Cadmium in PDB 3qpx: Crystal Structure of Fab C2507

The structure of Crystal Structure of Fab C2507, PDB code: 3qpx was solved by J.Luo, A.Teplyakov, O.Obmolova, T.Malia, G.L.Gilliland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.52 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.150, 87.050, 100.310, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.4

The structure of Crystal Structure of Fab C2507 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Crystal Structure of Fab C2507 (pdb code 3qpx). 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 Fab C2507, PDB code: 3qpx:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd226 b:45.5 occ:0.62 ND1 L:HIS188 2.4 47.4 1.0 OD2 L:ASP150 2.5 41.1 1.0 CE1 L:HIS188 3.3 53.4 1.0 CG L:ASP150 3.4 41.8 1.0 CG L:HIS188 3.4 49.1 1.0 CB L:ASP150 3.6 45.1 1.0 CB L:HIS188 3.7 45.0 1.0 CA L:HIS188 4.2 42.6 1.0 O L:VAL149 4.3 37.4 1.0 O L:LYS187 4.4 40.8 1.0 NE2 L:HIS188 4.4 54.3 1.0 CD2 L:HIS188 4.5 52.9 1.0 OD1 L:ASP150 4.6 39.5 1.0 CG1 L:VAL149 4.6 37.9 1.0 O L:HOH272 4.6 47.2 1.0 C L:VAL149 4.8 40.2 1.0 CA L:ASP150 4.9 42.1 1.0 N L:ASP150 5.0 39.8 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd227 b:62.2 occ:0.54 O H:HOH410 2.4 40.3 1.0 O L:HOH264 2.4 45.1 1.0 NE2 H:HIS170 2.5 45.5 1.0 ND2 L:ASN137 2.5 55.7 1.0 OD1 L:ASN136 2.8 47.6 1.0 ND2 L:ASN136 3.0 53.6 1.0 CG L:ASN137 3.0 52.8 1.0 OD1 L:ASN137 3.0 58.7 1.0 CD2 H:HIS170 3.1 42.4 1.0 CG L:ASN136 3.3 50.0 1.0 CE1 H:HIS170 3.6 41.7 1.0 OG1 H:THR189 4.1 36.3 1.0 O H:GLY168 4.2 34.1 1.0 CB L:ASN137 4.3 45.0 1.0 CG H:HIS170 4.4 38.6 1.0 CA H:GLY168 4.5 33.8 1.0 OG L:SER173 4.5 33.7 1.0 ND1 H:HIS170 4.6 41.2 1.0 C H:GLY168 4.6 36.3 1.0 CB L:ASN136 4.7 40.1 1.0 CG2 H:THR189 4.8 28.3 1.0 O L:HOH282 4.8 28.4 1.0 N L:ASN137 4.8 30.9 1.0 O H:HOH400 5.0 51.0 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd228 b:40.9 occ:1.00 O L:ASP1 2.4 29.4 1.0 N L:ASP1 2.4 41.2 1.0 OD1 L:ASP1 2.5 42.7 1.0 O L:HOH326 2.5 40.4 1.0 C L:ASP1 3.1 32.3 1.0 CA L:ASP1 3.2 39.5 1.0 CG L:ASP1 3.5 41.4 1.0 CB L:ASP1 3.9 40.8 1.0 OE1 L:GLN3 4.2 40.0 1.0 N L:ILE2 4.4 31.1 1.0 O L:HOH331 4.5 55.8 1.0 O L:HOH274 4.6 33.4 1.0 OD2 L:ASP1 4.6 40.2 1.0 CD L:GLN3 4.9 37.1 1.0 CG L:GLN3 5.0 33.2 1.0 O4 L:SO4217 5.0 0.0 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd238 b:43.3 occ:0.51 NE2 H:HIS224 2.5 45.1 1.0 CD2 H:HIS224 3.2 47.0 1.0 CE1 H:HIS224 3.7 48.3 1.0 O L:GLU212 4.4 38.0 1.0 CG H:HIS224 4.5 47.9 1.0 O H:SER221 4.6 37.2 1.0 ND1 H:HIS224 4.7 46.2 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd239 b:40.1 occ:1.00 NE2 H:HIS227 2.4 39.4 1.0 OE1 L:GLU212 2.5 34.1 1.0 O H:HOH267 2.6 29.4 1.0 O H:HOH305 2.6 38.9 1.0 OE2 L:GLU212 2.6 34.4 1.0 O L:HOH371 2.7 38.2 1.0 NZ H:LYS135 2.7 41.8 1.0 CD L:GLU212 2.9 40.7 1.0 CE H:LYS135 3.3 41.0 1.0 CD2 H:HIS227 3.3 46.3 1.0 CE1 H:HIS227 3.5 39.9 1.0 O H:CYS222 4.1 40.2 1.0 O1 H:SO4232 4.1 55.6 1.0 CA L:PHE208 4.3 40.2 1.0 N L:ASN209 4.4 36.5 1.0 CG L:GLU212 4.4 42.9 1.0 OD1 L:ASN209 4.5 35.9 1.0 CG H:HIS227 4.5 46.5 1.0 ND1 H:HIS227 4.5 43.8 1.0 O L:SER207 4.6 35.8 1.0 ND1 H:HIS224 4.6 46.2 1.0 O H:HOH359 4.7 67.9 1.0 O H:HIS224 4.7 46.2 1.0 CD H:LYS135 4.7 37.0 1.0 CB L:PHE208 4.8 40.7 1.0 C L:PHE208 4.9 36.6 1.0 CB H:HIS224 4.9 43.6 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd240 b:36.7 occ:1.00 O H:HOH268 2.4 36.7 1.0 NE2 H:HIS225 2.4 43.9 1.0 NE2 H:HIS223 2.4 37.3 1.0 O H:HOH274 2.7 30.0 1.0 CD2 H:HIS225 3.3 43.6 1.0 CD2 H:HIS223 3.3 31.7 1.0 CE1 H:HIS225 3.4 47.2 1.0 CE1 H:HIS223 3.4 36.2 1.0 ND1 H:HIS225 4.5 50.0 1.0 CG H:HIS225 4.5 47.9 1.0 CG H:HIS223 4.5 36.5 1.0 ND1 H:HIS223 4.5 39.2 1.0

J.Luo, A.Teplyakov, O.Obmolova, T.Malia, G.L.Gilliland. Crystal Structure of Fab C2507 To Be Published.