Zinc in PDB 3fx6: X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group
Enzymatic activity of X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group
All present enzymatic activity of X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group:
3.4.17.1;
Protein crystallography data
The structure of X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group, PDB code: 3fx6
was solved by
S.F.Wang,
J.Y.Jin,
G.R.Tian,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.37 /
1.85
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.356,
59.752,
99.514,
90.00,
104.04,
90.00
|
R / Rfree (%)
|
20.7 /
23.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group
(pdb code 3fx6). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group, PDB code: 3fx6:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 3fx6
Go back to
Zinc Binding Sites List in 3fx6
Zinc binding site 1 out
of 3 in the X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn309
b:11.1
occ:1.00
|
ND1
|
A:HIS69
|
2.1
|
8.4
|
1.0
|
ND1
|
A:HIS196
|
2.1
|
8.0
|
1.0
|
OE1
|
A:GLU72
|
2.2
|
9.0
|
1.0
|
OAQ
|
A:BPX311
|
2.2
|
45.8
|
1.0
|
OE2
|
A:GLU72
|
2.3
|
8.3
|
1.0
|
OAP
|
A:BPX311
|
2.6
|
39.6
|
1.0
|
CD
|
A:GLU72
|
2.6
|
10.3
|
1.0
|
CAG
|
A:BPX311
|
2.9
|
44.9
|
1.0
|
CE1
|
A:HIS69
|
3.0
|
8.4
|
1.0
|
CG
|
A:HIS196
|
3.0
|
8.2
|
1.0
|
CG
|
A:HIS69
|
3.1
|
6.2
|
1.0
|
CE1
|
A:HIS196
|
3.1
|
10.5
|
1.0
|
CB
|
A:HIS196
|
3.3
|
6.7
|
1.0
|
CB
|
A:HIS69
|
3.4
|
8.4
|
1.0
|
CAH
|
A:BPX311
|
3.8
|
41.6
|
1.0
|
O
|
A:HOH316
|
3.9
|
8.9
|
1.0
|
CG
|
A:GLU72
|
4.1
|
8.1
|
1.0
|
CA
|
A:HIS196
|
4.1
|
7.5
|
1.0
|
NE2
|
A:HIS69
|
4.1
|
7.2
|
1.0
|
CAA
|
A:BPX311
|
4.1
|
46.0
|
1.0
|
CAB
|
A:BPX311
|
4.2
|
48.2
|
1.0
|
OE2
|
A:GLU270
|
4.2
|
11.2
|
1.0
|
CD2
|
A:HIS196
|
4.2
|
10.0
|
1.0
|
CD2
|
A:HIS69
|
4.2
|
5.3
|
1.0
|
NE2
|
A:HIS196
|
4.2
|
9.0
|
1.0
|
N
|
A:SER197
|
4.4
|
9.5
|
1.0
|
OAS
|
A:BPX311
|
4.5
|
39.0
|
1.0
|
NH2
|
A:ARG127
|
4.5
|
15.6
|
1.0
|
NAM
|
A:BPX311
|
4.5
|
43.4
|
1.0
|
O
|
A:HOH334
|
4.6
|
24.8
|
1.0
|
OE1
|
A:GLU270
|
4.7
|
13.3
|
1.0
|
CA
|
A:HIS69
|
4.8
|
8.9
|
1.0
|
C
|
A:HIS196
|
4.8
|
8.0
|
1.0
|
CD
|
A:GLU270
|
4.9
|
12.9
|
1.0
|
CG2
|
A:ILE68
|
4.9
|
11.6
|
1.0
|
N
|
A:HIS69
|
4.9
|
7.4
|
1.0
|
CB
|
A:GLU72
|
4.9
|
8.0
|
1.0
|
|
Zinc binding site 2 out
of 3 in 3fx6
Go back to
Zinc Binding Sites List in 3fx6
Zinc binding site 2 out
of 3 in the X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn309
b:14.8
occ:1.00
|
ND1
|
C:HIS69
|
2.2
|
10.5
|
1.0
|
ND1
|
C:HIS196
|
2.2
|
11.2
|
1.0
|
OE1
|
C:GLU72
|
2.2
|
12.2
|
1.0
|
OAQ
|
C:BPX311
|
2.3
|
49.7
|
1.0
|
OE2
|
C:GLU72
|
2.4
|
11.3
|
1.0
|
OAP
|
C:BPX311
|
2.6
|
45.8
|
1.0
|
CD
|
C:GLU72
|
2.6
|
12.6
|
1.0
|
CAG
|
C:BPX311
|
2.9
|
48.9
|
1.0
|
CG
|
C:HIS196
|
3.0
|
10.9
|
1.0
|
CG
|
C:HIS69
|
3.1
|
9.4
|
1.0
|
CE1
|
C:HIS69
|
3.2
|
12.6
|
1.0
|
CB
|
C:HIS196
|
3.2
|
10.8
|
1.0
|
CE1
|
C:HIS196
|
3.3
|
12.5
|
1.0
|
CB
|
C:HIS69
|
3.4
|
9.6
|
1.0
|
CAH
|
C:BPX311
|
3.8
|
46.7
|
1.0
|
O
|
C:HOH329
|
3.9
|
11.8
|
1.0
|
CA
|
C:HIS196
|
4.1
|
9.5
|
1.0
|
CG
|
C:GLU72
|
4.2
|
11.2
|
1.0
|
CAA
|
C:BPX311
|
4.2
|
49.7
|
1.0
|
OE2
|
C:GLU270
|
4.2
|
16.8
|
1.0
|
CD2
|
C:HIS196
|
4.2
|
11.5
|
1.0
|
CAB
|
C:BPX311
|
4.3
|
50.8
|
1.0
|
NE2
|
C:HIS69
|
4.3
|
11.6
|
1.0
|
CD2
|
C:HIS69
|
4.3
|
9.1
|
1.0
|
NE2
|
C:HIS196
|
4.3
|
12.8
|
1.0
|
N
|
C:SER197
|
4.4
|
11.2
|
1.0
|
NH2
|
C:ARG127
|
4.5
|
17.9
|
1.0
|
NAM
|
C:BPX311
|
4.5
|
47.7
|
1.0
|
OAS
|
C:BPX311
|
4.6
|
44.9
|
1.0
|
O
|
C:HOH363
|
4.6
|
27.3
|
1.0
|
OE1
|
C:GLU270
|
4.7
|
17.8
|
1.0
|
CA
|
C:HIS69
|
4.8
|
10.2
|
1.0
|
C
|
C:HIS196
|
4.8
|
11.5
|
1.0
|
CG2
|
C:ILE68
|
4.9
|
12.0
|
1.0
|
CD
|
C:GLU270
|
4.9
|
15.5
|
1.0
|
N
|
C:HIS69
|
4.9
|
9.7
|
1.0
|
CB
|
C:GLU72
|
5.0
|
9.4
|
1.0
|
|
Zinc binding site 3 out
of 3 in 3fx6
Go back to
Zinc Binding Sites List in 3fx6
Zinc binding site 3 out
of 3 in the X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of X-Ray Crystallographic Studies on the Complex of Carboxypeptidase A with the Inhibitor Using Alpha-Nitro Ketone As the Zinc-Binding Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn309
b:14.3
occ:1.00
|
ND1
|
E:HIS69
|
2.1
|
7.9
|
1.0
|
ND1
|
E:HIS196
|
2.1
|
10.8
|
1.0
|
OE1
|
E:GLU72
|
2.3
|
10.6
|
1.0
|
OAQ
|
E:BPX311
|
2.3
|
48.9
|
1.0
|
OE2
|
E:GLU72
|
2.3
|
11.0
|
1.0
|
OAP
|
E:BPX311
|
2.6
|
43.7
|
1.0
|
CD
|
E:GLU72
|
2.6
|
12.3
|
1.0
|
CAG
|
E:BPX311
|
3.0
|
47.0
|
1.0
|
CG
|
E:HIS196
|
3.1
|
11.9
|
1.0
|
CG
|
E:HIS69
|
3.1
|
6.4
|
1.0
|
CE1
|
E:HIS69
|
3.1
|
10.8
|
1.0
|
CE1
|
E:HIS196
|
3.2
|
14.9
|
1.0
|
CB
|
E:HIS196
|
3.3
|
10.6
|
1.0
|
CB
|
E:HIS69
|
3.4
|
7.5
|
1.0
|
CAH
|
E:BPX311
|
3.8
|
43.0
|
1.0
|
O
|
E:HOH312
|
3.9
|
9.7
|
1.0
|
CG
|
E:GLU72
|
4.1
|
10.1
|
1.0
|
CA
|
E:HIS196
|
4.2
|
11.1
|
1.0
|
CAA
|
E:BPX311
|
4.2
|
48.1
|
1.0
|
CD2
|
E:HIS196
|
4.2
|
13.0
|
1.0
|
NE2
|
E:HIS69
|
4.2
|
8.7
|
1.0
|
CD2
|
E:HIS69
|
4.2
|
9.0
|
1.0
|
OE2
|
E:GLU270
|
4.2
|
14.7
|
1.0
|
CAB
|
E:BPX311
|
4.3
|
50.6
|
1.0
|
NE2
|
E:HIS196
|
4.3
|
11.9
|
1.0
|
OAS
|
E:BPX311
|
4.4
|
39.4
|
1.0
|
N
|
E:SER197
|
4.5
|
12.0
|
1.0
|
NAM
|
E:BPX311
|
4.5
|
43.7
|
1.0
|
O
|
E:HOH322
|
4.6
|
26.9
|
1.0
|
NH2
|
E:ARG127
|
4.6
|
16.7
|
1.0
|
OE1
|
E:GLU270
|
4.7
|
14.8
|
1.0
|
CA
|
E:HIS69
|
4.7
|
9.4
|
1.0
|
OAO
|
E:BPX311
|
4.8
|
50.8
|
1.0
|
C
|
E:HIS196
|
4.9
|
11.4
|
1.0
|
CD
|
E:GLU270
|
4.9
|
16.3
|
1.0
|
N
|
E:HIS69
|
4.9
|
8.5
|
1.0
|
CG2
|
E:ILE68
|
5.0
|
12.6
|
1.0
|
CB
|
E:GLU72
|
5.0
|
9.4
|
1.0
|
|
Reference:
S.F.Wang,
G.R.Tian,
W.Z.Zhang,
J.Y.Jin.
Characterization of Alpha-Nitromethyl Ketone As A New Zinc-Binding Group Based on Structural Analysis of Its Complex with Carboxypeptidase A Bioorg.Med.Chem.Lett. V. 19 5009 2009.
ISSN: ISSN 0960-894X
PubMed: 19646864
DOI: 10.1016/J.BMCL.2009.07.060
Page generated: Thu Oct 24 13:27:48 2024
|