Zinc in PDB 1hee: Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A
Enzymatic activity of Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A
All present enzymatic activity of Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A:
3.4.17.1;
Protein crystallography data
The structure of Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A, PDB code: 1hee
was solved by
J.H.Cho,
N.-C.Ha,
S.J.Chung,
D.H.Kim,
K.Y.Choi,
B.-H.Oh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
100 /
1.75
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.570,
60.524,
74.410,
90.00,
97.84,
90.00
|
R / Rfree (%)
|
19.8 /
22.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A
(pdb code 1hee). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A, PDB code: 1hee:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1hee
Go back to
Zinc Binding Sites List in 1hee
Zinc binding site 1 out
of 4 in the Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1308
b:10.6
occ:1.00
|
O1
|
A:LHY1309
|
2.0
|
17.6
|
1.0
|
OE2
|
A:GLU72
|
2.1
|
6.9
|
1.0
|
ND1
|
A:HIS69
|
2.1
|
8.6
|
1.0
|
ND1
|
A:HIS196
|
2.2
|
6.6
|
1.0
|
OE1
|
A:GLU72
|
2.5
|
7.8
|
1.0
|
CD
|
A:GLU72
|
2.6
|
6.6
|
1.0
|
C1
|
A:LHY1309
|
3.1
|
17.8
|
1.0
|
CE1
|
A:HIS69
|
3.1
|
7.7
|
1.0
|
CG
|
A:HIS69
|
3.1
|
8.6
|
1.0
|
CG
|
A:HIS196
|
3.1
|
5.2
|
1.0
|
CE1
|
A:HIS196
|
3.2
|
8.7
|
1.0
|
CB
|
A:HIS196
|
3.4
|
5.7
|
1.0
|
CB
|
A:HIS69
|
3.4
|
6.8
|
1.0
|
N2
|
A:LHY1309
|
3.7
|
18.8
|
1.0
|
N
|
A:LHY1309
|
4.1
|
14.4
|
1.0
|
O
|
A:HOH2040
|
4.1
|
8.5
|
1.0
|
O
|
A:HOH2041
|
4.1
|
8.5
|
1.0
|
CG
|
A:GLU72
|
4.1
|
5.1
|
1.0
|
NH1
|
A:ARG127
|
4.2
|
5.8
|
1.0
|
NE2
|
A:HIS69
|
4.2
|
8.7
|
1.0
|
O
|
A:SER197
|
4.2
|
5.3
|
1.0
|
CD2
|
A:HIS69
|
4.3
|
8.1
|
1.0
|
CD2
|
A:HIS196
|
4.3
|
6.8
|
1.0
|
NE2
|
A:HIS196
|
4.3
|
6.9
|
1.0
|
CA
|
A:HIS196
|
4.3
|
5.5
|
1.0
|
CA
|
A:LHY1309
|
4.3
|
13.9
|
1.0
|
C
|
A:LHY1309
|
4.4
|
12.3
|
1.0
|
OXT
|
A:LHY1309
|
4.4
|
10.8
|
1.0
|
N
|
A:SER197
|
4.6
|
6.5
|
1.0
|
CA
|
A:HIS69
|
4.8
|
7.2
|
1.0
|
O
|
A:LHY1309
|
4.8
|
12.3
|
1.0
|
N
|
A:HIS69
|
5.0
|
5.5
|
1.0
|
CZ
|
A:ARG127
|
5.0
|
8.0
|
1.0
|
CG2
|
A:ILE68
|
5.0
|
8.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1hee
Go back to
Zinc Binding Sites List in 1hee
Zinc binding site 2 out
of 4 in the Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1308
b:9.9
occ:1.00
|
O1
|
B:LHY1309
|
2.1
|
19.5
|
1.0
|
ND1
|
B:HIS69
|
2.1
|
6.8
|
1.0
|
OE2
|
B:GLU72
|
2.2
|
5.4
|
1.0
|
ND1
|
B:HIS196
|
2.2
|
4.6
|
1.0
|
OE1
|
B:GLU72
|
2.5
|
6.5
|
1.0
|
CD
|
B:GLU72
|
2.7
|
5.6
|
1.0
|
C1
|
B:LHY1309
|
3.0
|
19.9
|
1.0
|
CE1
|
B:HIS69
|
3.1
|
6.1
|
1.0
|
CG
|
B:HIS196
|
3.1
|
6.2
|
1.0
|
CG
|
B:HIS69
|
3.1
|
7.5
|
1.0
|
CE1
|
B:HIS196
|
3.2
|
7.1
|
1.0
|
CB
|
B:HIS196
|
3.3
|
6.3
|
1.0
|
CB
|
B:HIS69
|
3.5
|
5.3
|
1.0
|
N2
|
B:LHY1309
|
3.7
|
20.1
|
1.0
|
N
|
B:LHY1309
|
3.9
|
17.4
|
1.0
|
NH1
|
B:ARG127
|
4.1
|
16.0
|
1.0
|
CG
|
B:GLU72
|
4.2
|
5.2
|
1.0
|
O
|
B:HOH2043
|
4.2
|
13.0
|
1.0
|
O
|
B:SER197
|
4.2
|
6.0
|
1.0
|
NE2
|
B:HIS69
|
4.2
|
8.1
|
1.0
|
CA
|
B:LHY1309
|
4.2
|
16.6
|
1.0
|
CD2
|
B:HIS69
|
4.2
|
6.1
|
1.0
|
O
|
B:HOH2042
|
4.3
|
7.2
|
1.0
|
CD2
|
B:HIS196
|
4.3
|
5.8
|
1.0
|
NE2
|
B:HIS196
|
4.3
|
8.6
|
1.0
|
CA
|
B:HIS196
|
4.3
|
5.5
|
1.0
|
C
|
B:LHY1309
|
4.4
|
15.7
|
1.0
|
OXT
|
B:LHY1309
|
4.4
|
15.8
|
1.0
|
N
|
B:SER197
|
4.6
|
6.2
|
1.0
|
CA
|
B:HIS69
|
4.8
|
6.3
|
1.0
|
O2
|
B:LHY1309
|
4.9
|
20.2
|
1.0
|
O
|
B:LHY1309
|
4.9
|
14.8
|
1.0
|
CZ
|
B:ARG127
|
5.0
|
16.6
|
1.0
|
N
|
B:HIS69
|
5.0
|
5.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1hee
Go back to
Zinc Binding Sites List in 1hee
Zinc binding site 3 out
of 4 in the Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1308
b:10.4
occ:1.00
|
O1
|
D:LHY1309
|
2.1
|
19.2
|
1.0
|
OE2
|
D:GLU72
|
2.1
|
3.9
|
1.0
|
ND1
|
D:HIS69
|
2.1
|
6.0
|
1.0
|
ND1
|
D:HIS196
|
2.2
|
5.6
|
1.0
|
OE1
|
D:GLU72
|
2.5
|
8.8
|
1.0
|
CD
|
D:GLU72
|
2.6
|
5.4
|
1.0
|
C1
|
D:LHY1309
|
3.0
|
20.1
|
1.0
|
CG
|
D:HIS69
|
3.1
|
6.7
|
1.0
|
CE1
|
D:HIS69
|
3.1
|
7.6
|
1.0
|
CG
|
D:HIS196
|
3.1
|
6.0
|
1.0
|
CE1
|
D:HIS196
|
3.1
|
6.5
|
1.0
|
CB
|
D:HIS196
|
3.4
|
5.3
|
1.0
|
CB
|
D:HIS69
|
3.4
|
6.3
|
1.0
|
N2
|
D:LHY1309
|
3.6
|
20.8
|
1.0
|
N
|
D:LHY1309
|
3.9
|
16.7
|
1.0
|
NH1
|
D:ARG127
|
4.0
|
14.5
|
1.0
|
CG
|
D:GLU72
|
4.1
|
5.6
|
1.0
|
O
|
D:HOH2046
|
4.2
|
10.9
|
1.0
|
O
|
D:SER197
|
4.2
|
6.7
|
1.0
|
NE2
|
D:HIS69
|
4.2
|
7.9
|
1.0
|
CD2
|
D:HIS69
|
4.2
|
6.0
|
1.0
|
NE2
|
D:HIS196
|
4.3
|
7.5
|
1.0
|
CD2
|
D:HIS196
|
4.3
|
4.8
|
1.0
|
CA
|
D:LHY1309
|
4.3
|
15.6
|
1.0
|
O
|
D:HOH2045
|
4.3
|
17.1
|
1.0
|
CA
|
D:HIS196
|
4.4
|
6.1
|
1.0
|
C
|
D:LHY1309
|
4.4
|
13.9
|
1.0
|
OXT
|
D:LHY1309
|
4.4
|
15.0
|
1.0
|
N
|
D:SER197
|
4.6
|
6.9
|
1.0
|
CA
|
D:HIS69
|
4.8
|
5.1
|
1.0
|
O
|
D:LHY1309
|
4.9
|
15.1
|
1.0
|
CZ
|
D:ARG127
|
4.9
|
15.5
|
1.0
|
O2
|
D:LHY1309
|
4.9
|
23.7
|
1.0
|
N
|
D:HIS69
|
5.0
|
6.0
|
1.0
|
CG2
|
D:ILE68
|
5.0
|
10.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1hee
Go back to
Zinc Binding Sites List in 1hee
Zinc binding site 4 out
of 4 in the Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Bovine Pancreatic Carboxypeptidase A Complexed with L-N-Hydroxyaminocarbonyl Phenylalanine at 2.3 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn1308
b:9.0
occ:1.00
|
O1
|
E:LHY1309
|
2.1
|
16.9
|
1.0
|
OE2
|
E:GLU72
|
2.1
|
6.7
|
1.0
|
ND1
|
E:HIS196
|
2.1
|
4.0
|
1.0
|
ND1
|
E:HIS69
|
2.1
|
8.0
|
1.0
|
OE1
|
E:GLU72
|
2.5
|
5.2
|
1.0
|
CD
|
E:GLU72
|
2.6
|
5.2
|
1.0
|
C1
|
E:LHY1309
|
3.1
|
17.6
|
1.0
|
CE1
|
E:HIS196
|
3.1
|
7.1
|
1.0
|
CE1
|
E:HIS69
|
3.1
|
8.0
|
1.0
|
CG
|
E:HIS69
|
3.1
|
7.0
|
1.0
|
CG
|
E:HIS196
|
3.1
|
5.5
|
1.0
|
CB
|
E:HIS69
|
3.4
|
6.3
|
1.0
|
CB
|
E:HIS196
|
3.4
|
4.1
|
1.0
|
N2
|
E:LHY1309
|
3.7
|
18.1
|
1.0
|
N
|
E:LHY1309
|
4.0
|
14.6
|
1.0
|
O
|
E:HOH2045
|
4.1
|
14.2
|
1.0
|
CG
|
E:GLU72
|
4.1
|
5.5
|
1.0
|
NH1
|
E:ARG127
|
4.1
|
13.2
|
1.0
|
O
|
E:HOH2046
|
4.1
|
7.9
|
1.0
|
NE2
|
E:HIS196
|
4.2
|
5.6
|
1.0
|
NE2
|
E:HIS69
|
4.2
|
8.2
|
1.0
|
O
|
E:SER197
|
4.2
|
6.5
|
1.0
|
CD2
|
E:HIS69
|
4.2
|
7.0
|
1.0
|
CD2
|
E:HIS196
|
4.2
|
4.4
|
1.0
|
CA
|
E:LHY1309
|
4.3
|
14.0
|
1.0
|
C
|
E:LHY1309
|
4.4
|
11.2
|
1.0
|
CA
|
E:HIS196
|
4.4
|
5.5
|
1.0
|
OXT
|
E:LHY1309
|
4.4
|
9.0
|
1.0
|
N
|
E:SER197
|
4.6
|
7.2
|
1.0
|
CA
|
E:HIS69
|
4.8
|
6.9
|
1.0
|
O
|
E:LHY1309
|
4.8
|
11.6
|
1.0
|
CZ
|
E:ARG127
|
4.9
|
13.1
|
1.0
|
N
|
E:HIS69
|
5.0
|
5.4
|
1.0
|
CG2
|
E:ILE68
|
5.0
|
8.0
|
1.0
|
|
Reference:
J.H.Cho,
D.H.Kim,
S.J.Chung,
N.-C.Ha,
B.-H.Oh,
K.Y.Choi.
Insight Into the Stereochemistry in the Inhibition of Carboxypeptidase A with N- (Hydroxyaminocarbonyl)Phenylalanine: Binding Modes of An Enantiomeric Pair of the Inhibitor to Carboxypeptidase A Bioorg.Med.Chem. V. 10 2015 2002.
ISSN: ISSN 0968-0896
PubMed: 11937361
DOI: 10.1016/S0968-0896(01)00429-1
Page generated: Sun Oct 13 02:13:13 2024
|