Cadmium in PDB 1kcq: Human Gelsolin Domain 2 with A CD2+ Bound

The structure of Human Gelsolin Domain 2 with A CD2+ Bound, PDB code: 1kcq was solved by S.L.Kazmirski, R.L.Isaacson, C.An, A.Buckle, C.M.Johnson, V.Daggett, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.25 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.968, 26.525, 50.294, 90.00, 121.19, 90.00
R / Rfree (%)	17.7 / 23.3

The binding sites of Cadmium atom in the Human Gelsolin Domain 2 with A CD2+ Bound (pdb code 1kcq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Human Gelsolin Domain 2 with A CD2+ Bound, PDB code: 1kcq:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Human Gelsolin Domain 2 with A CD2+ Bound


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Human Gelsolin Domain 2 with A CD2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd262 b:18.3 occ:0.50 OE2 A:GLU258 1.9 20.3 1.0 O A:HOH273 2.5 30.1 1.0 O A:HOH358 2.6 40.6 1.0 CD A:GLU258 2.8 20.0 1.0 OE1 A:GLU258 2.8 17.6 1.0 O A:HOH268 4.2 14.1 1.0 CG A:GLU258 4.2 19.7 1.0 OD1 A:ASP259 4.3 17.9 1.0 N A:ASP259 4.6 20.9 1.0 O A:HOH318 4.8 60.5 1.0 O A:HOH267 4.9 14.0 1.0 CA A:GLU258 4.9 17.3 1.0

Cadmium binding site 2 out of 5 in the Human Gelsolin Domain 2 with A CD2+ Bound


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Human Gelsolin Domain 2 with A CD2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd263 b:16.2 occ:1.00 O A:GLY186 2.2 13.8 1.0 OE2 A:GLU209 2.3 13.2 1.0 O A:HOH267 2.4 14.0 1.0 OD1 A:ASP187 2.4 14.3 1.0 OD1 A:ASP259 2.4 17.9 1.0 O A:HOH268 2.5 14.1 1.0 OE1 A:GLU209 2.7 14.1 1.0 CD A:GLU209 2.8 11.6 1.0 OD2 A:ASP259 2.8 16.5 1.0 CG A:ASP259 3.0 16.9 1.0 C A:GLY186 3.2 12.4 1.0 CG A:ASP187 3.6 16.8 1.0 CA A:ASP187 3.8 11.9 1.0 N A:ASP187 3.9 14.0 1.0 ND2 A:ASN206 4.0 19.2 1.0 CB A:ASP187 4.2 13.1 1.0 NZ A:LYS166 4.2 19.9 1.0 CG A:GLU209 4.3 14.1 1.0 CA A:GLY186 4.3 13.9 1.0 CB A:ASP259 4.5 17.7 1.0 OD2 A:ASP187 4.5 13.6 1.0 CA A:SER205 4.7 15.5 1.0 CG A:LYS166 4.7 12.0 1.0 N A:ASN206 4.8 17.7 1.0 O A:THR257 4.8 22.1 1.0 N A:GLY167 4.8 14.8 1.0 O A:HOH358 4.8 40.6 1.0 O A:ASN204 4.8 16.8 1.0 O A:GLY167 4.9 16.4 1.0 CG A:ASN206 5.0 20.5 1.0

Cadmium binding site 3 out of 5 in the Human Gelsolin Domain 2 with A CD2+ Bound


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Human Gelsolin Domain 2 with A CD2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd264 b:20.9 occ:0.50 O A:HOH270 2.3 19.7 1.0 OE2 A:GLU175 2.4 19.1 1.0 OE1 A:GLU175 2.5 20.5 1.0 CD A:GLU175 2.7 18.9 1.0 CD A:ARG161 3.7 17.4 1.0 CG A:ARG161 4.2 20.2 1.0 CG A:GLU175 4.2 16.2 1.0 NH1 A:ARG161 4.7 15.6 1.0 CB A:GLU175 4.8 15.3 1.0 O A:HOH266 4.9 18.1 1.0 CB A:ARG161 5.0 14.9 1.0

Cadmium binding site 4 out of 5 in the Human Gelsolin Domain 2 with A CD2+ Bound


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Human Gelsolin Domain 2 with A CD2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd265 b:23.8 occ:0.50 CD A:CD265 0.0 23.8 0.5 CD A:CD265 1.5 38.9 0.5 ND1 A:HIS232 2.3 20.5 1.0 O A:HOH360 2.4 32.0 1.0 O A:HOH355 2.6 38.4 1.0 O A:HOH374 2.8 46.1 1.0 CE1 A:HIS232 3.1 21.1 1.0 CG A:HIS232 3.4 19.9 1.0 CB A:HIS232 3.8 16.6 1.0 O A:HOH331 4.1 28.9 1.0 NE2 A:HIS232 4.3 19.2 1.0 CA A:HIS232 4.4 16.7 1.0 O A:HOH282 4.4 21.5 1.0 CD2 A:HIS232 4.5 19.1 1.0 O A:HOH352 5.0 35.6 1.0

Cadmium binding site 5 out of 5 in the Human Gelsolin Domain 2 with A CD2+ Bound


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Human Gelsolin Domain 2 with A CD2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd265 b:38.9 occ:0.50 CD A:CD265 0.0 38.9 0.5 CD A:CD265 1.5 23.8 0.5 O A:HOH374 2.4 46.1 1.0 O A:HOH355 2.4 38.4 1.0 ND1 A:HIS232 2.6 20.5 1.0 CE1 A:HIS232 3.4 21.1 1.0 CG A:HIS232 3.6 19.9 1.0 O A:HOH360 3.8 32.0 1.0 O A:HOH352 3.8 35.6 1.0 CB A:HIS232 3.8 16.6 1.0 CA A:HIS232 3.9 16.7 1.0 O A:VAL231 4.2 18.8 1.0 O A:HOH331 4.5 28.9 1.0 NE2 A:HIS232 4.6 19.2 1.0 CD2 A:HIS232 4.6 19.1 1.0 N A:HIS232 4.8 17.2 1.0 C A:VAL231 4.9 18.8 1.0 C A:HIS232 4.9 19.0 1.0 CD A:ARG230 5.0 33.2 1.0 N A:VAL233 5.0 18.4 1.0

S.L.Kazmirski, R.L.Isaacson, C.An, A.Buckle, C.M.Johnson, V.Daggett, A.R.Fersht. Loss of A Metal-Binding Site in Gelsolin Leads to Familial Amyloidosis-Finnish Type. Nat.Struct.Biol. V. 9 112 2002.
ISSN: ISSN 1072-8368
PubMed: 11753432
DOI: 10.1038/NSB745