Cadmium in PDB 4qqp: Crystal Structure of C1QL3 Mutant D207A

The structure of Crystal Structure of C1QL3 Mutant D207A, PDB code: 4qqp was solved by S.Ressl, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.72 / 1.46
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	76.590, 76.590, 126.210, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20.3

The binding sites of Cadmium atom in the Crystal Structure of C1QL3 Mutant D207A (pdb code 4qqp). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of C1QL3 Mutant D207A, PDB code: 4qqp:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of C1QL3 Mutant D207A


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 C1QL3 Mutant D207A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:16.5 occ:0.33 O A:HOH372 2.3 22.4 1.0 OD2 A:ASP87 2.5 15.1 1.0 O A:HOH316 2.5 38.7 0.3 O A:HOH375 2.6 50.3 0.3 CG A:ASP87 3.3 12.9 1.0 OD1 A:ASP87 3.6 12.8 1.0 O A:HOH305 4.2 8.1 1.0 CB A:ASP87 4.5 10.9 1.0 OD1 A:ASN91 4.6 27.8 1.0 CA A:ASP87 4.8 11.6 1.0 O A:HOH374 4.9 40.2 1.0 N A:ALA88 5.0 12.3 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of C1QL3 Mutant D207A


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 C1QL3 Mutant D207A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:8.7 occ:0.33 O A:HOH305 2.2 8.1 1.0 OD2 A:ASP93 2.3 8.1 1.0 O A:HOH316 2.5 38.7 0.3 CG A:ASP93 3.3 7.0 1.0 OD1 A:ASP93 4.0 7.0 1.0 CD A:CD203 4.1 6.4 0.3 OD2 A:ASP87 4.2 15.1 1.0 O A:HOH301 4.3 7.0 1.0 CB A:ASP93 4.3 6.1 1.0 O A:GLN86 4.5 10.0 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of C1QL3 Mutant D207A


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 C1QL3 Mutant D207A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:6.4 occ:0.33 O A:HOH314 2.2 9.7 1.0 OD1 A:ASP93 2.3 7.0 1.0 O A:HOH323 2.6 52.9 0.3 CG A:ASP93 3.2 7.0 1.0 OD2 A:ASP93 3.3 8.1 1.0 CD A:CD202 4.1 8.7 0.3 O A:HOH307 4.2 8.7 1.0 N A:TYR94 4.6 5.0 1.0 CB A:ASP93 4.6 6.1 1.0 O A:HOH301 4.7 7.0 1.0 O A:TYR94 4.8 6.9 1.0 O A:HOH376 4.8 30.2 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of C1QL3 Mutant D207A


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 C1QL3 Mutant D207A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:11.3 occ:1.00 O A:HOH355 2.4 12.7 1.0 ND1 A:HIS19 2.4 10.6 1.0 OE2 A:GLU23 2.5 30.9 1.0 OE1 A:GLU23 3.1 24.4 1.0 CD A:GLU23 3.2 23.4 1.0 CE1 A:HIS19 3.3 12.2 1.0 CG A:HIS19 3.4 9.6 1.0 CB A:HIS19 3.7 8.6 1.0 CA A:HIS19 4.0 8.5 1.0 O A:GLN18 4.3 13.4 1.0 NE2 A:HIS19 4.4 17.2 1.0 NH2 A:ARG17 4.5 23.6 1.0 CD2 A:HIS19 4.5 11.9 1.0 O A:HOH317 4.5 13.2 1.0 CG A:GLU23 4.7 15.9 1.0 N A:GLU20 4.7 8.9 1.0 C A:HIS19 4.9 7.9 1.0 N A:HIS19 5.0 9.7 1.0 O A:HOH377 5.0 31.1 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of C1QL3 Mutant D207A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of C1QL3 Mutant D207A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:44.8 occ:1.00 O A:HOH322 2.4 16.1 1.0 O A:HOH331 2.4 19.1 1.0 OD2 A:ASP72 2.5 14.5 1.0 OD2 A:ASP114 2.6 30.1 1.0 CG A:ASP114 3.4 20.5 1.0 CG A:ASP72 3.5 13.2 1.0 OD1 A:ASP72 3.7 9.2 1.0 O A:HOH381 3.8 23.3 1.0 CB A:ASP114 4.0 13.8 1.0 OD1 A:ASP114 4.3 21.3 1.0 OG A:SER82 4.5 7.9 1.0 CB A:ASP72 4.8 7.4 1.0 CG2 A:VAL79 5.0 11.6 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of C1QL3 Mutant D207A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of C1QL3 Mutant D207A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:0.9 occ:1.00 O A:HOH392 2.6 15.3 1.0 O A:HOH302 2.7 6.8 1.0 NZ A:LYS117 3.6 26.6 1.0 CE A:LYS117 4.0 19.7 1.0 OE1 A:GLU20 4.6 11.4 1.0 OD2 A:ASP65 4.9 35.9 1.0 OE2 A:GLU20 4.9 10.4 1.0

S.Ressl, B.K.Vu, S.Vivona, D.C.Martinelli, T.C.Sudhof, A.T.Brunger. Structures of C1Q-Like Proteins Reveal Unique Features Among the C1Q/Tnf Superfamily. Structure V. 23 688 2015.
ISSN: ISSN 0969-2126
PubMed: 25752542
DOI: 10.1016/J.STR.2015.01.019