Cadmium in PDB 5k1f: Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex

All present enzymatic activity of Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex:
3.5.2.6;

The structure of Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex, PDB code: 5k1f was solved by Y.J.An, J.H.Na, S.S.Cha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.698, 59.377, 113.612, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.1

The binding sites of Cadmium atom in the Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex (pdb code 5k1f). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex, PDB code: 5k1f:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex


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 A Class C Beta Lactamase/COMPOUND2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:31.9 occ:1.00 NE2 A:HIS161 2.6 24.6 1.0 O A:HOH570 2.6 11.6 1.0 O A:HOH571 2.7 13.6 1.0 O A:HOH569 2.7 24.7 1.0 CD2 A:HIS161 3.3 23.3 1.0 CE1 A:HIS161 3.7 25.6 1.0 NH2 A:ARG133 4.1 26.3 1.0 CG A:HIS161 4.5 20.9 1.0 O A:HOH531 4.6 14.2 1.0 ND1 A:HIS161 4.6 22.1 1.0 NE1 A:TRP96 4.8 20.2 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex


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 A Class C Beta Lactamase/COMPOUND2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:22.7 occ:1.00 ND1 A:HIS259 2.5 15.4 1.0 O A:HOH579 2.6 16.8 1.0 O A:HOH581 2.6 17.6 1.0 O A:HOH572 2.7 18.1 1.0 CE1 A:HIS259 3.4 16.6 1.0 CG A:HIS259 3.4 19.5 1.0 CB A:HIS259 3.7 13.4 1.0 CA A:HIS259 4.5 13.3 1.0 NE2 A:HIS259 4.6 19.5 1.0 CD2 A:HIS259 4.6 17.2 1.0 O A:HOH549 4.9 18.6 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex


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 A Class C Beta Lactamase/COMPOUND2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:27.7 occ:1.00 O A:HOH577 2.5 14.8 1.0 O A:HOH580 2.6 10.5 1.0 ND1 A:HIS24 2.6 22.4 1.0 CG A:HIS24 3.5 22.7 1.0 CE1 A:HIS24 3.5 25.3 1.0 CB A:HIS24 3.7 25.4 1.0 CA A:HIS24 3.9 26.0 1.0 CD A:PRO342 4.2 18.5 1.0 O A:GLU23 4.6 28.2 1.0 O A:HIS24 4.6 22.5 1.0 NH2 A:ARG339 4.6 32.0 1.0 CG A:PRO342 4.7 22.0 1.0 NE2 A:HIS24 4.7 24.7 1.0 CD2 A:HIS24 4.7 26.9 1.0 C A:HIS24 4.7 20.5 1.0 N A:HIS24 4.9 22.2 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex


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 A Class C Beta Lactamase/COMPOUND2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:25.9 occ:1.00 NE2 A:HIS148 2.5 16.2 1.0 CE1 A:HIS148 3.4 20.3 1.0 CD2 A:HIS148 3.5 22.4 1.0 ND1 A:HIS148 4.6 15.6 1.0 CG A:HIS148 4.6 17.7 1.0 CB A:PRO297 4.8 18.3 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND2 Complex


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 A Class C Beta Lactamase/COMPOUND2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd406 b:33.6 occ:1.00 NE2 A:HIS351 2.5 25.2 1.0 O A:VAL278 2.5 18.3 1.0 O A:HOH575 2.6 16.3 1.0 O A:HOH582 2.9 30.4 1.0 CE1 A:HIS351 3.3 24.8 1.0 C A:VAL278 3.5 20.0 1.0 CD2 A:HIS351 3.5 20.4 1.0 N A:VAL278 4.0 19.1 1.0 CA A:THR279 4.2 18.9 1.0 N A:THR279 4.2 21.0 1.0 CA A:VAL278 4.4 18.4 1.0 ND1 A:HIS351 4.5 24.9 1.0 CG A:HIS351 4.6 21.0 1.0 C A:THR279 4.6 22.0 1.0 N A:GLU280 4.7 21.5 1.0 CB A:PRO277 4.7 15.5 1.0 C A:PRO277 4.8 19.6 1.0 CG1 A:VAL278 5.0 19.9 1.0

J.H.Na, Y.J.An, S.S.Cha. Gmp and Imp Are Competitive Inhibitors of Cmy-10, An Extended-Spectrum Class C Beta-Lactamase. Antimicrob. Agents V. 61 2017CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 28242658
DOI: 10.1128/AAC.00098-17