Zinc in PDB 7vb3: Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
Enzymatic activity of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
All present enzymatic activity of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum:
4.1.2.46;
Protein crystallography data
The structure of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum, PDB code: 7vb3
was solved by
D.Zheng,
M.Nakabayashi,
Y.Asano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
84.07 /
1.48
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.12,
52.18,
168.51,
90,
95.01,
90
|
R / Rfree (%)
|
15.6 /
18.3
|
Other elements in 7vb3:
The structure of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
(pdb code 7vb3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum, PDB code: 7vb3:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7vb3
Go back to
Zinc Binding Sites List in 7vb3
Zinc binding site 1 out
of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
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 Hydroxynitrile Lyase From Linum Usitatissimum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:12.3
occ:1.00
|
SG
|
A:CYS121
|
2.3
|
12.3
|
1.0
|
SG
|
A:CYS129
|
2.3
|
11.4
|
1.0
|
SG
|
A:CYS115
|
2.3
|
12.8
|
1.0
|
SG
|
A:CYS118
|
2.4
|
11.8
|
1.0
|
CB
|
A:CYS129
|
3.3
|
11.4
|
1.0
|
CB
|
A:CYS121
|
3.4
|
12.3
|
1.0
|
CB
|
A:CYS115
|
3.4
|
13.0
|
1.0
|
CB
|
A:CYS118
|
3.5
|
13.1
|
1.0
|
N
|
A:CYS115
|
3.5
|
12.6
|
1.0
|
CA
|
A:CYS129
|
3.7
|
11.0
|
1.0
|
N
|
A:GLN116
|
3.8
|
13.6
|
1.0
|
CA
|
A:CYS115
|
3.9
|
12.4
|
1.0
|
N
|
A:CYS118
|
3.9
|
12.9
|
1.0
|
N
|
A:GLN130
|
3.9
|
11.3
|
1.0
|
N
|
A:CYS121
|
4.2
|
11.0
|
1.0
|
C
|
A:CYS129
|
4.2
|
11.4
|
1.0
|
CA
|
A:CYS118
|
4.2
|
12.0
|
1.0
|
C
|
A:CYS115
|
4.3
|
12.9
|
1.0
|
CA
|
A:CYS121
|
4.3
|
11.4
|
1.0
|
N
|
A:ASN131
|
4.5
|
11.9
|
1.0
|
N
|
A:THR117
|
4.5
|
13.9
|
1.0
|
C
|
A:GLU114
|
4.6
|
12.4
|
1.0
|
ND2
|
A:ASN131
|
4.7
|
14.5
|
1.0
|
O
|
A:HOH955
|
4.7
|
15.9
|
1.0
|
CA
|
A:GLN116
|
4.9
|
13.6
|
1.0
|
CB
|
A:ASN131
|
4.9
|
14.1
|
1.0
|
C
|
A:CYS118
|
4.9
|
11.6
|
1.0
|
O
|
A:CYS118
|
4.9
|
12.3
|
1.0
|
CA
|
A:GLU114
|
4.9
|
11.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7vb3
Go back to
Zinc Binding Sites List in 7vb3
Zinc binding site 2 out
of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
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 Hydroxynitrile Lyase From Linum Usitatissimum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:10.3
occ:0.89
|
NE2
|
A:HIS85
|
2.0
|
10.3
|
1.0
|
O
|
A:HOH606
|
2.1
|
13.3
|
1.0
|
SG
|
A:CYS199
|
2.2
|
10.6
|
1.0
|
SG
|
A:CYS63
|
2.4
|
11.0
|
1.0
|
CE1
|
A:HIS85
|
3.0
|
11.3
|
1.0
|
CD2
|
A:HIS85
|
3.0
|
11.5
|
1.0
|
CB
|
A:CYS63
|
3.2
|
10.9
|
1.0
|
CB
|
A:CYS199
|
3.4
|
9.3
|
1.0
|
C5N
|
A:NAD501
|
3.4
|
10.5
|
1.0
|
C4N
|
A:NAD501
|
3.7
|
9.7
|
1.0
|
C6N
|
A:NAD501
|
4.0
|
9.9
|
1.0
|
ND1
|
A:HIS85
|
4.1
|
11.3
|
1.0
|
CG
|
A:HIS85
|
4.2
|
10.4
|
1.0
|
OE2
|
A:GLU86
|
4.2
|
13.4
|
1.0
|
CB
|
A:THR65
|
4.2
|
12.0
|
1.0
|
O
|
A:HOH804
|
4.2
|
17.2
|
1.0
|
OG1
|
A:THR65
|
4.3
|
12.9
|
1.0
|
O1
|
A:GOL504
|
4.4
|
21.9
|
1.0
|
C3N
|
A:NAD501
|
4.6
|
9.1
|
1.0
|
CA
|
A:CYS63
|
4.7
|
10.6
|
1.0
|
CA
|
A:CYS199
|
4.7
|
8.6
|
1.0
|
O
|
A:HOH669
|
4.7
|
10.7
|
1.0
|
N1N
|
A:NAD501
|
4.8
|
9.8
|
1.0
|
N
|
A:ALA200
|
4.9
|
10.2
|
1.0
|
C3
|
A:GOL504
|
4.9
|
22.0
|
1.0
|
C
|
A:CYS199
|
5.0
|
10.3
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7vb3
Go back to
Zinc Binding Sites List in 7vb3
Zinc binding site 3 out
of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
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 Hydroxynitrile Lyase From Linum Usitatissimum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:12.8
occ:1.00
|
SG
|
B:CYS115
|
2.3
|
12.1
|
1.0
|
SG
|
B:CYS118
|
2.4
|
12.5
|
1.0
|
SG
|
B:CYS121
|
2.4
|
13.5
|
1.0
|
SG
|
B:CYS129
|
2.4
|
11.5
|
1.0
|
CB
|
B:CYS121
|
3.3
|
13.5
|
1.0
|
CB
|
B:CYS129
|
3.4
|
10.6
|
1.0
|
CB
|
B:CYS118
|
3.4
|
11.9
|
1.0
|
CB
|
B:CYS115
|
3.4
|
11.7
|
1.0
|
N
|
B:CYS115
|
3.5
|
12.5
|
1.0
|
CA
|
B:CYS129
|
3.7
|
10.8
|
1.0
|
CA
|
B:CYS115
|
3.9
|
12.8
|
1.0
|
N
|
B:CYS118
|
3.9
|
13.5
|
1.0
|
N
|
B:GLN130
|
3.9
|
12.0
|
1.0
|
N
|
B:GLN116
|
3.9
|
14.2
|
1.0
|
CA
|
B:CYS118
|
4.2
|
14.0
|
1.0
|
N
|
B:CYS121
|
4.2
|
13.2
|
1.0
|
C
|
B:CYS129
|
4.2
|
12.0
|
1.0
|
C
|
B:CYS115
|
4.3
|
14.3
|
1.0
|
CA
|
B:CYS121
|
4.4
|
13.0
|
1.0
|
N
|
B:ASN131
|
4.5
|
13.0
|
1.0
|
C
|
B:GLU114
|
4.6
|
13.2
|
1.0
|
N
|
B:THR117
|
4.6
|
17.4
|
1.0
|
ND2
|
B:ASN131
|
4.7
|
16.3
|
1.0
|
O
|
B:HOH943
|
4.7
|
14.8
|
1.0
|
C
|
B:CYS118
|
4.8
|
11.9
|
1.0
|
O
|
B:CYS118
|
4.9
|
12.6
|
1.0
|
CA
|
B:GLU114
|
4.9
|
12.7
|
1.0
|
CA
|
B:GLN116
|
4.9
|
16.2
|
1.0
|
CB
|
B:ASN131
|
5.0
|
15.2
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7vb3
Go back to
Zinc Binding Sites List in 7vb3
Zinc binding site 4 out
of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
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 Hydroxynitrile Lyase From Linum Usitatissimum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn503
b:12.0
occ:1.00
|
NE2
|
B:HIS85
|
2.0
|
10.6
|
1.0
|
O
|
B:HOH614
|
2.1
|
10.8
|
1.0
|
SG
|
B:CYS199
|
2.2
|
11.8
|
1.0
|
SG
|
B:CYS63
|
2.3
|
11.0
|
1.0
|
CE1
|
B:HIS85
|
3.0
|
10.6
|
1.0
|
CD2
|
B:HIS85
|
3.1
|
11.2
|
1.0
|
CB
|
B:CYS63
|
3.1
|
10.2
|
1.0
|
CB
|
B:CYS199
|
3.4
|
11.2
|
1.0
|
C5N
|
B:NAD501
|
3.5
|
8.9
|
1.0
|
C4N
|
B:NAD501
|
3.7
|
10.0
|
1.0
|
C6N
|
B:NAD501
|
4.0
|
9.4
|
1.0
|
OE2
|
B:GLU86
|
4.1
|
13.7
|
1.0
|
ND1
|
B:HIS85
|
4.1
|
11.2
|
1.0
|
CG
|
B:HIS85
|
4.2
|
10.3
|
1.0
|
CB
|
B:THR65
|
4.2
|
11.1
|
1.0
|
O
|
B:HOH838
|
4.3
|
15.8
|
1.0
|
OG1
|
B:THR65
|
4.3
|
11.0
|
1.0
|
O1
|
B:GOL504
|
4.5
|
20.6
|
1.0
|
C3N
|
B:NAD501
|
4.5
|
9.4
|
1.0
|
CA
|
B:CYS63
|
4.6
|
10.2
|
1.0
|
CA
|
B:CYS199
|
4.7
|
10.3
|
1.0
|
O
|
B:HOH720
|
4.8
|
11.6
|
1.0
|
N1N
|
B:NAD501
|
4.8
|
9.8
|
1.0
|
C3
|
B:GOL504
|
4.9
|
19.6
|
1.0
|
N
|
B:ALA200
|
4.9
|
9.7
|
1.0
|
C2N
|
B:NAD501
|
5.0
|
9.5
|
1.0
|
C
|
B:CYS199
|
5.0
|
9.6
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7vb3
Go back to
Zinc Binding Sites List in 7vb3
Zinc binding site 5 out
of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn502
b:17.0
occ:1.00
|
SG
|
C:CYS121
|
2.3
|
16.7
|
1.0
|
SG
|
C:CYS115
|
2.3
|
18.4
|
1.0
|
SG
|
C:CYS118
|
2.3
|
16.1
|
1.0
|
SG
|
C:CYS129
|
2.4
|
16.9
|
1.0
|
CB
|
C:CYS121
|
3.3
|
17.2
|
1.0
|
CB
|
C:CYS129
|
3.4
|
14.9
|
1.0
|
CB
|
C:CYS118
|
3.4
|
16.4
|
1.0
|
CB
|
C:CYS115
|
3.4
|
18.9
|
1.0
|
N
|
C:CYS115
|
3.5
|
19.2
|
1.0
|
CA
|
C:CYS129
|
3.7
|
15.8
|
1.0
|
CA
|
C:CYS115
|
3.9
|
19.2
|
1.0
|
N
|
C:CYS118
|
3.9
|
18.6
|
1.0
|
N
|
C:GLN116
|
3.9
|
18.6
|
1.0
|
N
|
C:GLN130
|
4.0
|
15.3
|
1.0
|
N
|
C:CYS121
|
4.2
|
15.2
|
1.0
|
CA
|
C:CYS118
|
4.2
|
16.9
|
1.0
|
C
|
C:CYS129
|
4.3
|
15.6
|
1.0
|
C
|
C:CYS115
|
4.3
|
20.2
|
1.0
|
CA
|
C:CYS121
|
4.3
|
16.8
|
1.0
|
N
|
C:ASN131
|
4.5
|
17.4
|
1.0
|
N
|
C:THR117
|
4.6
|
20.9
|
1.0
|
C
|
C:GLU114
|
4.6
|
20.5
|
1.0
|
ND2
|
C:ASN131
|
4.6
|
23.4
|
1.0
|
O
|
C:HOH859
|
4.7
|
21.4
|
1.0
|
C
|
C:CYS118
|
4.9
|
16.3
|
1.0
|
CA
|
C:GLN116
|
4.9
|
20.3
|
1.0
|
O
|
C:CYS118
|
4.9
|
16.1
|
1.0
|
CA
|
C:GLU114
|
4.9
|
18.0
|
1.0
|
CB
|
C:ASN131
|
4.9
|
20.7
|
1.0
|
N
|
C:CYS129
|
5.0
|
14.8
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7vb3
Go back to
Zinc Binding Sites List in 7vb3
Zinc binding site 6 out
of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn503
b:13.7
occ:0.86
|
NE2
|
C:HIS85
|
2.0
|
13.4
|
1.0
|
O
|
C:HOH602
|
2.1
|
15.6
|
1.0
|
SG
|
C:CYS199
|
2.2
|
14.2
|
1.0
|
SG
|
C:CYS63
|
2.3
|
15.5
|
1.0
|
CE1
|
C:HIS85
|
2.9
|
15.6
|
1.0
|
CD2
|
C:HIS85
|
3.0
|
14.2
|
1.0
|
CB
|
C:CYS63
|
3.2
|
15.3
|
1.0
|
CB
|
C:CYS199
|
3.3
|
14.8
|
1.0
|
C5N
|
C:NAD501
|
3.4
|
15.6
|
1.0
|
C4N
|
C:NAD501
|
3.7
|
14.8
|
1.0
|
C6N
|
C:NAD501
|
4.0
|
14.3
|
1.0
|
ND1
|
C:HIS85
|
4.1
|
16.5
|
1.0
|
CG
|
C:HIS85
|
4.1
|
13.9
|
1.0
|
OE2
|
C:GLU86
|
4.2
|
19.1
|
1.0
|
CB
|
C:THR65
|
4.2
|
15.4
|
1.0
|
O
|
C:HOH757
|
4.3
|
20.9
|
1.0
|
OG1
|
C:THR65
|
4.4
|
15.3
|
1.0
|
O3
|
C:GOL504
|
4.4
|
26.6
|
1.0
|
C3N
|
C:NAD501
|
4.6
|
13.9
|
1.0
|
CA
|
C:CYS63
|
4.6
|
13.6
|
1.0
|
CA
|
C:CYS199
|
4.7
|
12.9
|
1.0
|
O
|
C:HOH694
|
4.8
|
17.7
|
1.0
|
N1N
|
C:NAD501
|
4.8
|
14.6
|
1.0
|
N
|
C:ALA200
|
4.9
|
12.7
|
1.0
|
C2N
|
C:NAD501
|
5.0
|
14.1
|
1.0
|
C1
|
C:GOL504
|
5.0
|
25.1
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7vb3
Go back to
Zinc Binding Sites List in 7vb3
Zinc binding site 7 out
of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn502
b:14.7
occ:0.86
|
SG
|
D:CYS121
|
2.3
|
17.6
|
1.0
|
SG
|
D:CYS115
|
2.3
|
15.8
|
1.0
|
SG
|
D:CYS118
|
2.4
|
17.0
|
1.0
|
SG
|
D:CYS129
|
2.4
|
16.1
|
1.0
|
CB
|
D:CYS121
|
3.3
|
19.2
|
1.0
|
CB
|
D:CYS115
|
3.4
|
17.9
|
1.0
|
CB
|
D:CYS129
|
3.4
|
14.6
|
1.0
|
CB
|
D:CYS118
|
3.4
|
18.7
|
1.0
|
N
|
D:CYS115
|
3.5
|
16.5
|
1.0
|
CA
|
D:CYS129
|
3.7
|
16.2
|
1.0
|
CA
|
D:CYS115
|
3.9
|
16.6
|
1.0
|
N
|
D:GLN130
|
3.9
|
16.3
|
1.0
|
N
|
D:GLN116
|
3.9
|
16.6
|
1.0
|
N
|
D:CYS118
|
3.9
|
19.0
|
1.0
|
CA
|
D:CYS118
|
4.2
|
17.9
|
1.0
|
C
|
D:CYS129
|
4.2
|
17.8
|
1.0
|
N
|
D:CYS121
|
4.2
|
17.1
|
1.0
|
C
|
D:CYS115
|
4.3
|
18.1
|
1.0
|
CA
|
D:CYS121
|
4.3
|
17.2
|
1.0
|
N
|
D:ASN131
|
4.5
|
18.2
|
1.0
|
C
|
D:GLU114
|
4.5
|
16.4
|
1.0
|
N
|
D:THR117
|
4.6
|
18.1
|
1.0
|
ND2
|
D:ASN131
|
4.6
|
20.9
|
1.0
|
O
|
D:HOH861
|
4.8
|
21.3
|
1.0
|
C
|
D:CYS118
|
4.8
|
18.5
|
1.0
|
O
|
D:CYS118
|
4.8
|
18.4
|
1.0
|
CA
|
D:GLU114
|
4.9
|
15.7
|
1.0
|
CA
|
D:GLN116
|
4.9
|
16.8
|
1.0
|
CB
|
D:ASN131
|
4.9
|
19.9
|
1.0
|
N
|
D:CYS129
|
5.0
|
15.3
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7vb3
Go back to
Zinc Binding Sites List in 7vb3
Zinc binding site 8 out
of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn503
b:14.3
occ:0.86
|
NE2
|
D:HIS85
|
2.0
|
13.5
|
1.0
|
O
|
D:HOH612
|
2.1
|
17.5
|
1.0
|
SG
|
D:CYS199
|
2.2
|
15.9
|
1.0
|
SG
|
D:CYS63
|
2.3
|
15.0
|
1.0
|
CE1
|
D:HIS85
|
3.0
|
16.7
|
1.0
|
CD2
|
D:HIS85
|
3.0
|
16.8
|
1.0
|
CB
|
D:CYS63
|
3.2
|
15.9
|
1.0
|
CB
|
D:CYS199
|
3.4
|
15.8
|
1.0
|
C5N
|
D:NAD501
|
3.4
|
13.3
|
1.0
|
C4N
|
D:NAD501
|
3.7
|
13.6
|
1.0
|
C6N
|
D:NAD501
|
4.1
|
13.0
|
1.0
|
ND1
|
D:HIS85
|
4.1
|
15.6
|
1.0
|
CG
|
D:HIS85
|
4.1
|
14.7
|
1.0
|
OE2
|
D:GLU86
|
4.1
|
18.2
|
1.0
|
CB
|
D:THR65
|
4.3
|
16.6
|
1.0
|
OG1
|
D:THR65
|
4.3
|
16.7
|
1.0
|
O
|
D:HOH762
|
4.3
|
20.6
|
1.0
|
O3
|
D:GOL504
|
4.5
|
27.3
|
1.0
|
C3N
|
D:NAD501
|
4.6
|
12.7
|
1.0
|
CA
|
D:CYS63
|
4.6
|
14.9
|
1.0
|
O
|
D:HOH648
|
4.7
|
16.2
|
1.0
|
CA
|
D:CYS199
|
4.7
|
14.1
|
1.0
|
N1N
|
D:NAD501
|
4.8
|
13.9
|
1.0
|
N
|
D:ALA200
|
4.9
|
14.4
|
1.0
|
C1
|
D:GOL504
|
4.9
|
28.6
|
1.0
|
C2N
|
D:NAD501
|
5.0
|
13.2
|
1.0
|
|
Reference:
D.Zheng,
M.Nakabayashi,
Y.Asano.
Structural Characterization of Linum Usitatissimum Hydroxynitrile Lyase: A New Cyanohydrin Decomposition Mechanism Involving A Cyano-Zinc Complex. J.Biol.Chem. V. 298 01650 2022.
ISSN: ESSN 1083-351X
PubMed: 35101448
DOI: 10.1016/J.JBC.2022.101650
Page generated: Wed Oct 30 12:37:17 2024
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