Zinc in PDB 6ok1: LTP2-CHSH2(DUF35) Aldolase
Protein crystallography data
The structure of LTP2-CHSH2(DUF35) Aldolase, PDB code: 6ok1
was solved by
M.S.Kimber,
E.Mallette,
R.Aggett,
S.Y.K.Seah,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.83 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.680,
110.560,
120.140,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.4 /
16.8
|
Other elements in 6ok1:
The structure of LTP2-CHSH2(DUF35) Aldolase also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the LTP2-CHSH2(DUF35) Aldolase
(pdb code 6ok1). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
LTP2-CHSH2(DUF35) Aldolase, PDB code: 6ok1:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 6ok1
Go back to
Zinc Binding Sites List in 6ok1
Zinc binding site 1 out
of 2 in the LTP2-CHSH2(DUF35) Aldolase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of LTP2-CHSH2(DUF35) Aldolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:27.8
occ:1.00
|
SG
|
B:CYS215
|
2.3
|
27.9
|
1.0
|
SG
|
B:CYS229
|
2.3
|
28.3
|
1.0
|
SG
|
B:CYS212
|
2.3
|
26.6
|
1.0
|
SG
|
B:CYS226
|
2.4
|
24.4
|
1.0
|
H
|
B:CYS215
|
3.0
|
34.0
|
1.0
|
HB2
|
B:CYS212
|
3.1
|
27.2
|
1.0
|
CB
|
B:CYS212
|
3.1
|
22.6
|
1.0
|
HB3
|
B:CYS226
|
3.1
|
29.5
|
1.0
|
HB3
|
B:CYS212
|
3.1
|
27.2
|
1.0
|
HB3
|
B:CYS215
|
3.1
|
36.6
|
1.0
|
CB
|
B:CYS226
|
3.2
|
24.5
|
1.0
|
HB3
|
B:CYS229
|
3.2
|
38.7
|
1.0
|
HB2
|
B:CYS226
|
3.2
|
29.5
|
1.0
|
CB
|
B:CYS215
|
3.3
|
30.5
|
1.0
|
H
|
B:CYS229
|
3.3
|
32.0
|
1.0
|
CB
|
B:CYS229
|
3.4
|
32.2
|
1.0
|
HB3
|
B:ALA214
|
3.7
|
34.4
|
1.0
|
HB2
|
B:HIS228
|
3.7
|
30.8
|
1.0
|
N
|
B:CYS215
|
3.7
|
28.4
|
1.0
|
HB3
|
B:SER231
|
3.8
|
34.1
|
1.0
|
N
|
B:CYS229
|
3.8
|
26.6
|
1.0
|
CA
|
B:CYS215
|
4.1
|
25.1
|
1.0
|
H
|
B:SER231
|
4.1
|
32.4
|
1.0
|
HB2
|
B:CYS215
|
4.1
|
36.6
|
1.0
|
CA
|
B:CYS229
|
4.1
|
31.4
|
1.0
|
HB2
|
B:CYS229
|
4.1
|
38.7
|
1.0
|
H
|
B:THR217
|
4.3
|
31.3
|
1.0
|
HB
|
B:THR217
|
4.3
|
34.1
|
1.0
|
H
|
B:HIS228
|
4.4
|
32.0
|
1.0
|
H
|
B:GLY230
|
4.5
|
31.5
|
1.0
|
H
|
B:ALA214
|
4.5
|
36.9
|
1.0
|
HB2
|
B:SER231
|
4.6
|
34.1
|
1.0
|
CA
|
B:CYS212
|
4.6
|
23.0
|
1.0
|
CB
|
B:ALA214
|
4.6
|
28.7
|
1.0
|
CA
|
B:CYS226
|
4.6
|
23.3
|
1.0
|
CB
|
B:SER231
|
4.6
|
28.4
|
1.0
|
H
|
B:LYS216
|
4.6
|
31.3
|
1.0
|
CB
|
B:HIS228
|
4.6
|
25.7
|
1.0
|
HG1
|
B:THR217
|
4.7
|
34.7
|
1.0
|
C
|
B:CYS215
|
4.7
|
32.4
|
1.0
|
C
|
B:CYS229
|
4.8
|
33.5
|
1.0
|
C
|
B:HIS228
|
4.8
|
35.1
|
1.0
|
C
|
B:ALA214
|
4.8
|
32.2
|
1.0
|
N
|
B:GLY230
|
4.8
|
26.2
|
1.0
|
HA
|
B:CYS212
|
4.9
|
27.6
|
1.0
|
O
|
B:HOH575
|
4.9
|
23.3
|
1.0
|
HA
|
B:CYS215
|
4.9
|
30.2
|
1.0
|
N
|
B:SER231
|
4.9
|
26.9
|
1.0
|
HD2
|
B:HIS228
|
4.9
|
82.1
|
1.0
|
N
|
B:LYS216
|
4.9
|
26.1
|
1.0
|
HA
|
B:CYS226
|
4.9
|
28.0
|
1.0
|
HB1
|
B:ALA214
|
5.0
|
34.4
|
1.0
|
HA
|
B:CYS229
|
5.0
|
37.7
|
1.0
|
|
Zinc binding site 2 out
of 2 in 6ok1
Go back to
Zinc Binding Sites List in 6ok1
Zinc binding site 2 out
of 2 in the LTP2-CHSH2(DUF35) Aldolase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of LTP2-CHSH2(DUF35) Aldolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn401
b:36.2
occ:1.00
|
SG
|
D:CYS229
|
2.3
|
40.7
|
1.0
|
SG
|
D:CYS215
|
2.4
|
40.4
|
1.0
|
SG
|
D:CYS212
|
2.4
|
36.4
|
1.0
|
SG
|
D:CYS226
|
2.4
|
34.9
|
1.0
|
H
|
D:CYS215
|
3.0
|
49.0
|
1.0
|
HB3
|
D:CYS229
|
3.0
|
54.2
|
1.0
|
HB3
|
D:CYS226
|
3.1
|
38.2
|
1.0
|
CB
|
D:CYS226
|
3.2
|
31.8
|
1.0
|
H
|
D:CYS229
|
3.2
|
46.9
|
1.0
|
HB3
|
D:CYS215
|
3.2
|
55.4
|
1.0
|
CB
|
D:CYS229
|
3.2
|
45.2
|
1.0
|
HB2
|
D:CYS226
|
3.2
|
38.2
|
1.0
|
CB
|
D:CYS212
|
3.3
|
33.4
|
1.0
|
HB2
|
D:CYS212
|
3.3
|
40.1
|
1.0
|
HB3
|
D:CYS212
|
3.3
|
40.1
|
1.0
|
CB
|
D:CYS215
|
3.4
|
46.2
|
1.0
|
HB3
|
D:ALA214
|
3.6
|
61.2
|
1.0
|
HB2
|
D:HIS228
|
3.7
|
46.8
|
1.0
|
N
|
D:CYS215
|
3.7
|
40.8
|
1.0
|
N
|
D:CYS229
|
3.7
|
39.1
|
1.0
|
HB3
|
D:SER231
|
3.8
|
45.7
|
1.0
|
H
|
D:SER231
|
4.0
|
41.8
|
1.0
|
CA
|
D:CYS229
|
4.0
|
34.8
|
1.0
|
HB2
|
D:CYS229
|
4.0
|
54.2
|
1.0
|
CA
|
D:CYS215
|
4.1
|
43.8
|
1.0
|
HB2
|
D:CYS215
|
4.2
|
55.4
|
1.0
|
H
|
D:THR217
|
4.4
|
47.2
|
1.0
|
H
|
D:ALA214
|
4.5
|
52.4
|
1.0
|
H
|
D:HIS228
|
4.5
|
37.5
|
1.0
|
CB
|
D:ALA214
|
4.5
|
51.0
|
1.0
|
H
|
D:GLY230
|
4.5
|
43.2
|
1.0
|
HB
|
D:THR217
|
4.5
|
43.5
|
1.0
|
CA
|
D:CYS226
|
4.6
|
31.3
|
1.0
|
C
|
D:CYS229
|
4.6
|
43.9
|
1.0
|
CB
|
D:SER231
|
4.6
|
38.1
|
1.0
|
CB
|
D:HIS228
|
4.6
|
39.0
|
1.0
|
HB2
|
D:SER231
|
4.6
|
45.7
|
1.0
|
H
|
D:LYS216
|
4.7
|
53.4
|
1.0
|
C
|
D:HIS228
|
4.7
|
43.2
|
1.0
|
CA
|
D:CYS212
|
4.7
|
39.0
|
1.0
|
N
|
D:GLY230
|
4.8
|
36.0
|
1.0
|
HG1
|
D:THR217
|
4.8
|
49.7
|
1.0
|
N
|
D:SER231
|
4.8
|
34.8
|
1.0
|
C
|
D:ALA214
|
4.8
|
55.1
|
1.0
|
C
|
D:CYS215
|
4.8
|
40.6
|
1.0
|
HB1
|
D:ALA214
|
4.8
|
61.2
|
1.0
|
HA
|
D:CYS229
|
4.9
|
41.7
|
1.0
|
HD2
|
D:HIS228
|
4.9
|
99.7
|
1.0
|
O
|
D:HOH537
|
4.9
|
32.6
|
1.0
|
HA
|
D:CYS215
|
4.9
|
52.5
|
1.0
|
HA
|
D:CYS226
|
5.0
|
37.6
|
1.0
|
N
|
D:LYS216
|
5.0
|
44.5
|
1.0
|
|
Reference:
R.Aggett,
E.Mallette,
S.E.Gilbert,
M.A.Vachon,
K.L.Schroeter,
M.S.Kimber,
S.Y.K.Seah.
The Steroid Side-Chain-Cleaving Aldolase LTP2-CHSH2DUF35IS A Thiolase Superfamily Member with A Radically Repurposed Active Site. J.Biol.Chem. V. 294 11934 2019.
ISSN: ESSN 1083-351X
PubMed: 31209106
DOI: 10.1074/JBC.RA119.008889
Page generated: Tue Oct 29 04:25:52 2024
|