Zinc in PDB 7xe2: Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa

Enzymatic activity of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa

All present enzymatic activity of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa:
1.14.99.66;

Protein crystallography data

The structure of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa, PDB code: 7xe2 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) 46.56 / 2.05
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 143.582, 170.082, 201.107, 90, 90, 90
R / Rfree (%) 16.7 / 19.4

Other elements in 7xe2:

The structure of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa also contains other interesting chemical elements:

Bromine (Br) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa (pdb code 7xe2). 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 Trans-4-Br-Pcpa, PDB code: 7xe2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7xe2

Go back to Zinc Binding Sites List in 7xe2
Zinc binding site 1 out of 6 in the Crystal Structure of LSD2 in Complex with Trans-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 Trans-4-Br-Pcpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:35.6
occ:1.00
 SG A:CYS147 2.3 37.8 1.0
SG A:CYS169 2.3 35.5 1.0
SG A:CYS185 2.4 40.0 1.0
SG A:CYS142 2.4 35.8 1.0
CB A:CYS142 3.0 31.8 1.0
CB A:CYS185 3.2 41.1 1.0
CB A:CYS147 3.2 42.3 1.0
CB A:CYS169 3.3 38.7 1.0
CA A:CYS185 3.6 43.6 1.0
N A:CYS169 3.9 36.4 1.0
CA A:CYS169 4.2 40.4 1.0
CA A:CYS142 4.5 36.3 1.0
N A:CYS185 4.5 42.8 1.0
O A:HOH1084 4.6 48.8 1.0
CB A:LYS144 4.6 53.3 1.0
CA A:CYS147 4.6 45.2 1.0
C A:CYS185 4.7 44.8 1.0
O A:CYS185 4.7 35.5 1.0
N A:ARG148 4.8 39.9 1.0
N A:LYS149 4.9 35.3 1.0

Zinc binding site 2 out of 6 in 7xe2

Go back to Zinc Binding Sites List in 7xe2
Zinc binding site 2 out of 6 in the Crystal Structure of LSD2 in Complex with Trans-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 Trans-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 37.0 1.0
ND1 A:HIS84 2.1 36.6 1.0
SG A:CYS58 2.3 39.2 1.0
SG A:CYS53 2.3 42.0 1.0
CD2 A:HIS90 2.8 37.9 1.0
CE1 A:HIS84 3.1 32.8 1.0
CB A:CYS58 3.1 42.6 1.0
CE1 A:HIS90 3.2 42.3 1.0
CG A:HIS84 3.2 41.2 1.0
CB A:CYS53 3.2 38.9 1.0
CB A:HIS84 3.5 36.4 1.0
O A:SER86 3.9 33.2 1.0
CG A:HIS90 4.0 38.9 1.0
ND1 A:HIS90 4.2 38.1 1.0
NE2 A:HIS84 4.2 35.5 1.0
CD2 A:HIS84 4.3 32.0 1.0
CA A:HIS84 4.3 36.5 1.0
CB A:LYS55 4.5 40.2 1.0
CA A:CYS58 4.5 46.8 1.0
CA A:CYS53 4.6 42.9 1.0
CA A:CYS87 4.7 34.2 1.0
C A:SER86 4.7 33.5 1.0

Zinc binding site 3 out of 6 in 7xe2

Go back to Zinc Binding Sites List in 7xe2
Zinc binding site 3 out of 6 in the Crystal Structure of LSD2 in Complex with Trans-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 Trans-4-Br-Pcpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:48.4
occ:1.00
 SG A:CYS95 2.3 54.4 1.0
SG A:CYS92 2.3 55.7 1.0
SG A:CYS73 2.3 60.6 1.0
SG A:CYS65 2.4 45.7 1.0
CB A:CYS65 3.1 42.7 1.0
CB A:CYS73 3.2 58.7 1.0
CB A:CYS95 3.4 54.3 1.0
CB A:CYS92 3.6 58.1 1.0
CA A:CYS73 3.6 67.7 1.0
N A:CYS92 3.9 48.4 1.0
N A:ALA74 4.0 64.2 1.0
N A:SER68 4.0 54.4 1.0
C A:CYS73 4.2 71.2 1.0
CA A:SER68 4.2 65.4 1.0
N A:CYS95 4.3 53.9 1.0
CA A:CYS92 4.3 45.8 1.0
CA A:CYS95 4.4 54.8 1.0
CA A:CYS65 4.6 44.7 1.0
N A:LYS75 4.6 60.9 1.0
O A:CYS92 4.8 49.5 1.0
CB A:ALA67 4.8 45.3 1.0
N A:ALA69 4.9 64.3 1.0
C A:CYS92 4.9 53.2 1.0
N A:CYS73 4.9 63.8 1.0

Zinc binding site 4 out of 6 in 7xe2

Go back to Zinc Binding Sites List in 7xe2
Zinc binding site 4 out of 6 in the Crystal Structure of LSD2 in Complex with Trans-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 Trans-4-Br-Pcpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:43.8
occ:1.00
 SG B:CYS169 2.3 42.6 1.0
SG B:CYS147 2.3 43.2 1.0
SG B:CYS185 2.3 49.6 1.0
SG B:CYS142 2.4 41.2 1.0
CB B:CYS147 3.1 46.7 1.0
CB B:CYS142 3.1 38.9 1.0
CB B:CYS185 3.2 46.0 1.0
CB B:CYS169 3.3 44.6 1.0
CA B:CYS185 3.6 46.4 1.0
N B:CYS169 3.8 47.4 1.0
CA B:CYS169 4.2 48.6 1.0
CA B:CYS147 4.5 50.9 1.0
N B:CYS185 4.5 48.1 1.0
CA B:CYS142 4.6 42.0 1.0
C B:CYS185 4.7 46.8 1.0
O B:CYS185 4.7 45.6 1.0
CD B:LYS144 4.7 69.3 1.0
O B:HOH1037 4.8 47.3 1.0
N B:ARG148 4.8 44.1 1.0
CB B:LYS144 4.9 59.5 1.0
C B:ARG168 4.9 49.9 1.0
C B:CYS147 5.0 47.6 1.0
N B:LYS149 5.0 43.2 1.0

Zinc binding site 5 out of 6 in 7xe2

Go back to Zinc Binding Sites List in 7xe2
Zinc binding site 5 out of 6 in the Crystal Structure of LSD2 in Complex with Trans-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 Trans-4-Br-Pcpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:66.0
occ:1.00
 NE2 B:HIS90 2.0 59.6 1.0
ND1 B:HIS84 2.1 62.7 1.0
SG B:CYS58 2.3 59.8 1.0
SG B:CYS53 2.3 77.6 1.0
CE1 B:HIS90 2.9 59.0 1.0
CE1 B:HIS84 2.9 57.1 1.0
CD2 B:HIS90 3.0 66.4 1.0
CB B:CYS53 3.1 67.9 1.0
CG B:HIS84 3.1 62.8 1.0
CB B:CYS58 3.2 75.6 1.0
CB B:HIS84 3.6 61.0 1.0
O B:SER86 3.9 54.2 1.0
ND1 B:HIS90 4.0 60.7 1.0
NE2 B:HIS84 4.1 60.3 1.0
CG B:HIS90 4.1 64.0 1.0
CD2 B:HIS84 4.2 61.5 1.0
CA B:HIS84 4.4 62.4 1.0
CA B:CYS53 4.5 79.7 1.0
CA B:CYS58 4.6 76.5 1.0
CB B:LYS55 4.6 80.4 1.0
C B:SER86 4.8 51.9 1.0
CB B:ALA60 4.8 75.2 1.0
CA B:CYS87 4.8 55.1 1.0

Zinc binding site 6 out of 6 in 7xe2

Go back to Zinc Binding Sites List in 7xe2
Zinc binding site 6 out of 6 in the Crystal Structure of LSD2 in Complex with Trans-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 Trans-4-Br-Pcpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn903

b:78.3
occ:1.00
 SG B:CYS95 2.3 72.2 1.0
SG B:CYS92 2.3 78.3 1.0
SG B:CYS73 2.3 94.1 1.0
SG B:CYS65 2.3 74.0 1.0
CB B:CYS65 3.0 75.5 1.0
CB B:CYS73 3.2 86.6 1.0
CB B:CYS95 3.4 77.1 1.0
CA B:CYS73 3.7 91.6 1.0
CB B:CYS92 3.8 80.9 1.0
N B:SER68 3.9 73.0 1.0
N B:CYS92 4.0 71.5 1.0
N B:ALA74 4.1 91.4 1.0
CA B:SER68 4.2 81.2 1.0
C B:CYS73 4.2 93.5 1.0
N B:CYS95 4.3 77.5 1.0
CA B:CYS95 4.5 77.7 0.8
CA B:CYS92 4.5 82.3 1.0
CA B:CYS65 4.5 76.5 1.0
N B:LYS75 4.7 95.8 1.0
N B:ALA69 4.7 81.6 1.0
CB B:ALA67 4.8 74.0 1.0
O B:CYS92 4.9 75.3 1.0
C B:ALA67 4.9 75.4 1.0
N B:CYS73 5.0 94.1 1.0
C B:SER68 5.0 81.3 1.0
C B:CYS65 5.0 71.5 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 14:59:22 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy