Cadmium in PDB 3cfk: Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form

The structure of Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form, PDB code: 3cfk was solved by E.W.Debler, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.67 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	81.069, 106.299, 116.109, 89.89, 90.04, 89.48
R / Rfree (%)	22.1 / 24.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form (pdb code 3cfk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 23 binding sites of Cadmium where determined in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form, PDB code: 3cfk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


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 Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd301 b:77.0 occ:0.80 O L:HOH344 2.3 47.2 1.0 O L:HOH341 2.7 32.4 1.0 O J:GLY57 2.7 58.1 1.0 OE1 L:GLU81 2.8 58.8 1.0 NE2 L:GLN79 2.9 57.4 1.0 OE2 L:GLU81 3.3 60.1 1.0 CD L:GLU81 3.4 59.4 1.0 OG1 L:THR80 3.6 58.2 1.0 C J:GLY57 3.7 57.6 1.0 CA J:GLY57 3.9 57.5 1.0 CD L:GLN79 4.1 60.7 1.0 CB L:GLN79 4.4 58.2 1.0 CG L:GLN79 4.5 59.7 1.0 N L:THR80 4.5 57.9 1.0 CB L:THR80 4.9 57.6 1.0 CG L:GLU81 4.9 58.3 1.0 N J:VAL58 4.9 57.9 1.0

Cadmium binding site 2 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


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 Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd319 b:98.4 occ:0.50 O L:HOH330 2.3 38.0 1.0 O J:HOH332 2.4 50.1 1.0 O L:HOH335 2.5 59.7 1.0 O J:HOH324 2.6 36.9 1.0 OE2 L:GLU81 4.0 60.1 1.0 OE2 J:GLU81 4.2 60.3 1.0 O J:HOH341 4.4 51.6 1.0 CG J:GLU81 4.6 58.1 1.0 NH2 J:ARG61 4.7 57.6 1.0 OE1 L:GLN79 4.7 62.8 1.0 CG L:GLU81 4.7 58.3 1.0 NH1 J:ARG61 4.8 58.0 1.0 NH1 L:ARG61 4.8 58.1 1.0 CD L:GLU81 4.8 59.4 1.0 CD J:GLU81 4.9 59.4 1.0 NH2 L:ARG61 4.9 57.6 1.0 OE1 J:GLN79 5.0 59.2 1.0

Cadmium binding site 3 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


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 Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd323 b:93.0 occ:0.60 ND2 L:ASN138 2.1 58.4 1.0 NE2 H:HIS172 2.3 59.0 1.0 O L:HOH333 2.7 63.5 1.0 CG L:ASN138 2.8 59.2 1.0 OD1 L:ASN138 2.9 60.0 1.0 CE1 H:HIS172 3.0 58.5 1.0 CD2 H:HIS172 3.5 58.1 1.0 OD1 L:ASN137 3.9 60.8 1.0 O L:HOH337 3.9 44.5 1.0 OE2 K:GLU1 4.1 55.8 1.0 ND2 L:ASN137 4.1 59.1 1.0 ND1 H:HIS172 4.2 57.9 1.0 CB L:ASN138 4.3 57.9 1.0 CD K:GLU1 4.3 58.8 1.0 OD2 L:ASP170 4.3 60.6 1.0 OG L:SER174 4.4 58.0 1.0 CG L:ASN137 4.4 58.8 1.0 CG H:HIS172 4.5 58.0 1.0 N K:GLU1 4.6 57.0 1.0 OE1 K:GLU1 4.7 59.7 1.0 CG K:GLU1 4.7 58.8 1.0 OG1 L:THR172 4.8 58.1 1.0 OD2 L:ASP167 4.8 59.7 1.0 CA L:ASN138 4.8 57.7 1.0 N L:ASN138 4.9 57.8 1.0 CB K:GLU1 5.0 57.3 1.0

Cadmium binding site 4 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


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 Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd317 b:90.7 occ:0.80 O A:HOH416 2.0 47.7 1.0 O M:GLY57 2.3 58.3 1.0 NE2 A:GLN79 2.5 55.1 1.0 OE2 A:GLU81 2.6 60.2 1.0 O A:HOH411 3.0 41.7 1.0 OE1 A:GLU81 3.1 58.7 1.0 CD A:GLU81 3.2 59.3 1.0 C M:GLY57 3.3 57.7 1.0 CA M:GLY57 3.7 57.5 1.0 CD A:GLN79 3.8 59.0 1.0 OG1 A:THR80 4.4 57.8 1.0 CG A:GLN79 4.5 58.5 1.0 CB A:GLN79 4.5 58.0 1.0 N M:VAL58 4.5 57.9 1.0 O3 A:GOL402 4.6 67.9 1.0 CG A:GLU81 4.7 58.2 1.0 OE1 A:GLN79 4.7 58.6 1.0 CA M:VAL58 5.0 57.8 1.0

Cadmium binding site 5 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


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 Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd318 b:96.5 occ:0.60 O A:HOH403 2.2 73.8 1.0 OD2 A:ASP69 3.4 59.8 1.0 CG A:ASP69 3.8 58.8 1.0 CB A:ASP69 3.9 58.1 1.0 NE A:ARG70 4.3 57.9 1.0 N A:ASP69 4.5 57.9 1.0 NH2 A:ARG70 4.6 57.6 1.0 OD1 A:ASP69 4.6 60.0 1.0 CZ A:ARG70 4.9 57.8 1.0 CA A:ASP69 4.9 57.9 1.0

Cadmium binding site 6 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


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 Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd306 b:92.1 occ:0.75 OE1 B:GLU226 2.6 65.0 1.0 CD B:GLU226 2.6 63.3 1.0 OE2 B:GLU226 2.7 66.9 1.0 OE2 H:GLU226 2.8 62.8 1.0 CD H:GLU226 2.8 62.9 1.0 OE1 H:GLU226 3.0 64.6 1.0 CG B:GLU226 3.5 62.4 1.0 CG H:GLU226 3.7 62.3 1.0 NZ B:LYS222 4.0 58.2 1.0 CE B:LYS222 4.7 57.8 1.0 CB B:GLU226 4.7 61.5 1.0 CB H:GLU226 4.9 62.1 1.0

Cadmium binding site 7 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd308 b:76.1 occ:0.75 O G:GLY57 2.5 58.1 1.0 O C:HOH322 2.6 34.9 1.0 NE2 C:GLN79 2.8 58.5 1.0 OE1 C:GLU81 3.0 58.7 1.0 OE2 C:GLU81 3.3 60.3 1.0 C G:GLY57 3.4 57.6 1.0 CD C:GLU81 3.5 59.4 1.0 OG1 C:THR80 3.7 57.9 1.0 CA G:GLY57 3.8 57.6 1.0 CD C:GLN79 3.8 59.7 1.0 CG C:GLN79 4.5 58.7 1.0 OE1 C:GLN79 4.6 61.7 1.0 CB C:GLN79 4.6 58.6 1.0 N G:VAL58 4.6 57.8 1.0 N C:THR80 4.7 57.9 1.0 CB C:THR80 5.0 57.6 1.0

Cadmium binding site 8 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd309 b:94.2 occ:0.50 ND2 C:ASN138 1.8 58.5 1.0 NE2 D:HIS172 2.2 58.9 1.0 CG C:ASN138 2.8 59.1 1.0 CE1 D:HIS172 2.8 58.4 1.0 OD1 C:ASN138 3.0 60.2 1.0 CD2 D:HIS172 3.4 58.0 1.0 O I:HOH238 3.7 47.6 1.0 OD1 C:ASN137 3.7 60.6 1.0 OG C:SER174 4.0 58.1 1.0 ND1 D:HIS172 4.1 57.9 1.0 CB C:ASN138 4.1 57.8 1.0 OD2 C:ASP170 4.2 60.4 1.0 ND2 C:ASN137 4.2 59.0 1.0 CG C:ASN137 4.3 58.9 1.0 OG1 C:THR172 4.3 58.0 1.0 CG D:HIS172 4.4 58.0 1.0 CA C:ASN138 4.6 57.8 1.0 OD2 C:ASP167 4.6 59.6 1.0 N C:ASN138 4.6 57.7 1.0 OE2 I:GLU1 4.8 58.2 1.0 N I:GLU1 4.8 57.3 1.0

Cadmium binding site 9 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd310 b:48.0 occ:1.00 ND2 C:ASN152 2.3 56.9 1.0 O C:HOH341 2.3 28.8 1.0 O C:HOH316 2.5 32.2 1.0 O C:HOH313 2.7 12.3 1.0 O C:HOH317 2.8 23.0 1.0 CG C:ASN152 3.2 57.5 1.0 OD1 C:ASN152 3.4 57.3 1.0 CB C:ASN152 4.6 57.4 1.0 O C:HOH323 4.7 40.5 1.0 CA C:ASN152 4.9 57.7 1.0

Cadmium binding site 10 out of 23 in the Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Catalytic Elimination Antibody 34E4, Triclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd311 b:84.7 occ:0.70 OD2 D:ASP65 2.3 60.2 1.0 CG D:ASP65 3.1 61.0 1.0 CB D:ASP65 3.5 61.5 1.0 OD1 D:ASP65 4.2 61.2 1.0 CE D:LYS64 4.3 62.5 1.0 CD D:LYS64 4.4 62.3 1.0 NZ D:LYS64 4.4 62.8 1.0 N D:ASP65 4.6 62.2 1.0 CA D:ASP65 4.7 61.8 1.0 CG D:LYS64 4.8 62.2 1.0 CB D:LYS64 4.8 62.2 1.0

E.W.Debler, R.Muller, D.Hilvert, I.A.Wilson. Conformational Isomerism Can Limit Antibody Catalysis. J.Biol.Chem. V. 283 16554 2008.
ISSN: ISSN 0021-9258
PubMed: 18417480
DOI: 10.1074/JBC.M710256200