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:

Bromine (Br) 2 atoms

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


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 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


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 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


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 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


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 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


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 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


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 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: Wed Oct 30 14:58:22 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy