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Cadmium in PDB 5f1f: Crystal Structure of A Class C Beta Lactamase

Enzymatic activity of Crystal Structure of A Class C Beta Lactamase

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

Protein crystallography data

The structure of Crystal Structure of A Class C Beta Lactamase, PDB code: 5f1f was solved by Y.J.An, M.K.Kim, 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) 38.18 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.874, 59.342, 111.841, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of A Class C Beta Lactamase (pdb code 5f1f). 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 A Class C Beta Lactamase, PDB code: 5f1f:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 5f1f

Go back to Cadmium Binding Sites List in 5f1f
Cadmium binding site 1 out of 6 in the Crystal Structure of A Class C Beta Lactamase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:17.8
occ:1.00
 NE2 A:HIS161 2.3 20.2 1.0
O A:HOH731 2.3 16.6 1.0
O A:HOH727 2.3 17.0 1.0
O A:HOH540 2.3 23.2 1.0
O A:HOH754 2.4 8.9 1.0
O A:HOH750 2.4 10.8 1.0
CD2 A:HIS161 2.6 16.9 1.0
CE1 A:HIS161 3.5 20.4 1.0
CG A:HIS161 4.0 15.8 1.0
NH2 A:ARG133 4.3 18.3 1.0
ND1 A:HIS161 4.3 14.1 1.0
O A:HOH551 4.4 24.9 1.0
O A:HOH651 4.4 11.6 1.0
O A:HOH790 4.6 22.3 1.0
O A:HOH627 4.6 26.1 1.0
NE1 A:TRP96 4.8 16.6 1.0

Cadmium binding site 2 out of 6 in 5f1f

Go back to Cadmium Binding Sites List in 5f1f
Cadmium binding site 2 out of 6 in the Crystal Structure of A Class C Beta Lactamase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:20.0
occ:1.00
 NE2 A:HIS351 2.3 14.6 1.0
O A:HOH758 2.3 25.5 1.0
O A:VAL278 2.4 15.9 1.0
O A:HOH752 2.4 8.6 1.0
CE1 A:HIS351 3.2 16.3 1.0
CD2 A:HIS351 3.4 12.6 1.0
C A:VAL278 3.4 13.2 1.0
CA A:THR279 4.0 17.4 1.0
N A:VAL278 4.1 14.3 1.0
N A:THR279 4.1 16.5 1.0
O A:HOH728 4.3 21.7 1.0
ND1 A:HIS351 4.3 15.8 1.0
CA A:VAL278 4.4 10.9 1.0
CG A:HIS351 4.5 11.0 1.0
O A:HOH622 4.5 13.4 1.0
C A:THR279 4.6 16.6 1.0
N A:GLU280 4.7 18.2 1.0
CB A:PRO277 4.7 14.4 1.0
C A:PRO277 4.8 13.2 1.0
O A:HOH733 5.0 22.3 1.0

Cadmium binding site 3 out of 6 in 5f1f

Go back to Cadmium Binding Sites List in 5f1f
Cadmium binding site 3 out of 6 in the Crystal Structure of A Class C Beta Lactamase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:20.3
occ:1.00
 ND1 A:HIS24 2.3 16.6 1.0
O A:HOH762 2.4 8.9 1.0
CE1 A:HIS24 3.1 19.4 1.0
CG A:HIS24 3.4 15.9 1.0
CB A:HIS24 3.8 16.9 1.0
CA A:HIS24 4.0 17.2 1.0
CD A:PRO342 4.1 14.0 1.0
NE2 A:HIS24 4.3 22.1 1.0
CD2 A:HIS24 4.5 19.8 1.0
CG A:PRO342 4.6 15.4 1.0
O A:HOH789 4.7 28.0 1.0
O A:GLU23 4.7 24.9 1.0
O A:HIS24 4.8 17.9 1.0
NH2 A:ARG339 4.8 29.6 1.0
C A:HIS24 4.9 18.4 1.0
O A:HOH729 4.9 26.5 1.0
NE A:ARG339 5.0 22.2 1.0
N A:HIS24 5.0 17.2 1.0

Cadmium binding site 4 out of 6 in 5f1f

Go back to Cadmium Binding Sites List in 5f1f
Cadmium binding site 4 out of 6 in the Crystal Structure of A Class C Beta Lactamase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:13.8
occ:1.00
 ND1 A:HIS259 2.3 11.0 1.0
O A:HOH748 2.3 17.8 1.0
O A:HOH763 2.4 7.9 1.0
CE1 A:HIS259 3.2 12.7 1.0
CG A:HIS259 3.4 9.3 1.0
CB A:HIS259 3.7 9.5 1.0
O A:HOH523 4.3 19.7 1.0
NE2 A:HIS259 4.3 14.2 1.0
O A:HOH665 4.4 14.8 1.0
CD2 A:HIS259 4.5 12.8 1.0
CA A:HIS259 4.5 8.5 1.0
O A:HOH761 4.5 25.1 1.0
O A:HOH702 4.8 23.0 1.0
O A:HOH539 4.8 15.1 1.0

Cadmium binding site 5 out of 6 in 5f1f

Go back to Cadmium Binding Sites List in 5f1f
Cadmium binding site 5 out of 6 in the Crystal Structure of A Class C Beta Lactamase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:36.0
occ:1.00
 OD2 A:ASP14 2.3 16.6 1.0
O A:HOH508 2.3 32.3 1.0
O A:HOH755 2.3 29.3 1.0
O A:HOH721 2.3 28.6 1.0
CG A:ASP14 3.2 18.2 1.0
CB A:ASP14 3.6 10.0 1.0
O A:HOH501 3.9 12.5 1.0
O A:HOH773 3.9 27.1 1.0
NE2 A:GLN18 4.0 29.7 1.0
OE1 A:GLN18 4.0 26.3 1.0
OD1 A:ASP14 4.3 15.5 1.0
CD A:GLN18 4.4 26.8 1.0
CG A:ARG10 4.9 20.4 1.0
CD A:ARG10 4.9 22.7 1.0

Cadmium binding site 6 out of 6 in 5f1f

Go back to Cadmium Binding Sites List in 5f1f
Cadmium binding site 6 out of 6 in the Crystal Structure of A Class C Beta Lactamase


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 A Class C Beta Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:20.1
occ:1.00
 O A:HOH568 2.2 21.2 1.0
ND1 A:HIS0 2.3 23.8 1.0
CB A:HIS0 2.4 28.9 1.0
CG A:HIS0 2.6 26.5 1.0
CA A:HIS0 3.4 22.5 1.0
CE1 A:HIS0 3.5 23.2 1.0
CD2 A:HIS0 3.9 26.4 1.0
NE2 A:HIS0 4.3 29.5 1.0
N A:HIS0 4.4 23.1 1.0
N A:GLY1 4.5 20.1 1.0
C A:HIS0 4.5 19.6 1.0

Reference:

M.K.Kim, Y.J.An, J.H.Na, J.H.Seol, J.Y.Ryu, K.M.Chung, J.H.Moon, J.S.Lee, S.S.Cha. Crystal Structure of A Class C Beta Lactamase To Be Published.
Page generated: Thu Jul 10 14:17:42 2025

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