Cadmium in PDB 4raw: Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin
Enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin
All present enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin:
3.5.2.6;
Protein crystallography data
The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin, PDB code: 4raw
was solved by
Y.Kim,
C.Tesar,
R.Jedrzejczak,
G.Babnigg,
J.Sacchettini,
A.Joachimiak,
Midwest Center For Structural Genomics (Mcsg),
Structures Of Mtbproteins Conferring Susceptibility To Known Mtb Inhibitors (Mtbi),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.41 /
1.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.114,
78.769,
133.815,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13 /
16.1
|
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin
(pdb code 4raw). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the
Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin, PDB code: 4raw:
Jump to Cadmium binding site number:
1;
2;
3;
4;
Cadmium binding site 1 out
of 4 in 4raw
Go back to
Cadmium Binding Sites List in 4raw
Cadmium binding site 1 out
of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed 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 Mutant M67V Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd302
b:8.6
occ:0.62
|
O
|
A:HOH570
|
2.1
|
8.8
|
1.0
|
ND1
|
A:HIS122
|
2.1
|
8.9
|
1.0
|
NE2
|
A:HIS189
|
2.1
|
8.3
|
1.0
|
NE2
|
A:HIS120
|
2.2
|
8.1
|
1.0
|
OXT
|
A:ZZ7301
|
2.4
|
10.0
|
1.0
|
CE1
|
A:HIS122
|
3.0
|
8.6
|
1.0
|
CD2
|
A:HIS189
|
3.1
|
7.7
|
1.0
|
CG
|
A:HIS122
|
3.1
|
8.4
|
1.0
|
CE1
|
A:HIS189
|
3.1
|
7.2
|
1.0
|
CE1
|
A:HIS120
|
3.2
|
7.9
|
1.0
|
CD2
|
A:HIS120
|
3.2
|
7.4
|
1.0
|
C15
|
A:ZZ7301
|
3.3
|
9.7
|
1.0
|
CB
|
A:HIS122
|
3.4
|
7.3
|
1.0
|
C14
|
A:ZZ7301
|
3.9
|
9.7
|
1.0
|
N3
|
A:ZZ7301
|
4.0
|
8.9
|
1.0
|
O4
|
A:ZZ7301
|
4.1
|
11.7
|
1.0
|
NE2
|
A:HIS122
|
4.1
|
9.4
|
1.0
|
ND1
|
A:HIS189
|
4.2
|
7.8
|
1.0
|
CD2
|
A:HIS122
|
4.2
|
8.6
|
1.0
|
CG
|
A:HIS189
|
4.2
|
7.5
|
1.0
|
OD1
|
A:ASP124
|
4.2
|
8.7
|
1.0
|
CG2
|
A:THR190
|
4.3
|
8.1
|
1.0
|
ND1
|
A:HIS120
|
4.3
|
7.3
|
1.0
|
CG
|
A:HIS120
|
4.3
|
6.5
|
1.0
|
SG
|
A:CYS208
|
4.4
|
8.0
|
1.0
|
CB
|
A:CYS208
|
4.4
|
8.0
|
1.0
|
CD
|
A:CD303
|
4.6
|
9.9
|
0.7
|
C13
|
A:ZZ7301
|
4.6
|
8.7
|
1.0
|
O
|
A:HOH585
|
4.8
|
30.2
|
1.0
|
CA
|
A:HIS122
|
4.8
|
7.9
|
1.0
|
C12
|
A:ZZ7301
|
4.9
|
8.4
|
1.0
|
|
Cadmium binding site 2 out
of 4 in 4raw
Go back to
Cadmium Binding Sites List in 4raw
Cadmium binding site 2 out
of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed 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 Mutant M67V Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd303
b:9.9
occ:0.69
|
NE2
|
A:HIS250
|
2.1
|
8.0
|
1.0
|
OD2
|
A:ASP124
|
2.2
|
9.2
|
1.0
|
O1
|
A:ZZ7301
|
2.2
|
9.1
|
1.0
|
N3
|
A:ZZ7301
|
2.2
|
8.9
|
1.0
|
SG
|
A:CYS208
|
2.4
|
8.0
|
1.0
|
O
|
A:HOH570
|
3.0
|
8.8
|
1.0
|
C2
|
A:ZZ7301
|
3.0
|
8.5
|
1.0
|
C12
|
A:ZZ7301
|
3.1
|
8.4
|
1.0
|
CD2
|
A:HIS250
|
3.1
|
7.7
|
1.0
|
CE1
|
A:HIS250
|
3.1
|
9.2
|
1.0
|
C13
|
A:ZZ7301
|
3.3
|
8.7
|
1.0
|
CG
|
A:ASP124
|
3.3
|
8.2
|
1.0
|
CB
|
A:CYS208
|
3.4
|
8.0
|
1.0
|
C16
|
A:ZZ7301
|
3.6
|
10.3
|
1.0
|
OD1
|
A:ASP124
|
3.8
|
8.7
|
1.0
|
C6
|
A:ZZ7301
|
3.9
|
9.2
|
1.0
|
CB
|
A:SER249
|
4.2
|
8.1
|
1.0
|
ND1
|
A:HIS250
|
4.2
|
9.8
|
1.0
|
O2
|
A:ZZ7301
|
4.2
|
9.7
|
1.0
|
CG
|
A:HIS250
|
4.2
|
9.1
|
1.0
|
C14
|
A:ZZ7301
|
4.3
|
9.7
|
1.0
|
OXT
|
A:ZZ7301
|
4.3
|
10.0
|
1.0
|
S1
|
A:ZZ7301
|
4.5
|
10.5
|
1.0
|
CA
|
A:CYS208
|
4.5
|
6.9
|
1.0
|
CB
|
A:ASP124
|
4.5
|
8.4
|
1.0
|
CD
|
A:CD302
|
4.6
|
8.6
|
0.6
|
OG
|
A:SER249
|
4.6
|
8.0
|
1.0
|
C15
|
A:ZZ7301
|
4.8
|
9.7
|
1.0
|
NE2
|
A:HIS189
|
4.9
|
8.3
|
1.0
|
CE1
|
A:HIS189
|
4.9
|
7.2
|
1.0
|
|
Cadmium binding site 3 out
of 4 in 4raw
Go back to
Cadmium Binding Sites List in 4raw
Cadmium binding site 3 out
of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed 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 Mutant M67V Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd302
b:8.2
occ:0.61
|
ND1
|
B:HIS122
|
2.1
|
7.3
|
1.0
|
O
|
B:HOH401
|
2.1
|
8.2
|
1.0
|
NE2
|
B:HIS189
|
2.1
|
6.9
|
1.0
|
NE2
|
B:HIS120
|
2.2
|
7.9
|
1.0
|
OXT
|
B:ZZ7301
|
2.4
|
9.2
|
1.0
|
CE1
|
B:HIS122
|
3.0
|
8.1
|
1.0
|
CG
|
B:HIS122
|
3.1
|
7.3
|
1.0
|
CD2
|
B:HIS189
|
3.1
|
6.9
|
1.0
|
CE1
|
B:HIS189
|
3.1
|
7.8
|
1.0
|
CE1
|
B:HIS120
|
3.1
|
8.5
|
1.0
|
CD2
|
B:HIS120
|
3.2
|
7.3
|
1.0
|
C15
|
B:ZZ7301
|
3.3
|
8.7
|
1.0
|
CB
|
B:HIS122
|
3.4
|
7.9
|
1.0
|
C14
|
B:ZZ7301
|
3.9
|
8.5
|
1.0
|
N3
|
B:ZZ7301
|
4.0
|
9.1
|
1.0
|
NE2
|
B:HIS122
|
4.1
|
8.9
|
1.0
|
O4
|
B:ZZ7301
|
4.2
|
12.2
|
1.0
|
CD2
|
B:HIS122
|
4.2
|
8.9
|
1.0
|
CG2
|
B:THR190
|
4.2
|
7.8
|
1.0
|
ND1
|
B:HIS189
|
4.2
|
8.4
|
1.0
|
CG
|
B:HIS189
|
4.2
|
7.1
|
1.0
|
OD1
|
B:ASP124
|
4.2
|
8.0
|
1.0
|
ND1
|
B:HIS120
|
4.3
|
8.4
|
1.0
|
CG
|
B:HIS120
|
4.3
|
7.0
|
1.0
|
SG
|
B:CYS208
|
4.4
|
7.5
|
1.0
|
CB
|
B:CYS208
|
4.5
|
6.9
|
1.0
|
C13
|
B:ZZ7301
|
4.6
|
8.3
|
1.0
|
CD
|
B:CD303
|
4.6
|
8.0
|
0.6
|
O
|
B:HOH488
|
4.7
|
16.9
|
1.0
|
CA
|
B:HIS122
|
4.9
|
7.5
|
1.0
|
C12
|
B:ZZ7301
|
4.9
|
8.7
|
1.0
|
|
Cadmium binding site 4 out
of 4 in 4raw
Go back to
Cadmium Binding Sites List in 4raw
Cadmium binding site 4 out
of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed 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 Mutant M67V Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd303
b:8.0
occ:0.61
|
NE2
|
B:HIS250
|
2.1
|
8.8
|
1.0
|
OD2
|
B:ASP124
|
2.2
|
8.3
|
1.0
|
O1
|
B:ZZ7301
|
2.2
|
9.0
|
1.0
|
N3
|
B:ZZ7301
|
2.2
|
9.1
|
1.0
|
SG
|
B:CYS208
|
2.4
|
7.5
|
1.0
|
O
|
B:HOH401
|
3.0
|
8.2
|
1.0
|
C2
|
B:ZZ7301
|
3.0
|
8.4
|
1.0
|
CD2
|
B:HIS250
|
3.0
|
9.5
|
1.0
|
C12
|
B:ZZ7301
|
3.0
|
8.7
|
1.0
|
CE1
|
B:HIS250
|
3.1
|
8.7
|
1.0
|
C13
|
B:ZZ7301
|
3.3
|
8.3
|
1.0
|
CG
|
B:ASP124
|
3.3
|
7.4
|
1.0
|
CB
|
B:CYS208
|
3.4
|
6.9
|
1.0
|
C16
|
B:ZZ7301
|
3.6
|
11.0
|
1.0
|
OD1
|
B:ASP124
|
3.8
|
8.0
|
1.0
|
C6
|
B:ZZ7301
|
3.9
|
9.5
|
1.0
|
CG
|
B:HIS250
|
4.2
|
9.7
|
1.0
|
CB
|
B:SER249
|
4.2
|
8.1
|
1.0
|
ND1
|
B:HIS250
|
4.2
|
8.7
|
1.0
|
O2
|
B:ZZ7301
|
4.2
|
10.0
|
1.0
|
C14
|
B:ZZ7301
|
4.3
|
8.5
|
1.0
|
OXT
|
B:ZZ7301
|
4.4
|
9.2
|
1.0
|
CA
|
B:CYS208
|
4.5
|
7.8
|
1.0
|
S1
|
B:ZZ7301
|
4.5
|
10.9
|
1.0
|
CB
|
B:ASP124
|
4.5
|
7.3
|
1.0
|
OG
|
B:SER249
|
4.6
|
8.0
|
1.0
|
CD
|
B:CD302
|
4.6
|
8.2
|
0.6
|
C15
|
B:ZZ7301
|
4.8
|
8.7
|
1.0
|
NE2
|
B:HIS189
|
4.9
|
6.9
|
1.0
|
CE1
|
B:HIS189
|
4.9
|
7.8
|
1.0
|
|
Reference:
Y.Kim,
C.Tesar,
R.Jedrzejczak,
G.Babnigg,
J.Sacchettini,
A.Joachimiak,
Midwest Center For Structural Genomics (Mcsg),
Structures Of Mtb Proteins Conferring Susceptibility Toknown Mtb Inhibitors (Mtbi).
Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin To Be Published.
Page generated: Fri Jul 19 17:56:44 2024
|