Cadmium in PDB 5ac3: Crystal Structure of PAM12A
Enzymatic activity of Crystal Structure of PAM12A
All present enzymatic activity of Crystal Structure of PAM12A:
3.5.1.4;
Protein crystallography data
The structure of Crystal Structure of PAM12A, PDB code: 5ac3
was solved by
B.Wu,
H.J.Wijma,
L.Song,
H.J.Rozeboom,
C.Poloni,
Y.Tian,
M.I.Arif,
T.Nuijens,
P.J.L.M.Quadflieg,
W.Szymanski,
B.L.Feringa,
D.B.Janssen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
71.77 /
1.80
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.870,
82.870,
112.891,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16 /
19.6
|
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Structure of PAM12A
(pdb code 5ac3). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the
Crystal Structure of PAM12A, PDB code: 5ac3:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Cadmium binding site 1 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 1 out
of 9 in the Crystal Structure of PAM12A
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 PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1532
b:20.5
occ:1.00
|
O
|
A:HOH2124
|
2.3
|
16.9
|
1.0
|
OD1
|
A:ASP156
|
2.3
|
19.7
|
1.0
|
OD2
|
A:ASP156
|
2.5
|
19.8
|
1.0
|
O
|
A:HOH2114
|
2.5
|
19.1
|
1.0
|
CG
|
A:ASP156
|
2.8
|
19.3
|
1.0
|
CB
|
A:ASP156
|
4.3
|
18.7
|
1.0
|
O
|
A:HOH2340
|
4.4
|
32.4
|
1.0
|
O
|
A:ARG152
|
4.6
|
18.1
|
1.0
|
O
|
A:HOH2115
|
4.6
|
32.4
|
1.0
|
O
|
A:HOH2111
|
4.7
|
33.3
|
1.0
|
CA
|
A:ASP156
|
5.0
|
18.6
|
1.0
|
|
Cadmium binding site 2 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 2 out
of 9 in the Crystal Structure of PAM12A
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 PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1533
b:30.1
occ:0.75
|
O
|
A:ACY1544
|
2.2
|
31.6
|
1.0
|
O
|
A:HOH2230
|
2.4
|
33.7
|
1.0
|
NE2
|
A:HIS445
|
2.5
|
30.9
|
1.0
|
O
|
A:HOH2302
|
2.6
|
35.5
|
1.0
|
O
|
A:HOH2337
|
2.6
|
40.1
|
1.0
|
C
|
A:ACY1544
|
2.9
|
33.7
|
1.0
|
OXT
|
A:ACY1544
|
3.0
|
32.6
|
1.0
|
CD2
|
A:HIS445
|
3.5
|
29.7
|
1.0
|
CE1
|
A:HIS445
|
3.5
|
31.2
|
1.0
|
CH3
|
A:ACY1544
|
4.4
|
32.1
|
1.0
|
O
|
A:GLU348
|
4.5
|
31.0
|
1.0
|
N
|
A:GLU348
|
4.5
|
28.1
|
1.0
|
ND1
|
A:HIS445
|
4.6
|
30.4
|
1.0
|
CG
|
A:HIS445
|
4.6
|
28.9
|
1.0
|
CB
|
A:ALA444
|
4.7
|
27.5
|
1.0
|
CB
|
A:GLU348
|
5.0
|
34.0
|
1.0
|
|
Cadmium binding site 3 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 3 out
of 9 in the Crystal Structure of PAM12A
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 PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1534
b:29.6
occ:0.75
|
O
|
A:HOH2055
|
2.0
|
38.0
|
1.0
|
O
|
A:ACY1545
|
2.3
|
36.5
|
1.0
|
NE2
|
A:HIS86
|
2.3
|
20.4
|
1.0
|
O
|
A:HOH2338
|
2.4
|
23.0
|
0.5
|
O
|
A:HOH2052
|
2.5
|
32.6
|
1.0
|
O
|
A:HOH2053
|
2.7
|
42.8
|
1.0
|
OXT
|
A:ACY1545
|
2.8
|
34.9
|
1.0
|
C
|
A:ACY1545
|
2.9
|
36.5
|
1.0
|
CE1
|
A:HIS86
|
3.1
|
20.2
|
1.0
|
CD2
|
A:HIS86
|
3.5
|
19.8
|
1.0
|
O
|
A:HOH2054
|
4.0
|
27.1
|
1.0
|
CD
|
A:ARG80
|
4.3
|
31.4
|
1.0
|
ND1
|
A:HIS86
|
4.3
|
19.2
|
1.0
|
NE
|
A:ARG80
|
4.4
|
32.4
|
1.0
|
CH3
|
A:ACY1545
|
4.4
|
35.2
|
1.0
|
CG
|
A:HIS86
|
4.5
|
18.7
|
1.0
|
|
Cadmium binding site 4 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 4 out
of 9 in the Crystal Structure of PAM12A
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 PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1535
b:36.0
occ:0.50
|
NE2
|
A:HIS197
|
2.4
|
21.4
|
1.0
|
O
|
A:HOH2307
|
2.7
|
27.7
|
1.0
|
CD2
|
A:HIS197
|
3.4
|
20.7
|
1.0
|
CE1
|
A:HIS197
|
3.4
|
21.6
|
1.0
|
CD
|
A:CD1536
|
3.5
|
46.1
|
0.5
|
CD
|
A:PRO460
|
4.3
|
22.9
|
1.0
|
CG
|
A:PRO460
|
4.4
|
23.7
|
1.0
|
ND1
|
A:HIS197
|
4.5
|
21.1
|
1.0
|
CG
|
A:HIS197
|
4.5
|
20.1
|
1.0
|
O
|
A:ALA458
|
4.6
|
18.2
|
1.0
|
CD1
|
A:LEU494
|
4.7
|
18.4
|
1.0
|
|
Cadmium binding site 5 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 5 out
of 9 in the Crystal Structure of PAM12A
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 PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1536
b:46.1
occ:0.50
|
CE1
|
A:HIS197
|
2.4
|
21.6
|
1.0
|
NE2
|
A:HIS197
|
3.0
|
21.4
|
1.0
|
CD
|
A:CD1535
|
3.5
|
36.0
|
0.5
|
ND1
|
A:HIS197
|
3.6
|
21.1
|
1.0
|
CG
|
A:PRO460
|
3.9
|
23.7
|
1.0
|
CD2
|
A:HIS197
|
4.3
|
20.7
|
1.0
|
OG
|
A:SER196
|
4.3
|
20.1
|
1.0
|
CB
|
A:PRO460
|
4.5
|
23.7
|
1.0
|
O
|
A:HOH2156
|
4.5
|
34.9
|
1.0
|
CG
|
A:HIS197
|
4.6
|
20.1
|
1.0
|
CD
|
A:ARG194
|
4.8
|
28.9
|
1.0
|
CD
|
A:PRO460
|
4.9
|
22.9
|
1.0
|
|
Cadmium binding site 6 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 6 out
of 9 in the Crystal Structure of PAM12A
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 PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1537
b:74.2
occ:0.50
|
OE2
|
A:GLU331
|
2.6
|
32.1
|
1.0
|
OE1
|
A:GLU331
|
2.7
|
32.4
|
1.0
|
CD
|
A:GLU331
|
3.0
|
30.1
|
1.0
|
CG
|
A:GLU331
|
4.4
|
26.8
|
1.0
|
|
Cadmium binding site 7 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 7 out
of 9 in the Crystal Structure of PAM12A
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 PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1538
b:22.9
occ:0.50
|
O
|
A:HOH2069
|
2.1
|
14.6
|
1.0
|
OE1
|
A:GLU98
|
2.2
|
28.9
|
1.0
|
OE1
|
A:GLU101
|
2.2
|
24.8
|
1.0
|
OXT
|
A:ACY1542
|
2.2
|
35.2
|
1.0
|
OE2
|
A:GLU98
|
2.5
|
30.2
|
1.0
|
CD
|
A:GLU98
|
2.7
|
26.9
|
1.0
|
C
|
A:ACY1542
|
3.0
|
36.0
|
1.0
|
O
|
A:ACY1542
|
3.0
|
37.4
|
1.0
|
CD
|
A:GLU101
|
3.2
|
24.0
|
1.0
|
OE2
|
A:GLU101
|
3.7
|
25.2
|
1.0
|
NH1
|
A:ARG102
|
3.9
|
23.4
|
1.0
|
NZ
|
A:LYS97
|
4.2
|
27.0
|
1.0
|
CG
|
A:GLU98
|
4.2
|
23.8
|
1.0
|
NH2
|
A:ARG102
|
4.3
|
24.3
|
1.0
|
CH3
|
A:ACY1542
|
4.4
|
35.2
|
1.0
|
CG
|
A:GLU101
|
4.5
|
22.7
|
1.0
|
O
|
A:HOH2068
|
4.5
|
26.3
|
1.0
|
CZ
|
A:ARG102
|
4.6
|
23.3
|
1.0
|
CB
|
A:GLU101
|
4.7
|
21.6
|
1.0
|
|
Cadmium binding site 8 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 8 out
of 9 in the Crystal Structure of PAM12A
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 PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1539
b:56.1
occ:1.00
|
O
|
A:HOH2261
|
2.2
|
36.0
|
1.0
|
NE2
|
A:HIS395
|
2.4
|
31.0
|
1.0
|
O
|
A:HOH2263
|
2.7
|
43.0
|
1.0
|
O
|
A:HOH2262
|
2.9
|
41.3
|
1.0
|
CE1
|
A:HIS395
|
3.1
|
30.6
|
1.0
|
O
|
A:HOH2339
|
3.3
|
39.2
|
1.0
|
O
|
A:HOH2264
|
3.3
|
45.5
|
1.0
|
CD2
|
A:HIS395
|
3.6
|
30.8
|
1.0
|
ND1
|
A:HIS395
|
4.4
|
30.2
|
1.0
|
CG
|
A:HIS395
|
4.6
|
30.2
|
1.0
|
CE2
|
A:PHE391
|
4.8
|
26.0
|
1.0
|
|
Cadmium binding site 9 out
of 9 in 5ac3
Go back to
Cadmium Binding Sites List in 5ac3
Cadmium binding site 9 out
of 9 in the Crystal Structure of PAM12A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Crystal Structure of PAM12A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1540
b:54.1
occ:0.50
|
O
|
A:HOH2107
|
2.6
|
28.1
|
1.0
|
ND1
|
A:HIS378
|
2.6
|
23.5
|
1.0
|
CE1
|
A:HIS378
|
3.1
|
22.9
|
1.0
|
O
|
A:HOH2091
|
3.4
|
37.4
|
1.0
|
CG
|
A:HIS378
|
3.8
|
23.1
|
1.0
|
CB
|
A:ASP146
|
4.3
|
21.9
|
1.0
|
NE2
|
A:HIS378
|
4.4
|
23.4
|
1.0
|
CB
|
A:HIS378
|
4.4
|
23.2
|
1.0
|
OD2
|
A:ASP146
|
4.4
|
25.7
|
1.0
|
CA
|
A:HIS378
|
4.5
|
24.3
|
1.0
|
N
|
A:ASP146
|
4.5
|
20.2
|
1.0
|
CG
|
A:ASP146
|
4.7
|
23.6
|
1.0
|
O
|
A:ASP146
|
4.7
|
18.5
|
1.0
|
CD2
|
A:HIS378
|
4.8
|
22.8
|
1.0
|
O
|
A:THR377
|
4.8
|
24.2
|
1.0
|
ND2
|
A:ASN127
|
4.8
|
17.8
|
1.0
|
CA
|
A:ASP146
|
4.9
|
20.7
|
1.0
|
CB
|
A:PRO145
|
4.9
|
19.2
|
1.0
|
|
Reference:
B.Wu,
H.J.Wijma,
L.Song,
H.J.Rozeboom,
C.Poloni,
Y.Tian,
M.I.Arif,
T.Nuijens,
P.J.L.M.Quadflieg,
W.Szymanski,
B.L.Feringa,
D.B.Janssen.
Versatile Peptide C-Terminal Functionalization Via A Computationally Peptide Amidase Acs Catalysis 2016.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.6B01062
Page generated: Fri Jul 19 18:08:44 2024
|