Zinc in PDB 7xe1: Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
Enzymatic activity of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
All present enzymatic activity of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa:
1.14.99.66;
Protein crystallography data
The structure of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa, PDB code: 7xe1
was solved by
H.Niwa,
S.Sato,
T.Umehara,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.75 /
2.07
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
144.121,
170.76,
202.669,
90,
90,
90
|
R / Rfree (%)
|
16.4 /
19.2
|
Other elements in 7xe1:
The structure of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
(pdb code 7xe1). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa, PDB code: 7xe1:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 7xe1
Go back to
Zinc Binding Sites List in 7xe1
Zinc binding site 1 out
of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn901
b:40.1
occ:1.00
|
SG
|
A:CYS147
|
2.2
|
39.6
|
1.0
|
SG
|
A:CYS169
|
2.3
|
38.0
|
1.0
|
SG
|
A:CYS185
|
2.3
|
47.7
|
1.0
|
SG
|
A:CYS142
|
2.4
|
38.3
|
1.0
|
CB
|
A:CYS142
|
3.0
|
34.2
|
1.0
|
CB
|
A:CYS185
|
3.2
|
49.6
|
1.0
|
CB
|
A:CYS147
|
3.2
|
52.2
|
1.0
|
CB
|
A:CYS169
|
3.3
|
41.5
|
1.0
|
CA
|
A:CYS185
|
3.6
|
46.2
|
1.0
|
N
|
A:CYS169
|
3.8
|
43.8
|
1.0
|
CA
|
A:CYS169
|
4.1
|
43.8
|
1.0
|
CA
|
A:CYS142
|
4.5
|
41.5
|
1.0
|
N
|
A:CYS185
|
4.5
|
50.8
|
1.0
|
O
|
A:HOH1100
|
4.5
|
55.1
|
1.0
|
CB
|
A:LYS144
|
4.6
|
56.1
|
1.0
|
CA
|
A:CYS147
|
4.6
|
49.2
|
1.0
|
C
|
A:CYS185
|
4.7
|
46.4
|
1.0
|
O
|
A:CYS185
|
4.7
|
37.9
|
1.0
|
N
|
A:ARG148
|
4.9
|
41.4
|
1.0
|
C
|
A:ARG168
|
4.9
|
49.5
|
1.0
|
O
|
A:HOH1518
|
5.0
|
49.1
|
1.0
|
N
|
A:LYS149
|
5.0
|
38.8
|
1.0
|
|
Zinc binding site 2 out
of 6 in 7xe1
Go back to
Zinc Binding Sites List in 7xe1
Zinc binding site 2 out
of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn902
b:36.1
occ:1.00
|
NE2
|
A:HIS90
|
2.0
|
34.2
|
1.0
|
ND1
|
A:HIS84
|
2.2
|
33.3
|
1.0
|
SG
|
A:CYS58
|
2.2
|
36.6
|
1.0
|
SG
|
A:CYS53
|
2.3
|
40.6
|
1.0
|
CD2
|
A:HIS90
|
2.9
|
31.5
|
1.0
|
CE1
|
A:HIS90
|
3.0
|
35.9
|
1.0
|
CE1
|
A:HIS84
|
3.1
|
30.7
|
1.0
|
CB
|
A:CYS58
|
3.2
|
37.9
|
1.0
|
CB
|
A:CYS53
|
3.2
|
37.8
|
1.0
|
CG
|
A:HIS84
|
3.2
|
35.8
|
1.0
|
CB
|
A:HIS84
|
3.5
|
35.4
|
1.0
|
O
|
A:SER86
|
3.9
|
31.8
|
1.0
|
CG
|
A:HIS90
|
4.1
|
34.1
|
1.0
|
ND1
|
A:HIS90
|
4.1
|
34.6
|
1.0
|
NE2
|
A:HIS84
|
4.2
|
38.0
|
1.0
|
CA
|
A:HIS84
|
4.3
|
36.8
|
1.0
|
CD2
|
A:HIS84
|
4.3
|
35.8
|
1.0
|
CA
|
A:CYS58
|
4.6
|
39.3
|
1.0
|
CA
|
A:CYS53
|
4.6
|
41.5
|
1.0
|
CB
|
A:LYS55
|
4.6
|
43.4
|
1.0
|
CA
|
A:CYS87
|
4.7
|
34.9
|
1.0
|
C
|
A:SER86
|
4.7
|
35.3
|
1.0
|
CB
|
A:ALA60
|
5.0
|
41.3
|
1.0
|
O
|
A:CYS87
|
5.0
|
34.5
|
1.0
|
|
Zinc binding site 3 out
of 6 in 7xe1
Go back to
Zinc Binding Sites List in 7xe1
Zinc binding site 3 out
of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn903
b:45.5
occ:1.00
|
SG
|
A:CYS92
|
2.2
|
48.1
|
1.0
|
SG
|
A:CYS95
|
2.3
|
50.1
|
1.0
|
SG
|
A:CYS73
|
2.3
|
54.7
|
1.0
|
SG
|
A:CYS65
|
2.4
|
41.5
|
1.0
|
CB
|
A:CYS65
|
3.1
|
40.8
|
1.0
|
CB
|
A:CYS73
|
3.1
|
51.9
|
1.0
|
CB
|
A:CYS95
|
3.4
|
51.2
|
1.0
|
CA
|
A:CYS73
|
3.6
|
57.0
|
1.0
|
CB
|
A:CYS92
|
3.6
|
52.7
|
1.0
|
N
|
A:CYS92
|
3.9
|
43.8
|
1.0
|
N
|
A:ALA74
|
3.9
|
59.9
|
1.0
|
N
|
A:SER68
|
4.0
|
50.5
|
1.0
|
CA
|
A:SER68
|
4.1
|
57.9
|
1.0
|
C
|
A:CYS73
|
4.1
|
61.4
|
1.0
|
N
|
A:CYS95
|
4.3
|
50.4
|
1.0
|
CA
|
A:CYS92
|
4.3
|
42.8
|
1.0
|
CA
|
A:CYS95
|
4.5
|
49.5
|
1.0
|
CA
|
A:CYS65
|
4.5
|
42.9
|
1.0
|
N
|
A:LYS75
|
4.7
|
57.2
|
1.0
|
N
|
A:ALA69
|
4.8
|
54.6
|
1.0
|
O
|
A:CYS92
|
4.8
|
44.6
|
1.0
|
N
|
A:CYS73
|
4.9
|
58.3
|
1.0
|
C
|
A:CYS92
|
4.9
|
47.6
|
1.0
|
CB
|
A:ALA67
|
4.9
|
43.5
|
1.0
|
|
Zinc binding site 4 out
of 6 in 7xe1
Go back to
Zinc Binding Sites List in 7xe1
Zinc binding site 4 out
of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn901
b:42.4
occ:1.00
|
SG
|
B:CYS169
|
2.2
|
40.0
|
1.0
|
SG
|
B:CYS147
|
2.3
|
42.3
|
1.0
|
SG
|
B:CYS185
|
2.3
|
42.3
|
1.0
|
SG
|
B:CYS142
|
2.4
|
41.4
|
1.0
|
CB
|
B:CYS142
|
3.1
|
38.6
|
1.0
|
CB
|
B:CYS147
|
3.1
|
48.4
|
1.0
|
CB
|
B:CYS185
|
3.2
|
41.9
|
1.0
|
CB
|
B:CYS169
|
3.2
|
42.5
|
1.0
|
CA
|
B:CYS185
|
3.6
|
41.8
|
1.0
|
N
|
B:CYS169
|
3.8
|
45.0
|
1.0
|
CA
|
B:CYS169
|
4.1
|
48.2
|
1.0
|
N
|
B:CYS185
|
4.6
|
44.3
|
1.0
|
CA
|
B:CYS147
|
4.6
|
50.1
|
1.0
|
CA
|
B:CYS142
|
4.6
|
41.4
|
1.0
|
O
|
B:HOH1036
|
4.6
|
48.8
|
1.0
|
CD
|
B:LYS144
|
4.6
|
58.6
|
1.0
|
C
|
B:CYS185
|
4.7
|
42.1
|
1.0
|
O
|
B:CYS185
|
4.7
|
40.9
|
1.0
|
CB
|
B:LYS144
|
4.8
|
51.7
|
1.0
|
N
|
B:ARG148
|
4.8
|
46.2
|
1.0
|
C
|
B:ARG168
|
4.9
|
48.3
|
1.0
|
N
|
B:LYS149
|
5.0
|
40.9
|
1.0
|
|
Zinc binding site 5 out
of 6 in 7xe1
Go back to
Zinc Binding Sites List in 7xe1
Zinc binding site 5 out
of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn902
b:59.8
occ:1.00
|
NE2
|
B:HIS90
|
2.0
|
59.6
|
1.0
|
ND1
|
B:HIS84
|
2.1
|
62.4
|
1.0
|
SG
|
B:CYS58
|
2.2
|
61.1
|
1.0
|
SG
|
B:CYS53
|
2.3
|
69.8
|
1.0
|
CE1
|
B:HIS90
|
2.9
|
59.8
|
1.0
|
CE1
|
B:HIS84
|
3.0
|
60.2
|
1.0
|
CD2
|
B:HIS90
|
3.0
|
62.7
|
1.0
|
CB
|
B:CYS53
|
3.2
|
69.5
|
1.0
|
CG
|
B:HIS84
|
3.2
|
58.8
|
1.0
|
CB
|
B:CYS58
|
3.2
|
76.9
|
1.0
|
CB
|
B:HIS84
|
3.6
|
57.6
|
1.0
|
O
|
B:SER86
|
3.9
|
55.1
|
1.0
|
ND1
|
B:HIS90
|
4.0
|
58.0
|
1.0
|
CG
|
B:HIS90
|
4.1
|
62.8
|
1.0
|
NE2
|
B:HIS84
|
4.2
|
55.7
|
1.0
|
CD2
|
B:HIS84
|
4.3
|
60.5
|
1.0
|
CA
|
B:HIS84
|
4.4
|
59.5
|
1.0
|
CB
|
B:ALA60
|
4.5
|
75.3
|
1.0
|
CA
|
B:CYS53
|
4.6
|
80.3
|
1.0
|
CA
|
B:CYS58
|
4.6
|
79.1
|
1.0
|
C
|
B:SER86
|
4.8
|
54.2
|
1.0
|
CB
|
B:LYS55
|
4.8
|
75.2
|
1.0
|
CA
|
B:CYS87
|
4.8
|
54.0
|
1.0
|
|
Zinc binding site 6 out
of 6 in 7xe1
Go back to
Zinc Binding Sites List in 7xe1
Zinc binding site 6 out
of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_06.jpg) Mono view
![](/pictures/ZN/pdb/xe/7xe1-ZN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of LSD2 in Complex with Cis-4-Br-Pcpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn903
b:73.1
occ:1.00
|
SG
|
B:CYS95
|
2.2
|
78.8
|
1.0
|
SG
|
B:CYS92
|
2.2
|
74.4
|
1.0
|
SG
|
B:CYS65
|
2.5
|
67.6
|
1.0
|
SG
|
B:CYS73
|
2.6
|
86.6
|
1.0
|
CB
|
B:CYS65
|
3.3
|
67.4
|
1.0
|
CB
|
B:CYS95
|
3.3
|
76.4
|
1.0
|
CB
|
B:CYS73
|
3.4
|
87.0
|
1.0
|
CA
|
B:CYS73
|
3.7
|
86.2
|
1.0
|
CB
|
B:CYS92
|
3.7
|
75.2
|
1.0
|
N
|
B:SER68
|
3.9
|
73.0
|
1.0
|
N
|
B:CYS92
|
4.0
|
69.2
|
1.0
|
N
|
B:ALA74
|
4.0
|
87.7
|
1.0
|
N
|
B:CYS95
|
4.1
|
82.6
|
1.0
|
CA
|
B:SER68
|
4.2
|
79.7
|
1.0
|
C
|
B:CYS73
|
4.3
|
88.3
|
1.0
|
CA
|
B:CYS95
|
4.3
|
78.7
|
0.7
|
CA
|
B:CYS92
|
4.4
|
77.5
|
1.0
|
CA
|
B:CYS65
|
4.7
|
65.2
|
1.0
|
CB
|
B:ALA67
|
4.8
|
66.9
|
1.0
|
O
|
B:CYS92
|
4.8
|
73.6
|
1.0
|
N
|
B:LYS75
|
4.8
|
91.5
|
1.0
|
C
|
B:CYS92
|
4.9
|
78.6
|
1.0
|
N
|
B:ALA69
|
4.9
|
83.6
|
1.0
|
N
|
B:CYS73
|
4.9
|
92.0
|
1.0
|
|
Reference:
H.Niwa,
C.Watanabe,
S.Sato,
T.Harada,
H.Watanabe,
R.Tabusa,
S.Fukasawa,
A.Shiobara,
T.Hashimoto,
O.Ohno,
K.Nakamura,
K.Tsuganezawa,
A.Tanaka,
M.Shirouzu,
T.Honma,
K.Matsuno,
T.Umehara.
Structure-Activity Relationship and in Silico Evaluation of Cis- and Trans-Pcpa-Derived Inhibitors of LSD1 and LSD2 Acs Med.Chem.Lett. V. 13 1485 2022.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.2C00294
Page generated: Sat Apr 8 05:51:16 2023
|