1.0 HD3 D:LYS41 4.3 84.6 1.0 HD2 D:ARG53 4.4 76.4 1.0 H D:LYS41 4.4 52.1 1.0 HE1 D:TRP40 4.5 48.9 1.0 HG3 D:LYS41 4.5 69.9 1.0 CD D:ARG53 4.6 63.6 1.0 NE1 D:TRP40 4.6 40.7 1.0 CB D:LYS41 4.6 49.8 1.0 HZ2 D:TRP40 4.6 40.1 1.0 CG D:LYS41 4.7 58.2 1.0 CE2 D:TRP40 4.7 36.8 1.0 CZ2 D:TRP40 4.7 33.4 1.0 HB3 D:ASP49 4.9 54.1 1.0 HD3 D:ARG53 4.9 76.4 1.0 CA D:HIS44 4.9 45.9 1.0 HE3 D:LYS41 5.0 82.3 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