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Cadmium in PDB 5k1d: Crystal Structure of A Class C Beta Lactamase/COMPOUND1 Complex

Enzymatic activity of Crystal Structure of A Class C Beta Lactamase/COMPOUND1 Complex

All present enzymatic activity of Crystal Structure of A Class C Beta Lactamase/COMPOUND1 Complex:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of A Class C Beta Lactamase/COMPOUND1 Complex, PDB code: 5k1d 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) 38.08 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.625, 59.381, 112.833, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of A Class C Beta Lactamase/COMPOUND1 Complex (pdb code 5k1d). 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/COMPOUND1 Complex, PDB code: 5k1d:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5k1d

Go back to Cadmium Binding Sites List in 5k1d
Cadmium binding site 1 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND1 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/COMPOUND1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:21.4
occ:1.00
ND1 A:HIS259 2.5 14.3 1.0
O A:HOH675 2.6 11.7 1.0
CE1 A:HIS259 3.4 13.5 1.0
CG A:HIS259 3.5 18.9 1.0
CB A:HIS259 3.7 11.4 1.0
O A:HOH649 4.2 24.2 1.0
O A:HOH533 4.3 21.3 1.0
CA A:HIS259 4.5 12.4 1.0
NE2 A:HIS259 4.5 16.8 1.0
CD2 A:HIS259 4.6 18.9 1.0
O A:HOH625 4.7 19.4 1.0
O A:HIS259 5.0 14.6 1.0

Cadmium binding site 2 out of 5 in 5k1d

Go back to Cadmium Binding Sites List in 5k1d
Cadmium binding site 2 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND1 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/COMPOUND1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:35.1
occ:1.00
O A:HOH676 2.6 16.6 1.0
CE1 A:HIS351 2.6 26.3 1.0
O A:VAL278 2.7 21.9 1.0
NE2 A:HIS351 3.0 30.6 1.0
O A:HOH674 3.2 29.2 1.0
C A:VAL278 3.5 20.8 1.0
O A:HOH657 3.8 27.1 1.0
ND1 A:HIS351 3.9 33.4 1.0
N A:VAL278 4.1 22.3 1.0
CA A:THR279 4.1 20.4 1.0
O A:HOH648 4.1 17.3 1.0
N A:THR279 4.2 21.5 1.0
CD2 A:HIS351 4.3 32.5 1.0
CA A:VAL278 4.5 19.2 1.0
C A:THR279 4.6 23.7 1.0
N A:GLU280 4.6 25.4 1.0
O A:HOH678 4.7 26.2 1.0
CB A:PRO277 4.7 22.2 1.0
CG A:HIS351 4.8 20.7 1.0
C A:PRO277 4.9 21.8 1.0

Cadmium binding site 3 out of 5 in 5k1d

Go back to Cadmium Binding Sites List in 5k1d
Cadmium binding site 3 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND1 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/COMPOUND1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:26.7
occ:1.00
OXT A:GLY359 2.7 28.9 1.0
O A:GLY359 2.7 25.5 1.0
C A:GLY359 3.1 30.5 1.0
CA A:GLY359 4.6 21.4 1.0

Cadmium binding site 4 out of 5 in 5k1d

Go back to Cadmium Binding Sites List in 5k1d
Cadmium binding site 4 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND1 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/COMPOUND1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:27.7
occ:1.00
NE2 A:HIS148 2.5 16.3 1.0
CD2 A:HIS148 3.4 18.9 1.0
CE1 A:HIS148 3.6 17.5 1.0
O A:HOH556 4.1 31.6 1.0
CG A:HIS148 4.6 17.2 1.0
ND1 A:HIS148 4.7 17.8 1.0
CB A:PRO297 4.8 18.6 1.0

Cadmium binding site 5 out of 5 in 5k1d

Go back to Cadmium Binding Sites List in 5k1d
Cadmium binding site 5 out of 5 in the Crystal Structure of A Class C Beta Lactamase/COMPOUND1 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/COMPOUND1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:29.1
occ:1.00
NE2 A:HIS161 2.5 20.9 1.0
O A:HOH660 2.6 18.9 1.0
O A:HOH636 2.6 28.7 1.0
O A:HOH655 2.7 8.7 1.0
O A:HOH667 2.7 9.8 1.0
O A:HOH686 2.7 23.9 1.0
CD2 A:HIS161 3.2 16.7 1.0
CE1 A:HIS161 3.7 21.4 1.0
O A:HOH677 3.9 29.9 1.0
NH2 A:ARG133 4.1 25.3 1.0
O A:HOH647 4.4 23.6 1.0
O A:HOH651 4.4 24.2 1.0
O A:HOH620 4.4 14.1 1.0
CG A:HIS161 4.4 19.4 1.0
O A:HOH695 4.5 22.7 1.0
ND1 A:HIS161 4.6 25.7 1.0
NE1 A:TRP96 4.9 23.7 1.0
CZ A:ARG133 5.0 23.8 1.0

Reference:

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
Page generated: Sat Dec 12 08:26:55 2020

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