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Cadmium in PDB 4hl1: Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin

Enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin

All present enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin, PDB code: 4hl1 was solved by Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, J.Mire, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility To Known Mtbinhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.94 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.997, 78.700, 134.377, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 14.9

Other elements in 4hl1:

The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin (pdb code 4hl1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin, PDB code: 4hl1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 4hl1

Go back to Cadmium Binding Sites List in 4hl1
Cadmium binding site 1 out of 8 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:11.2
occ:0.64
 CD A:CD302 0.0 11.2 0.6
CD A:CD302 1.0 21.1 0.4
ND1 A:HIS122 2.2 16.9 1.0
NE2 A:HIS189 2.3 11.0 1.0
O A:HOH484 2.5 16.7 1.0
NE2 A:HIS120 2.6 17.9 1.0
CL A:CL305 2.6 19.1 1.0
CE1 A:HIS122 3.2 15.0 1.0
CG A:HIS122 3.2 12.6 1.0
CE1 A:HIS189 3.3 10.7 1.0
CD2 A:HIS189 3.3 10.0 1.0
CB A:HIS122 3.5 10.1 1.0
CD2 A:HIS120 3.5 12.8 1.0
CE1 A:HIS120 3.6 16.4 1.0
O A:HOH425 4.2 23.6 1.0
O3 A:ZZ7301 4.2 26.3 1.0
NE2 A:HIS122 4.3 17.7 1.0
CD A:CD303 4.3 10.9 0.9
CD2 A:HIS122 4.3 15.7 1.0
ND1 A:HIS189 4.4 11.3 1.0
CG2 A:THR190 4.5 12.7 1.0
OD1 A:ASP124 4.5 17.4 1.0
CG A:HIS189 4.5 10.8 1.0
SG A:CYS208 4.5 13.4 1.0
N2 A:ZZ7301 4.5 27.2 1.0
N3 A:ZZ7301 4.6 18.4 1.0
C3 A:ZZ7301 4.6 26.1 1.0
ND1 A:HIS120 4.7 17.2 1.0
CG A:HIS120 4.7 11.7 1.0
CB A:CYS208 4.7 10.9 1.0
O1 A:ZZ7301 4.8 16.1 1.0
CA A:HIS122 5.0 9.0 1.0

Cadmium binding site 2 out of 8 in 4hl1

Go back to Cadmium Binding Sites List in 4hl1
Cadmium binding site 2 out of 8 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:21.1
occ:0.36
 CD A:CD302 0.0 21.1 0.4
CD A:CD302 1.0 11.2 0.6
NE2 A:HIS120 2.1 17.9 1.0
O A:HOH484 2.2 16.7 1.0
NE2 A:HIS189 2.4 11.0 1.0
CE1 A:HIS120 2.7 16.4 1.0
ND1 A:HIS122 3.0 16.9 1.0
CD2 A:HIS189 3.2 10.0 1.0
CD2 A:HIS120 3.3 12.8 1.0
CL A:CL305 3.3 19.1 1.0
CE1 A:HIS189 3.4 10.7 1.0
SG A:CYS208 3.5 13.4 1.0
CB A:HIS122 3.7 10.1 1.0
CD A:CD303 3.7 10.9 0.9
CG A:HIS122 3.7 12.6 1.0
CB A:CYS208 3.9 10.9 1.0
OD1 A:ASP124 3.9 17.4 1.0
ND1 A:HIS120 4.0 17.2 1.0
CE1 A:HIS122 4.0 15.0 1.0
CG A:HIS120 4.2 11.7 1.0
CG A:HIS189 4.4 10.8 1.0
ND1 A:HIS189 4.4 11.3 1.0
O1 A:ZZ7301 4.4 16.1 1.0
O3 A:ZZ7301 4.5 26.3 1.0
N3 A:ZZ7301 4.6 18.4 1.0
OD2 A:ASP124 4.7 12.7 1.0
CG A:ASP124 4.8 12.7 1.0
CG2 A:THR190 4.8 12.7 1.0
CD2 A:HIS122 5.0 15.7 1.0
C2 A:ZZ7301 5.0 15.8 1.0

Cadmium binding site 3 out of 8 in 4hl1

Go back to Cadmium Binding Sites List in 4hl1
Cadmium binding site 3 out of 8 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:10.9
occ:0.90
 O1 A:ZZ7301 2.2 16.1 1.0
NE2 A:HIS250 2.3 10.2 1.0
OD2 A:ASP124 2.4 12.7 1.0
SG A:CYS208 2.5 13.4 1.0
O A:HOH484 2.6 16.7 1.0
N3 A:ZZ7301 2.6 18.4 1.0
C2 A:ZZ7301 3.1 15.8 1.0
CD2 A:HIS250 3.2 11.0 1.0
C12 A:ZZ7301 3.3 16.7 1.0
C13 A:ZZ7301 3.3 21.2 1.0
CE1 A:HIS250 3.4 9.7 1.0
CG A:ASP124 3.4 12.7 1.0
CB A:CYS208 3.5 10.9 1.0
OD1 A:ASP124 3.6 17.4 1.0
C14 A:ZZ7301 3.7 23.4 1.0
CD A:CD302 3.7 21.1 0.4
C16 A:ZZ7301 4.2 20.1 1.0
C6 A:ZZ7301 4.3 19.0 1.0
O2 A:ZZ7301 4.3 15.1 1.0
CD A:CD302 4.3 11.2 0.6
CG A:HIS250 4.4 9.8 1.0
ND1 A:HIS250 4.4 10.2 1.0
CB A:SER249 4.5 11.5 1.0
CL A:CL305 4.5 19.1 1.0
CA A:CYS208 4.6 13.0 1.0
NE2 A:HIS189 4.7 11.0 1.0
CB A:ASP124 4.7 12.6 1.0
O3 A:ZZ7301 4.8 26.3 1.0
OG A:SER249 4.8 13.4 1.0
N1 A:ZZ7301 4.8 24.6 1.0
S1 A:ZZ7301 4.8 22.1 1.0
CE1 A:HIS189 4.8 10.7 1.0

Cadmium binding site 4 out of 8 in 4hl1

Go back to Cadmium Binding Sites List in 4hl1
Cadmium binding site 4 out of 8 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:14.2
occ:0.62
 O A:HOH413 2.3 29.4 1.0
OD2 A:ASP223 2.3 21.3 1.0
OE2 A:GLU152 2.4 19.8 1.0
OE1 B:GLU227 2.5 24.0 0.9
OE2 B:GLU227 2.5 30.8 0.9
OE1 A:GLU152 2.6 21.8 1.0
O B:HOH463 2.8 50.4 1.0
CD B:GLU227 2.8 22.3 0.9
CD A:GLU152 2.9 21.8 1.0
OD1 A:ASP223 2.9 19.2 1.0
CG A:ASP223 3.0 20.1 1.0
NE2 A:HIS122 3.9 17.7 1.0
NE2 B:HIS228 4.2 14.9 1.0
O A:HOH440 4.3 16.8 1.0
CG B:GLU227 4.3 16.2 0.9
CG A:GLU152 4.4 15.0 1.0
CE1 B:HIS228 4.5 15.3 1.0
CB A:ASP223 4.5 15.5 1.0
O A:HOH505 4.6 30.1 1.0
O A:HOH576 4.6 39.1 1.0
O B:HOH455 4.7 26.1 1.0
CD2 A:HIS122 4.7 15.7 1.0
O A:HOH494 4.7 26.5 1.0
CE1 A:HIS122 4.8 15.0 1.0

Cadmium binding site 5 out of 8 in 4hl1

Go back to Cadmium Binding Sites List in 4hl1
Cadmium binding site 5 out of 8 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:10.7
occ:0.65
 CD B:CD302 0.0 10.7 0.7
CD B:CD302 1.2 26.1 0.3
ND1 B:HIS122 2.2 15.2 1.0
NE2 B:HIS189 2.3 12.2 1.0
NE2 B:HIS120 2.6 16.1 1.0
O B:HOH624 2.6 17.8 1.0
CL B:CL305 2.7 19.0 1.0
CE1 B:HIS122 3.2 14.4 1.0
CG B:HIS122 3.2 10.6 1.0
CD2 B:HIS189 3.3 10.1 1.0
CE1 B:HIS189 3.3 13.1 1.0
CB B:HIS122 3.5 10.4 1.0
CE1 B:HIS120 3.5 13.6 1.0
CD2 B:HIS120 3.5 13.5 1.0
O3 B:ZZ7301 4.2 30.4 1.0
CD B:CD303 4.3 10.9 0.9
NE2 B:HIS122 4.3 18.2 1.0
CD2 B:HIS122 4.3 14.7 1.0
ND1 B:HIS189 4.4 11.6 1.0
CG B:HIS189 4.4 8.5 1.0
CG2 B:THR190 4.4 12.6 1.0
OD1 B:ASP124 4.4 16.3 1.0
O B:HOH418 4.4 20.8 1.0
SG B:CYS208 4.5 12.9 1.0
N2 B:ZZ7301 4.5 29.9 1.0
ND1 B:HIS120 4.6 15.3 1.0
CB B:CYS208 4.6 12.9 1.0
CG B:HIS120 4.7 12.4 1.0
C3 B:ZZ7301 4.7 29.7 1.0
N3 B:ZZ7301 4.7 22.8 1.0
O1 B:ZZ7301 4.9 17.3 1.0
CA B:HIS122 5.0 9.7 1.0

Cadmium binding site 6 out of 8 in 4hl1

Go back to Cadmium Binding Sites List in 4hl1
Cadmium binding site 6 out of 8 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:26.1
occ:0.35
 CD B:CD302 0.0 26.1 0.3
CD B:CD302 1.2 10.7 0.7
NE2 B:HIS120 2.1 16.1 1.0
O B:HOH624 2.2 17.8 1.0
NE2 B:HIS189 2.5 12.2 1.0
CE1 B:HIS120 2.7 13.6 1.0
CD2 B:HIS189 3.2 10.1 1.0
ND1 B:HIS122 3.2 15.2 1.0
SG B:CYS208 3.4 12.9 1.0
CD2 B:HIS120 3.4 13.5 1.0
CL B:CL305 3.5 19.0 1.0
CE1 B:HIS189 3.5 13.1 1.0
CD B:CD303 3.5 10.9 0.9
CB B:CYS208 3.7 12.9 1.0
OD1 B:ASP124 3.8 16.3 1.0
CB B:HIS122 3.8 10.4 1.0
CG B:HIS122 3.9 10.6 1.0
ND1 B:HIS120 3.9 15.3 1.0
CE1 B:HIS122 4.3 14.4 1.0
CG B:HIS120 4.3 12.4 1.0
O3 B:ZZ7301 4.4 30.4 1.0
CG B:HIS189 4.4 8.5 1.0
O1 B:ZZ7301 4.4 17.3 1.0
ND1 B:HIS189 4.5 11.6 1.0
OD2 B:ASP124 4.5 13.7 1.0
CG B:ASP124 4.6 16.1 1.0
N3 B:ZZ7301 4.6 22.8 1.0
C2 B:ZZ7301 4.9 18.3 1.0
CG B:LYS125 4.9 13.2 1.0

Cadmium binding site 7 out of 8 in 4hl1

Go back to Cadmium Binding Sites List in 4hl1
Cadmium binding site 7 out of 8 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:10.9
occ:0.88
 O1 B:ZZ7301 2.3 17.3 1.0
NE2 B:HIS250 2.3 10.8 1.0
OD2 B:ASP124 2.4 13.7 1.0
SG B:CYS208 2.5 12.9 1.0
O B:HOH624 2.6 17.8 1.0
N3 B:ZZ7301 2.6 22.8 1.0
C2 B:ZZ7301 3.1 18.3 1.0
CD2 B:HIS250 3.3 11.2 1.0
C12 B:ZZ7301 3.3 20.8 1.0
C13 B:ZZ7301 3.3 25.4 1.0
CE1 B:HIS250 3.3 10.8 1.0
CG B:ASP124 3.4 16.1 1.0
CD B:CD302 3.5 26.1 0.3
CB B:CYS208 3.6 12.9 1.0
C14 B:ZZ7301 3.6 27.6 1.0
OD1 B:ASP124 3.7 16.3 1.0
C16 B:ZZ7301 4.2 23.4 1.0
C6 B:ZZ7301 4.2 23.0 1.0
CD B:CD302 4.3 10.7 0.7
O2 B:ZZ7301 4.4 17.1 1.0
CB B:SER249 4.4 12.0 1.0
ND1 B:HIS250 4.4 12.7 1.0
CG B:HIS250 4.4 12.2 1.0
CL B:CL305 4.5 19.0 1.0
CA B:CYS208 4.6 10.7 1.0
NE2 B:HIS189 4.7 12.2 1.0
CB B:ASP124 4.7 12.7 1.0
N1 B:ZZ7301 4.7 28.8 1.0
O3 B:ZZ7301 4.8 30.4 1.0
OG B:SER249 4.8 13.8 1.0
S1 B:ZZ7301 4.8 25.7 1.0
CE1 B:HIS189 4.9 13.1 1.0

Cadmium binding site 8 out of 8 in 4hl1

Go back to Cadmium Binding Sites List in 4hl1
Cadmium binding site 8 out of 8 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd304

b:14.1
occ:0.82
 O B:HOH462 2.1 24.4 1.0
OD2 B:ASP223 2.3 17.6 1.0
OE1 A:GLU227 2.4 17.7 0.9
OE2 B:GLU152 2.4 19.8 1.0
OE2 A:GLU227 2.5 21.0 0.9
OE1 B:GLU152 2.5 15.9 1.0
CD A:GLU227 2.8 19.3 0.9
CD B:GLU152 2.8 17.6 1.0
OD1 B:ASP223 2.9 19.8 1.0
CG B:ASP223 3.0 17.1 1.0
NE2 B:HIS122 4.0 18.2 1.0
O B:HOH563 4.2 38.9 1.0
O B:HOH428 4.2 16.4 1.0
NE2 A:HIS228 4.3 14.6 1.0
CG A:GLU227 4.3 14.5 0.9
CG B:GLU152 4.3 13.1 1.0
O B:HOH539 4.3 35.4 1.0
CE1 A:HIS228 4.4 18.1 1.0
CB B:ASP223 4.4 12.6 1.0
O B:HOH458 4.5 26.3 1.0
O A:HOH490 4.6 25.6 1.0
O B:HOH477 4.8 27.5 1.0
CD2 B:HIS122 4.8 14.7 1.0
CE1 B:HIS122 4.9 14.4 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, J.Mire, J.Sacchettini, A.Joachimiak. Crystal Structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Ampicillin To Be Published.
Page generated: Fri Jul 19 17:26:44 2024

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