Cadmium in PDB 2gyd: Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent

The structure of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent, PDB code: 2gyd was solved by P.J.Loll, M.J.Rossi, R.Eckenhoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.13 / 1.72
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.890, 181.890, 181.890, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 21.7

The structure of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent also contains other interesting chemical elements:

Fluorine

(F)

5 atoms

The binding sites of Cadmium atom in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent (pdb code 2gyd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent, PDB code: 2gyd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:20.3 occ:0.50 OD2 A:ASP80 2.3 21.5 1.0 OD1 A:ASP80 2.5 17.4 1.0 CG A:ASP80 2.8 20.1 1.0 O A:HOH1008 4.2 0.2 0.5 CB A:ASP80 4.3 18.7 1.0 O A:HOH1061 4.5 22.5 1.0 O A:HOH1064 4.6 27.2 1.0

Cadmium binding site 2 out of 7 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:26.4 occ:0.33 OE2 A:GLU130 2.4 34.7 1.0 OE1 A:GLU130 3.0 31.0 1.0 CD A:GLU130 3.1 33.0 1.0 CD A:CD1007 3.2 65.2 0.3 CD A:CD1006 3.6 21.5 0.3 SG A:CYS126 3.7 31.6 1.0 NE2 A:HIS114 4.4 25.3 1.0 CG A:GLU130 4.6 30.6 1.0

Cadmium binding site 3 out of 7 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1003 b:0.1 occ:1.00 OE1 A:GLU53 2.6 37.0 1.0 OE1 A:GLU56 2.6 33.9 1.0 OE2 A:GLU53 3.2 38.5 1.0 CD A:GLU56 3.2 31.9 1.0 OE2 A:GLU56 3.2 35.2 1.0 CD A:GLU53 3.3 33.1 1.0 O A:HOH1184 3.7 44.1 1.0 CG A:GLU56 4.6 25.7 1.0 CG A:GLU53 4.7 26.6 1.0 CB A:GLU56 5.0 20.3 1.0

Cadmium binding site 4 out of 7 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1004 b:68.1 occ:1.00 OE2 A:GLU88 2.5 26.9 1.0 OE1 A:GLU88 2.6 29.3 1.0 CD A:GLU88 2.8 27.0 1.0 O A:HOH1117 3.5 46.3 1.0 O A:HOH1009 4.3 54.6 1.0 NH2 A:ARG39 4.3 20.8 1.0 CG A:GLU88 4.3 22.5 1.0 NH1 A:ARG39 4.7 19.4 1.0 CB A:GLU88 5.0 19.7 1.0

Cadmium binding site 5 out of 7 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1005 b:83.9 occ:1.00 O A:HOH1156 2.1 0.0 1.0 OE2 A:GLU60 2.4 33.1 1.0 OE1 A:GLU57 2.7 34.1 1.0 OE1 A:GLU60 3.0 35.4 1.0 CD A:GLU60 3.0 30.5 1.0 OE2 A:GLU56 3.2 35.2 1.0 O A:HOH1067 3.3 46.9 1.0 CD A:GLU57 3.6 30.3 1.0 OE2 A:GLU57 3.8 32.8 1.0 O A:HOH1184 4.0 44.1 1.0 CD A:GLU56 4.0 31.9 1.0 CG A:GLU56 4.1 25.7 1.0 O A:HOH1010 4.4 71.9 1.0 CG A:GLU60 4.5 26.0 1.0 CG A:GLU57 4.9 25.5 1.0

Cadmium binding site 6 out of 7 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1006 b:21.5 occ:0.33 NE2 A:HIS114 2.1 25.3 1.0 SG A:CYS126 2.6 31.6 1.0 CE1 A:HIS114 2.6 25.9 1.0 CD2 A:HIS114 3.3 25.8 1.0 O A:HOH1174 3.3 36.2 1.0 OG A:SER118 3.5 30.0 1.0 CB A:CYS126 3.5 25.4 1.0 CD A:CD1002 3.6 26.4 0.3 OE2 A:GLU130 3.7 34.7 1.0 ND1 A:HIS114 3.8 26.2 1.0 CG A:HIS114 4.2 23.7 1.0 CA A:CYS126 4.6 24.8 1.0 CD A:GLU130 4.6 33.0 1.0 CB A:SER118 4.8 25.9 1.0

Cadmium binding site 7 out of 7 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1007 b:65.2 occ:0.33 OE1 A:GLU130 2.5 31.0 1.0 CD A:CD1002 3.2 26.4 0.3 CD A:GLU130 3.5 33.0 1.0 O A:HOH1158 3.9 26.0 0.3 OE2 A:GLU130 4.0 34.7 1.0 SG A:CYS126 4.3 31.6 1.0 CG A:GLU130 4.7 30.6 1.0 CB A:GLU130 4.9 30.0 1.0

J.Xi, R.Liu, M.J.Rossi, J.Yang, P.J.Loll, W.P.Dailey, R.G.Eckenhoff. Photoactive Analogues of the Haloether Anesthetics Provide High-Resolution Features From Low-Affinity Interactions. Acs Chem.Biol. V. 1 377 2006.
ISSN: ISSN 1554-8929
PubMed: 17163775
DOI: 10.1021/CB600207D