Zinc in PDB 5zmy: Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
Protein crystallography data
The structure of Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids, PDB code: 5zmy
was solved by
S.Dong,
X.Liu,
X.Wang,
Y.Feng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.11 /
1.87
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.159,
158.348,
134.090,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.8 /
19.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
(pdb code 5zmy). 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids, PDB code: 5zmy:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5zmy
Go back to
Zinc Binding Sites List in 5zmy
Zinc binding site 1 out
of 8 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn400
b:15.7
occ:0.45
|
O2
|
A:TAR401
|
2.1
|
18.4
|
1.0
|
|
NE2
|
A:HIS69
|
2.1
|
22.6
|
1.0
|
|
NE2
|
A:HIS67
|
2.1
|
17.9
|
1.0
|
|
OE2
|
A:GLU34
|
2.1
|
20.4
|
1.0
|
|
O1
|
A:TAR401
|
2.2
|
18.3
|
1.0
|
|
O3
|
A:TAR401
|
2.2
|
20.4
|
1.0
|
|
HO2
|
A:TAR401
|
2.4
|
22.1
|
1.0
|
|
C2
|
A:TAR401
|
2.7
|
20.3
|
1.0
|
|
C1
|
A:TAR401
|
2.8
|
19.9
|
1.0
|
|
CD
|
A:GLU34
|
2.8
|
18.6
|
1.0
|
|
HO3
|
A:TAR401
|
2.8
|
24.5
|
1.0
|
|
OE1
|
A:GLU34
|
2.9
|
19.9
|
1.0
|
|
CE1
|
A:HIS69
|
3.0
|
23.4
|
1.0
|
|
C3
|
A:TAR401
|
3.0
|
21.5
|
1.0
|
|
CE1
|
A:HIS67
|
3.1
|
17.3
|
1.0
|
|
HE1
|
A:HIS69
|
3.1
|
28.2
|
1.0
|
|
CD2
|
A:HIS67
|
3.1
|
15.4
|
1.0
|
|
CD2
|
A:HIS69
|
3.2
|
20.8
|
1.0
|
|
HE1
|
A:HIS67
|
3.2
|
20.8
|
1.0
|
|
HD2
|
A:HIS67
|
3.3
|
18.6
|
1.0
|
|
HD2
|
A:HIS69
|
3.4
|
25.0
|
1.0
|
|
H2
|
A:TAR401
|
3.6
|
24.4
|
1.0
|
|
HH12
|
A:ARG31
|
3.6
|
18.1
|
1.0
|
|
H3
|
A:TAR401
|
3.8
|
25.9
|
1.0
|
|
HB
|
A:THR102
|
3.8
|
28.1
|
1.0
|
|
HG1
|
A:THR102
|
3.8
|
28.8
|
1.0
|
|
C4
|
A:TAR401
|
3.9
|
23.4
|
1.0
|
|
O4
|
A:TAR401
|
4.0
|
23.8
|
1.0
|
|
O
|
A:HOH536
|
4.0
|
23.7
|
1.0
|
|
O11
|
A:TAR401
|
4.0
|
19.9
|
1.0
|
|
HH22
|
A:ARG31
|
4.1
|
18.5
|
1.0
|
|
ND1
|
A:HIS69
|
4.2
|
23.3
|
1.0
|
|
ND1
|
A:HIS67
|
4.2
|
15.8
|
1.0
|
|
NH1
|
A:ARG31
|
4.2
|
15.0
|
1.0
|
|
OG1
|
A:THR102
|
4.2
|
24.0
|
1.0
|
|
CG
|
A:HIS67
|
4.3
|
14.3
|
1.0
|
|
CG
|
A:HIS69
|
4.3
|
20.3
|
1.0
|
|
HA
|
A:GLU34
|
4.3
|
18.5
|
1.0
|
|
CG
|
A:GLU34
|
4.3
|
16.9
|
1.0
|
|
HZ2
|
A:LYS247
|
4.4
|
26.1
|
1.0
|
|
CB
|
A:THR102
|
4.5
|
23.3
|
1.0
|
|
HG2
|
A:GLU34
|
4.5
|
20.4
|
1.0
|
|
NH2
|
A:ARG31
|
4.6
|
15.3
|
1.0
|
|
O
|
A:HOH671
|
4.6
|
16.0
|
1.0
|
|
HH11
|
A:ARG31
|
4.6
|
18.1
|
1.0
|
|
CZ
|
A:ARG31
|
4.7
|
14.7
|
1.0
|
|
HG3
|
A:GLU34
|
4.8
|
20.4
|
1.0
|
|
HA
|
A:THR102
|
4.9
|
26.4
|
1.0
|
|
HD1
|
A:HIS69
|
4.9
|
28.0
|
1.0
|
|
HG3
|
A:PRO133
|
4.9
|
18.3
|
1.0
|
|
HD1
|
A:HIS67
|
5.0
|
19.1
|
1.0
|
|
HB3
|
A:GLU34
|
5.0
|
20.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5zmy
Go back to
Zinc Binding Sites List in 5zmy
Zinc binding site 2 out
of 8 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn400
b:15.0
occ:0.41
|
NE2
|
B:HIS67
|
2.1
|
19.4
|
1.0
|
|
OE2
|
B:GLU34
|
2.1
|
18.8
|
1.0
|
|
NE2
|
B:HIS69
|
2.1
|
21.7
|
1.0
|
|
O2
|
B:TAR401
|
2.1
|
18.3
|
1.0
|
|
O11
|
B:TAR401
|
2.2
|
20.6
|
1.0
|
|
O3
|
B:TAR401
|
2.2
|
20.4
|
1.0
|
|
HO2
|
B:TAR401
|
2.5
|
22.1
|
1.0
|
|
C2
|
B:TAR401
|
2.8
|
21.0
|
1.0
|
|
C1
|
B:TAR401
|
2.9
|
22.3
|
1.0
|
|
CD
|
B:GLU34
|
2.9
|
17.0
|
1.0
|
|
HO3
|
B:TAR401
|
2.9
|
24.6
|
1.0
|
|
CE1
|
B:HIS69
|
2.9
|
22.8
|
1.0
|
|
C3
|
B:TAR401
|
3.0
|
22.3
|
1.0
|
|
CD2
|
B:HIS67
|
3.0
|
17.1
|
1.0
|
|
HE1
|
B:HIS69
|
3.0
|
27.4
|
1.0
|
|
OE1
|
B:GLU34
|
3.0
|
17.3
|
1.0
|
|
CE1
|
B:HIS67
|
3.1
|
18.8
|
1.0
|
|
HD2
|
B:HIS67
|
3.2
|
20.6
|
1.0
|
|
CD2
|
B:HIS69
|
3.2
|
20.9
|
1.0
|
|
HE1
|
B:HIS67
|
3.3
|
22.6
|
1.0
|
|
HD2
|
B:HIS69
|
3.4
|
25.2
|
1.0
|
|
HH12
|
B:ARG31
|
3.6
|
20.4
|
1.0
|
|
H2
|
B:TAR401
|
3.7
|
25.2
|
1.0
|
|
H3
|
B:TAR401
|
3.8
|
26.9
|
1.0
|
|
HG1
|
B:THR102
|
3.8
|
28.6
|
1.0
|
|
HB
|
B:THR102
|
3.8
|
26.9
|
1.0
|
|
C4
|
B:TAR401
|
3.9
|
23.9
|
1.0
|
|
O41
|
B:TAR401
|
4.1
|
24.2
|
1.0
|
|
HH22
|
B:ARG31
|
4.1
|
20.9
|
1.0
|
|
O
|
B:HOH570
|
4.1
|
24.5
|
1.0
|
|
ND1
|
B:HIS69
|
4.1
|
23.2
|
1.0
|
|
O1
|
B:TAR401
|
4.1
|
23.8
|
1.0
|
|
CG
|
B:HIS67
|
4.2
|
15.9
|
1.0
|
|
NH1
|
B:ARG31
|
4.2
|
16.9
|
1.0
|
|
ND1
|
B:HIS67
|
4.2
|
18.3
|
1.0
|
|
HA
|
B:GLU34
|
4.2
|
17.7
|
1.0
|
|
OG1
|
B:THR102
|
4.3
|
23.8
|
1.0
|
|
CG
|
B:HIS69
|
4.3
|
21.2
|
1.0
|
|
CG
|
B:GLU34
|
4.3
|
15.2
|
1.0
|
|
HG2
|
B:GLU34
|
4.5
|
18.3
|
1.0
|
|
CB
|
B:THR102
|
4.5
|
22.3
|
1.0
|
|
HZ2
|
B:LYS247
|
4.6
|
27.9
|
1.0
|
|
NH2
|
B:ARG31
|
4.6
|
17.4
|
1.0
|
|
O
|
B:HOH677
|
4.6
|
13.3
|
1.0
|
|
HH11
|
B:ARG31
|
4.7
|
20.4
|
1.0
|
|
CZ
|
B:ARG31
|
4.8
|
16.4
|
1.0
|
|
HG3
|
B:PRO133
|
4.8
|
18.2
|
1.0
|
|
HD1
|
B:HIS69
|
4.9
|
27.9
|
1.0
|
|
HG3
|
B:GLU34
|
4.9
|
18.3
|
1.0
|
|
HA
|
B:THR102
|
4.9
|
25.9
|
1.0
|
|
HB3
|
B:GLU34
|
5.0
|
19.4
|
1.0
|
|
O4
|
B:TAR401
|
5.0
|
24.0
|
1.0
|
|
HD1
|
B:HIS67
|
5.0
|
22.0
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5zmy
Go back to
Zinc Binding Sites List in 5zmy
Zinc binding site 3 out
of 8 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn400
b:14.0
occ:0.41
|
NE2
|
C:HIS67
|
2.0
|
22.4
|
1.0
|
|
O2
|
C:TAR401
|
2.0
|
20.4
|
1.0
|
|
NE2
|
C:HIS69
|
2.1
|
24.6
|
1.0
|
|
OE2
|
C:GLU34
|
2.2
|
21.7
|
1.0
|
|
O11
|
C:TAR401
|
2.2
|
20.6
|
1.0
|
|
HO2
|
C:TAR401
|
2.3
|
24.5
|
1.0
|
|
O3
|
C:TAR401
|
2.4
|
26.6
|
1.0
|
|
C2
|
C:TAR401
|
2.7
|
23.5
|
1.0
|
|
C1
|
C:TAR401
|
2.7
|
23.6
|
1.0
|
|
CD
|
C:GLU34
|
2.9
|
19.7
|
1.0
|
|
CE1
|
C:HIS69
|
3.0
|
24.7
|
1.0
|
|
OE1
|
C:GLU34
|
3.0
|
21.2
|
1.0
|
|
CD2
|
C:HIS67
|
3.0
|
19.5
|
1.0
|
|
HO3
|
C:TAR401
|
3.1
|
32.0
|
1.0
|
|
HE1
|
C:HIS69
|
3.1
|
29.7
|
1.0
|
|
C3
|
C:TAR401
|
3.1
|
26.9
|
1.0
|
|
CE1
|
C:HIS67
|
3.1
|
20.5
|
1.0
|
|
HD2
|
C:HIS67
|
3.1
|
23.5
|
1.0
|
|
CD2
|
C:HIS69
|
3.1
|
22.6
|
1.0
|
|
HE1
|
C:HIS67
|
3.3
|
24.7
|
1.0
|
|
HD2
|
C:HIS69
|
3.4
|
27.2
|
1.0
|
|
HH12
|
C:ARG31
|
3.6
|
23.0
|
1.0
|
|
H2
|
C:TAR401
|
3.6
|
28.3
|
1.0
|
|
HB
|
C:THR102
|
3.7
|
26.5
|
1.0
|
|
HG1
|
C:THR102
|
3.7
|
27.3
|
1.0
|
|
H3
|
C:TAR401
|
3.8
|
32.3
|
1.0
|
|
C4
|
C:TAR401
|
4.0
|
29.6
|
1.0
|
|
O1
|
C:TAR401
|
4.0
|
24.6
|
1.0
|
|
O
|
C:HOH615
|
4.0
|
28.6
|
1.0
|
|
HH22
|
C:ARG31
|
4.1
|
19.8
|
1.0
|
|
ND1
|
C:HIS69
|
4.1
|
24.7
|
1.0
|
|
HA
|
C:GLU34
|
4.1
|
19.1
|
1.0
|
|
NH1
|
C:ARG31
|
4.1
|
19.1
|
1.0
|
|
CG
|
C:HIS67
|
4.1
|
18.0
|
1.0
|
|
O41
|
C:TAR401
|
4.2
|
29.9
|
1.0
|
|
ND1
|
C:HIS67
|
4.2
|
19.6
|
1.0
|
|
OG1
|
C:THR102
|
4.2
|
22.7
|
1.0
|
|
CG
|
C:HIS69
|
4.2
|
21.9
|
1.0
|
|
CG
|
C:GLU34
|
4.3
|
17.1
|
1.0
|
|
CB
|
C:THR102
|
4.4
|
22.0
|
1.0
|
|
O
|
C:HOH667
|
4.4
|
15.0
|
1.0
|
|
HZ2
|
C:LYS247
|
4.5
|
31.3
|
1.0
|
|
HG2
|
C:GLU34
|
4.5
|
20.6
|
1.0
|
|
HH11
|
C:ARG31
|
4.6
|
23.0
|
1.0
|
|
NH2
|
C:ARG31
|
4.6
|
16.4
|
1.0
|
|
CZ
|
C:ARG31
|
4.7
|
16.7
|
1.0
|
|
HA
|
C:THR102
|
4.9
|
25.0
|
1.0
|
|
HD1
|
C:HIS69
|
4.9
|
29.8
|
1.0
|
|
O4
|
C:TAR401
|
4.9
|
30.7
|
1.0
|
|
HG3
|
C:PRO133
|
4.9
|
21.0
|
1.0
|
|
HG3
|
C:GLU34
|
4.9
|
20.6
|
1.0
|
|
HD1
|
C:HIS67
|
5.0
|
23.6
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5zmy
Go back to
Zinc Binding Sites List in 5zmy
Zinc binding site 4 out
of 8 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn400
b:17.9
occ:0.41
|
O2
|
D:TAR401
|
2.0
|
24.4
|
1.0
|
|
NE2
|
D:HIS69
|
2.0
|
27.2
|
1.0
|
|
OE2
|
D:GLU34
|
2.1
|
23.2
|
1.0
|
|
NE2
|
D:HIS67
|
2.1
|
20.3
|
1.0
|
|
O3
|
D:TAR401
|
2.2
|
29.1
|
1.0
|
|
O1
|
D:TAR401
|
2.3
|
32.0
|
1.0
|
|
HO2
|
D:TAR401
|
2.5
|
29.4
|
1.0
|
|
C2
|
D:TAR401
|
2.7
|
29.0
|
1.0
|
|
C1
|
D:TAR401
|
2.8
|
31.5
|
1.0
|
|
CD
|
D:GLU34
|
2.8
|
20.8
|
1.0
|
|
HO3
|
D:TAR401
|
2.8
|
35.0
|
1.0
|
|
OE1
|
D:GLU34
|
2.8
|
21.4
|
1.0
|
|
CE1
|
D:HIS69
|
3.0
|
27.8
|
1.0
|
|
C3
|
D:TAR401
|
3.0
|
30.8
|
1.0
|
|
HE1
|
D:HIS69
|
3.1
|
33.5
|
1.0
|
|
CD2
|
D:HIS69
|
3.1
|
25.5
|
1.0
|
|
CD2
|
D:HIS67
|
3.1
|
17.0
|
1.0
|
|
CE1
|
D:HIS67
|
3.1
|
19.1
|
1.0
|
|
HD2
|
D:HIS67
|
3.3
|
20.5
|
1.0
|
|
HE1
|
D:HIS67
|
3.3
|
23.1
|
1.0
|
|
HD2
|
D:HIS69
|
3.3
|
30.7
|
1.0
|
|
HB
|
D:THR102
|
3.5
|
29.8
|
1.0
|
|
H2
|
D:TAR401
|
3.6
|
34.9
|
1.0
|
|
H3
|
D:TAR401
|
3.7
|
37.1
|
1.0
|
|
HG1
|
D:THR102
|
3.9
|
32.0
|
1.0
|
|
HH12
|
D:ARG31
|
3.9
|
19.1
|
1.0
|
|
C4
|
D:TAR401
|
3.9
|
34.1
|
1.0
|
|
O11
|
D:TAR401
|
4.0
|
32.6
|
1.0
|
|
ND1
|
D:HIS69
|
4.1
|
27.4
|
1.0
|
|
O4
|
D:TAR401
|
4.1
|
35.5
|
1.0
|
|
O
|
D:HOH632
|
4.2
|
33.2
|
1.0
|
|
OG1
|
D:THR102
|
4.2
|
26.6
|
1.0
|
|
HA
|
D:GLU34
|
4.2
|
18.9
|
1.0
|
|
CG
|
D:HIS69
|
4.2
|
23.8
|
1.0
|
|
HH22
|
D:ARG31
|
4.2
|
20.3
|
1.0
|
|
CB
|
D:THR102
|
4.2
|
24.8
|
1.0
|
|
ND1
|
D:HIS67
|
4.2
|
17.7
|
1.0
|
|
CG
|
D:HIS67
|
4.3
|
16.6
|
1.0
|
|
HZ2
|
D:LYS247
|
4.3
|
34.0
|
1.0
|
|
CG
|
D:GLU34
|
4.3
|
17.8
|
1.0
|
|
NH1
|
D:ARG31
|
4.4
|
15.9
|
1.0
|
|
HG2
|
D:GLU34
|
4.5
|
21.5
|
1.0
|
|
O
|
D:HOH692
|
4.6
|
18.1
|
1.0
|
|
NH2
|
D:ARG31
|
4.7
|
16.8
|
1.0
|
|
HA
|
D:THR102
|
4.8
|
28.0
|
1.0
|
|
HH11
|
D:ARG31
|
4.8
|
19.1
|
1.0
|
|
CZ
|
D:ARG31
|
4.8
|
15.5
|
1.0
|
|
HG3
|
D:GLU34
|
4.9
|
21.5
|
1.0
|
|
HD1
|
D:HIS69
|
4.9
|
33.0
|
1.0
|
|
HB3
|
D:GLU34
|
4.9
|
20.1
|
1.0
|
|
O41
|
D:TAR401
|
4.9
|
35.9
|
1.0
|
|
HG3
|
D:PRO133
|
5.0
|
21.2
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5zmy
Go back to
Zinc Binding Sites List in 5zmy
Zinc binding site 5 out
of 8 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn400
b:21.3
occ:0.21
|
O1
|
E:TAR401
|
2.0
|
29.0
|
1.0
|
|
O2
|
E:TAR401
|
2.0
|
28.9
|
1.0
|
|
OE2
|
E:GLU34
|
2.1
|
49.9
|
1.0
|
|
NE2
|
E:HIS67
|
2.1
|
43.1
|
1.0
|
|
NE2
|
E:HIS69
|
2.1
|
46.5
|
1.0
|
|
O3
|
E:TAR401
|
2.4
|
29.1
|
1.0
|
|
C1
|
E:TAR401
|
2.6
|
29.2
|
1.0
|
|
C2
|
E:TAR401
|
2.6
|
29.4
|
1.0
|
|
HO2
|
E:TAR401
|
2.7
|
34.8
|
1.0
|
|
CD
|
E:GLU34
|
2.9
|
48.9
|
1.0
|
|
C3
|
E:TAR401
|
3.0
|
31.3
|
1.0
|
|
OE1
|
E:GLU34
|
3.0
|
53.2
|
1.0
|
|
CE1
|
E:HIS69
|
3.0
|
46.6
|
1.0
|
|
CE1
|
E:HIS67
|
3.0
|
41.2
|
1.0
|
|
CD2
|
E:HIS67
|
3.1
|
39.6
|
1.0
|
|
HO3
|
E:TAR401
|
3.1
|
35.0
|
1.0
|
|
HE1
|
E:HIS69
|
3.2
|
56.0
|
1.0
|
|
CD2
|
E:HIS69
|
3.2
|
45.2
|
1.0
|
|
HE1
|
E:HIS67
|
3.2
|
49.5
|
1.0
|
|
HD2
|
E:HIS67
|
3.3
|
47.6
|
1.0
|
|
HD2
|
E:HIS69
|
3.4
|
54.4
|
1.0
|
|
HG1
|
E:THR102
|
3.5
|
44.2
|
1.0
|
|
H2
|
E:TAR401
|
3.5
|
35.4
|
1.0
|
|
HB
|
E:THR102
|
3.6
|
44.9
|
1.0
|
|
H3
|
E:TAR401
|
3.7
|
37.6
|
1.0
|
|
HH12
|
E:ARG31
|
3.8
|
32.5
|
1.0
|
|
O11
|
E:TAR401
|
3.9
|
29.6
|
1.0
|
|
C4
|
E:TAR401
|
3.9
|
36.1
|
1.0
|
|
OG1
|
E:THR102
|
4.0
|
36.8
|
1.0
|
|
O
|
E:HOH580
|
4.0
|
38.4
|
1.0
|
|
ND1
|
E:HIS67
|
4.2
|
39.4
|
1.0
|
|
ND1
|
E:HIS69
|
4.2
|
47.0
|
1.0
|
|
CG
|
E:HIS67
|
4.2
|
36.5
|
1.0
|
|
CG
|
E:HIS69
|
4.3
|
46.0
|
1.0
|
|
CB
|
E:THR102
|
4.3
|
37.3
|
1.0
|
|
NH1
|
E:ARG31
|
4.3
|
27.5
|
1.0
|
|
HA
|
E:GLU34
|
4.3
|
45.2
|
1.0
|
|
CG
|
E:GLU34
|
4.3
|
44.5
|
1.0
|
|
O41
|
E:TAR401
|
4.4
|
38.3
|
1.0
|
|
HH22
|
E:ARG31
|
4.4
|
36.4
|
1.0
|
|
HG2
|
E:GLU34
|
4.5
|
53.4
|
1.0
|
|
O4
|
E:TAR401
|
4.6
|
38.6
|
1.0
|
|
HH11
|
E:ARG31
|
4.6
|
32.5
|
1.0
|
|
HZ2
|
E:LYS247
|
4.7
|
41.4
|
1.0
|
|
O
|
E:HOH589
|
4.7
|
24.3
|
1.0
|
|
HA
|
E:THR102
|
4.8
|
44.8
|
1.0
|
|
NH2
|
E:ARG31
|
4.9
|
30.2
|
1.0
|
|
HG3
|
E:GLU34
|
4.9
|
53.4
|
1.0
|
|
CZ
|
E:ARG31
|
4.9
|
29.1
|
1.0
|
|
HD1
|
E:HIS67
|
4.9
|
47.3
|
1.0
|
|
HG3
|
E:PRO133
|
4.9
|
34.2
|
1.0
|
|
HD1
|
E:HIS69
|
5.0
|
56.4
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5zmy
Go back to
Zinc Binding Sites List in 5zmy
Zinc binding site 6 out
of 8 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn400
b:17.0
occ:0.40
|
O2
|
F:TAR401
|
1.8
|
22.1
|
1.0
|
|
NE2
|
F:HIS69
|
2.0
|
31.5
|
1.0
|
|
O11
|
F:TAR401
|
2.1
|
23.5
|
1.0
|
|
OE2
|
F:GLU34
|
2.1
|
27.0
|
1.0
|
|
NE2
|
F:HIS67
|
2.1
|
27.1
|
1.0
|
|
O3
|
F:TAR401
|
2.2
|
26.4
|
1.0
|
|
HO2
|
F:TAR401
|
2.4
|
26.6
|
1.0
|
|
C2
|
F:TAR401
|
2.5
|
25.1
|
1.0
|
|
C1
|
F:TAR401
|
2.6
|
24.6
|
1.0
|
|
CD
|
F:GLU34
|
2.9
|
24.6
|
1.0
|
|
C3
|
F:TAR401
|
2.9
|
27.4
|
1.0
|
|
HO3
|
F:TAR401
|
2.9
|
31.8
|
1.0
|
|
CE1
|
F:HIS69
|
2.9
|
31.9
|
1.0
|
|
OE1
|
F:GLU34
|
3.0
|
26.6
|
1.0
|
|
HE1
|
F:HIS69
|
3.0
|
38.4
|
1.0
|
|
CD2
|
F:HIS67
|
3.1
|
23.4
|
1.0
|
|
CE1
|
F:HIS67
|
3.1
|
26.4
|
1.0
|
|
CD2
|
F:HIS69
|
3.1
|
29.4
|
1.0
|
|
HD2
|
F:HIS67
|
3.2
|
28.2
|
1.0
|
|
HE1
|
F:HIS67
|
3.3
|
31.8
|
1.0
|
|
HD2
|
F:HIS69
|
3.4
|
35.3
|
1.0
|
|
H2
|
F:TAR401
|
3.4
|
30.2
|
1.0
|
|
HB
|
F:THR102
|
3.6
|
31.2
|
1.0
|
|
H3
|
F:TAR401
|
3.6
|
33.0
|
1.0
|
|
HH12
|
F:ARG31
|
3.7
|
23.0
|
1.0
|
|
C4
|
F:TAR401
|
3.9
|
30.9
|
1.0
|
|
O1
|
F:TAR401
|
3.9
|
25.5
|
1.0
|
|
HG1
|
F:THR102
|
4.0
|
30.8
|
1.0
|
|
ND1
|
F:HIS69
|
4.1
|
31.9
|
1.0
|
|
HH22
|
F:ARG31
|
4.1
|
24.8
|
1.0
|
|
O41
|
F:TAR401
|
4.1
|
32.2
|
1.0
|
|
NH1
|
F:ARG31
|
4.2
|
19.1
|
1.0
|
|
ND1
|
F:HIS67
|
4.2
|
24.1
|
1.0
|
|
O
|
F:HOH640
|
4.2
|
32.4
|
1.0
|
|
CG
|
F:HIS69
|
4.2
|
28.3
|
1.0
|
|
HA
|
F:GLU34
|
4.2
|
25.0
|
1.0
|
|
CG
|
F:HIS67
|
4.2
|
21.9
|
1.0
|
|
OG1
|
F:THR102
|
4.3
|
25.6
|
1.0
|
|
CG
|
F:GLU34
|
4.3
|
21.8
|
1.0
|
|
CB
|
F:THR102
|
4.3
|
25.9
|
1.0
|
|
HZ2
|
F:LYS247
|
4.5
|
30.5
|
1.0
|
|
HG2
|
F:GLU34
|
4.5
|
26.3
|
1.0
|
|
NH2
|
F:ARG31
|
4.6
|
20.6
|
1.0
|
|
HH11
|
F:ARG31
|
4.6
|
23.0
|
1.0
|
|
O
|
F:HOH613
|
4.6
|
15.8
|
1.0
|
|
CZ
|
F:ARG31
|
4.7
|
19.9
|
1.0
|
|
HD1
|
F:HIS69
|
4.8
|
38.4
|
1.0
|
|
HG3
|
F:GLU34
|
4.9
|
26.3
|
1.0
|
|
O4
|
F:TAR401
|
4.9
|
31.6
|
1.0
|
|
HA
|
F:THR102
|
5.0
|
30.9
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5zmy
Go back to
Zinc Binding Sites List in 5zmy
Zinc binding site 7 out
of 8 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn400
b:13.5
occ:0.40
|
NE2
|
G:HIS67
|
2.0
|
19.9
|
1.0
|
|
O2
|
G:TAR401
|
2.1
|
20.5
|
1.0
|
|
OE2
|
G:GLU34
|
2.1
|
21.4
|
1.0
|
|
NE2
|
G:HIS69
|
2.1
|
23.7
|
1.0
|
|
O11
|
G:TAR401
|
2.2
|
25.9
|
1.0
|
|
O3
|
G:TAR401
|
2.2
|
26.7
|
1.0
|
|
HO2
|
G:TAR401
|
2.4
|
24.7
|
1.0
|
|
C2
|
G:TAR401
|
2.7
|
24.4
|
1.0
|
|
CD
|
G:GLU34
|
2.8
|
19.2
|
1.0
|
|
C1
|
G:TAR401
|
2.8
|
26.0
|
1.0
|
|
OE1
|
G:GLU34
|
2.8
|
19.4
|
1.0
|
|
HO3
|
G:TAR401
|
2.9
|
32.2
|
1.0
|
|
CE1
|
G:HIS69
|
3.0
|
24.0
|
1.0
|
|
C3
|
G:TAR401
|
3.0
|
27.0
|
1.0
|
|
CE1
|
G:HIS67
|
3.0
|
18.8
|
1.0
|
|
CD2
|
G:HIS67
|
3.1
|
17.8
|
1.0
|
|
HE1
|
G:HIS69
|
3.1
|
28.9
|
1.0
|
|
HE1
|
G:HIS67
|
3.2
|
22.6
|
1.0
|
|
CD2
|
G:HIS69
|
3.2
|
22.8
|
1.0
|
|
HD2
|
G:HIS67
|
3.3
|
21.5
|
1.0
|
|
HD2
|
G:HIS69
|
3.4
|
27.4
|
1.0
|
|
H2
|
G:TAR401
|
3.6
|
29.4
|
1.0
|
|
HB
|
G:THR102
|
3.6
|
28.1
|
1.0
|
|
H3
|
G:TAR401
|
3.7
|
32.5
|
1.0
|
|
HH12
|
G:ARG31
|
3.7
|
22.9
|
1.0
|
|
C4
|
G:TAR401
|
3.9
|
29.2
|
1.0
|
|
HG1
|
G:THR102
|
3.9
|
29.8
|
1.0
|
|
O1
|
G:TAR401
|
4.0
|
26.6
|
1.0
|
|
O
|
G:HOH655
|
4.1
|
27.9
|
1.0
|
|
O41
|
G:TAR401
|
4.1
|
29.7
|
1.0
|
|
HH22
|
G:ARG31
|
4.1
|
21.6
|
1.0
|
|
ND1
|
G:HIS69
|
4.1
|
24.0
|
1.0
|
|
ND1
|
G:HIS67
|
4.1
|
17.9
|
1.0
|
|
HA
|
G:GLU34
|
4.2
|
20.3
|
1.0
|
|
CG
|
G:HIS67
|
4.2
|
17.2
|
1.0
|
|
NH1
|
G:ARG31
|
4.2
|
19.0
|
1.0
|
|
CG
|
G:GLU34
|
4.2
|
17.5
|
1.0
|
|
OG1
|
G:THR102
|
4.3
|
24.8
|
1.0
|
|
CG
|
G:HIS69
|
4.3
|
22.6
|
1.0
|
|
CB
|
G:THR102
|
4.4
|
23.4
|
1.0
|
|
HG2
|
G:GLU34
|
4.5
|
21.1
|
1.0
|
|
HZ2
|
G:LYS247
|
4.5
|
27.3
|
1.0
|
|
NH2
|
G:ARG31
|
4.6
|
17.9
|
1.0
|
|
O
|
G:HOH613
|
4.6
|
18.7
|
1.0
|
|
HH11
|
G:ARG31
|
4.6
|
22.9
|
1.0
|
|
CZ
|
G:ARG31
|
4.7
|
18.4
|
1.0
|
|
O4
|
G:TAR401
|
4.8
|
30.1
|
1.0
|
|
HG3
|
G:GLU34
|
4.8
|
21.1
|
1.0
|
|
HA
|
G:THR102
|
4.8
|
26.1
|
1.0
|
|
HD1
|
G:HIS69
|
4.9
|
28.9
|
1.0
|
|
HG3
|
G:PRO133
|
4.9
|
21.7
|
1.0
|
|
HD1
|
G:HIS67
|
4.9
|
21.5
|
1.0
|
|
HB3
|
G:GLU34
|
4.9
|
21.7
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5zmy
Go back to
Zinc Binding Sites List in 5zmy
Zinc binding site 8 out
of 8 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids
 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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn400
b:14.0
occ:0.33
|
O2
|
H:TAR401
|
2.1
|
23.5
|
1.0
|
|
NE2
|
H:HIS69
|
2.1
|
27.5
|
1.0
|
|
NE2
|
H:HIS67
|
2.1
|
24.2
|
1.0
|
|
OE2
|
H:GLU34
|
2.1
|
23.9
|
1.0
|
|
O3
|
H:TAR401
|
2.2
|
30.6
|
1.0
|
|
O1
|
H:TAR401
|
2.3
|
29.5
|
1.0
|
|
HO2
|
H:TAR401
|
2.6
|
28.3
|
1.0
|
|
C2
|
H:TAR401
|
2.7
|
28.2
|
1.0
|
|
CD
|
H:GLU34
|
2.8
|
21.9
|
1.0
|
|
OE1
|
H:GLU34
|
2.8
|
21.9
|
1.0
|
|
C1
|
H:TAR401
|
2.8
|
29.4
|
1.0
|
|
HO3
|
H:TAR401
|
2.9
|
36.8
|
1.0
|
|
CE1
|
H:HIS69
|
2.9
|
28.1
|
1.0
|
|
C3
|
H:TAR401
|
3.0
|
30.9
|
1.0
|
|
HE1
|
H:HIS69
|
3.0
|
33.8
|
1.0
|
|
CD2
|
H:HIS67
|
3.0
|
22.4
|
1.0
|
|
HD2
|
H:HIS67
|
3.2
|
26.9
|
1.0
|
|
CE1
|
H:HIS67
|
3.2
|
23.9
|
1.0
|
|
CD2
|
H:HIS69
|
3.2
|
26.5
|
1.0
|
|
HE1
|
H:HIS67
|
3.4
|
28.8
|
1.0
|
|
HD2
|
H:HIS69
|
3.4
|
31.9
|
1.0
|
|
H2
|
H:TAR401
|
3.6
|
34.0
|
1.0
|
|
HB
|
H:THR102
|
3.6
|
32.1
|
1.0
|
|
HH12
|
H:ARG31
|
3.7
|
22.9
|
1.0
|
|
H3
|
H:TAR401
|
3.8
|
37.1
|
1.0
|
|
C4
|
H:TAR401
|
3.9
|
32.5
|
1.0
|
|
HG1
|
H:THR102
|
3.9
|
34.4
|
1.0
|
|
O4
|
H:TAR401
|
4.0
|
32.5
|
1.0
|
|
O11
|
H:TAR401
|
4.0
|
30.6
|
1.0
|
|
O
|
H:HOH627
|
4.1
|
33.6
|
1.0
|
|
ND1
|
H:HIS69
|
4.1
|
28.0
|
1.0
|
|
HH22
|
H:ARG31
|
4.2
|
22.0
|
1.0
|
|
NH1
|
H:ARG31
|
4.2
|
19.0
|
1.0
|
|
CG
|
H:HIS67
|
4.2
|
21.5
|
1.0
|
|
HA
|
H:GLU34
|
4.2
|
23.6
|
1.0
|
|
ND1
|
H:HIS67
|
4.3
|
23.0
|
1.0
|
|
CG
|
H:HIS69
|
4.3
|
26.0
|
1.0
|
|
CG
|
H:GLU34
|
4.3
|
19.9
|
1.0
|
|
OG1
|
H:THR102
|
4.3
|
28.6
|
1.0
|
|
HZ2
|
H:LYS247
|
4.4
|
32.7
|
1.0
|
|
CB
|
H:THR102
|
4.4
|
26.7
|
1.0
|
|
HG2
|
H:GLU34
|
4.5
|
24.0
|
1.0
|
|
O
|
H:HOH732
|
4.5
|
17.7
|
1.0
|
|
HH11
|
H:ARG31
|
4.6
|
22.9
|
1.0
|
|
NH2
|
H:ARG31
|
4.6
|
18.3
|
1.0
|
|
CZ
|
H:ARG31
|
4.7
|
17.7
|
1.0
|
|
HG3
|
H:GLU34
|
4.8
|
24.0
|
1.0
|
|
HB3
|
H:GLU34
|
4.8
|
24.2
|
1.0
|
|
HD1
|
H:HIS69
|
4.9
|
33.7
|
1.0
|
|
O41
|
H:TAR401
|
4.9
|
32.2
|
1.0
|
|
HA
|
H:THR102
|
5.0
|
31.5
|
1.0
|
|
CB
|
H:GLU34
|
5.0
|
20.1
|
1.0
|
|
Reference:
S.Dong,
X.Liu,
G.Z.Cui,
Q.Cui,
X.Wang,
Y.Feng.
Structural Insight Into the Catalytic Mechanism of A Cis-Epoxysuccinate Hydrolase Producing Enantiomerically Pure D(-)-Tartaric Acid. Chem. Commun. (Camb.) V. 54 8482 2018.
ISSN: ESSN 1364-548X
PubMed: 30003205
DOI: 10.1039/C8CC04398A
Page generated: Mon Oct 28 16:59:11 2024
|
