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

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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: Sat Apr 8 05:51:16 2023

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