Zinc in PDB 7xe3: Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)

Enzymatic activity of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)

All present enzymatic activity of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024):
1.14.99.66;

Protein crystallography data

The structure of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024), PDB code: 7xe3 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) 48.27 / 2.82
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 143.372, 171.226, 201.918, 90, 90, 90
R / Rfree (%) 17.7 / 22.2

Other elements in 7xe3:

The structure of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) also contains other interesting chemical elements:

Fluorine (F) 4 atoms
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-2,5-F2-Pcpa (S1024) (pdb code 7xe3). 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-2,5-F2-Pcpa (S1024), PDB code: 7xe3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7xe3

Go back to Zinc Binding Sites List in 7xe3
Zinc binding site 1 out of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)


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-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:70.5
occ:1.00
 SG A:CYS169 2.3 63.8 1.0
SG A:CYS147 2.3 68.1 1.0
SG A:CYS185 2.4 83.5 1.0
SG A:CYS142 2.4 75.3 1.0
CB A:CYS142 3.0 66.3 1.0
CB A:CYS169 3.1 71.3 1.0
CB A:CYS185 3.2 86.6 1.0
CB A:CYS147 3.3 81.9 1.0
CA A:CYS185 3.5 78.6 1.0
N A:CYS169 3.9 82.0 1.0
CA A:CYS169 4.1 78.3 1.0
N A:CYS185 4.4 86.2 1.0
CA A:CYS142 4.5 68.1 1.0
C A:CYS185 4.6 74.2 1.0
O A:CYS185 4.6 71.5 1.0
CA A:CYS147 4.7 86.4 1.0
CB A:LYS144 4.8 88.2 1.0
CD A:LYS144 5.0 98.4 1.0
CB A:LYS149 5.0 59.3 1.0

Zinc binding site 2 out of 6 in 7xe3

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Zinc binding site 2 out of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)


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-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:56.8
occ:1.00
 NE2 A:HIS90 2.0 50.4 1.0
ND1 A:HIS84 2.1 58.7 1.0
SG A:CYS58 2.3 58.1 1.0
SG A:CYS53 2.3 59.3 1.0
CD2 A:HIS90 2.8 50.9 1.0
CE1 A:HIS84 2.9 51.8 1.0
CB A:CYS53 3.1 61.0 1.0
CE1 A:HIS90 3.1 50.0 1.0
CB A:CYS58 3.2 54.3 1.0
CG A:HIS84 3.2 56.2 1.0
CB A:HIS84 3.6 58.6 1.0
O A:SER86 3.9 54.8 1.0
CG A:HIS90 4.0 55.0 1.0
NE2 A:HIS84 4.1 50.5 1.0
ND1 A:HIS90 4.1 52.2 1.0
CD2 A:HIS84 4.2 52.4 1.0
CA A:HIS84 4.4 58.2 1.0
CA A:CYS53 4.5 66.1 1.0
CA A:CYS58 4.6 58.9 1.0
CA A:CYS87 4.6 51.4 1.0
C A:SER86 4.8 51.7 1.0
CB A:ALA60 4.8 62.4 1.0
CB A:LYS55 4.9 69.3 1.0
O A:CYS87 4.9 61.0 1.0

Zinc binding site 3 out of 6 in 7xe3

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Zinc binding site 3 out of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)


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-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:77.3
occ:1.00
 SG A:CYS92 2.3 70.2 1.0
SG A:CYS73 2.3 85.6 1.0
SG A:CYS65 2.3 78.9 1.0
SG A:CYS95 2.3 78.6 1.0
CB A:CYS73 3.1 86.8 1.0
CB A:CYS65 3.1 71.9 1.0
CB A:CYS95 3.4 71.9 1.0
CA A:CYS73 3.5 81.0 1.0
CB A:CYS92 3.7 74.9 1.0
N A:SER68 3.9 82.6 1.0
N A:ALA74 3.9 87.6 1.0
N A:CYS92 4.1 66.2 1.0
CA A:SER68 4.2 82.9 1.0
C A:CYS73 4.2 87.3 1.0
N A:CYS95 4.3 80.8 1.0
CA A:CYS92 4.4 70.6 1.0
CA A:CYS95 4.5 75.1 1.0
CA A:CYS65 4.5 68.8 1.0
N A:LYS75 4.7 88.0 1.0
N A:ALA69 4.8 83.9 1.0
O A:CYS92 4.8 75.1 1.0
CB A:ALA67 4.8 76.7 1.0
N A:CYS73 4.8 93.5 1.0
C A:CYS92 4.9 72.9 1.0
OG A:SER68 5.0 91.4 1.0
C A:ALA67 5.0 85.2 1.0

Zinc binding site 4 out of 6 in 7xe3

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Zinc binding site 4 out of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)


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-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:76.7
occ:1.00
 SG B:CYS147 2.3 74.5 1.0
SG B:CYS169 2.3 62.8 1.0
SG B:CYS185 2.3 91.0 1.0
SG B:CYS142 2.3 80.3 1.0
CB B:CYS169 3.1 74.4 1.0
CB B:CYS142 3.1 71.1 1.0
CB B:CYS147 3.2 79.8 1.0
CB B:CYS185 3.4 82.7 1.0
CA B:CYS185 3.7 80.0 1.0
N B:CYS169 3.9 80.4 1.0
CA B:CYS169 4.1 79.6 1.0
O B:CYS185 4.5 69.1 1.0
C B:CYS185 4.6 77.0 1.0
CA B:CYS142 4.6 71.0 1.0
CA B:CYS147 4.6 80.4 1.0
N B:CYS185 4.8 84.0 1.0
CB B:LYS144 4.8 78.9 1.0
N B:ARG148 4.9 77.0 1.0
CD B:LYS144 5.0 87.3 1.0
N B:LYS149 5.0 72.4 1.0

Zinc binding site 5 out of 6 in 7xe3

Go back to Zinc Binding Sites List in 7xe3
Zinc binding site 5 out of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)


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-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:91.8
occ:1.00
 NE2 B:HIS90 2.0 88.9 1.0
ND1 B:HIS84 2.0 90.1 1.0
SG B:CYS58 2.3 100.8 1.0
SG B:CYS53 2.3 107.6 1.0
CE1 B:HIS90 2.6 92.1 1.0
CE1 B:HIS84 2.8 85.4 1.0
CG B:HIS84 3.2 86.3 1.0
CD2 B:HIS90 3.2 93.7 1.0
CB B:CYS58 3.4 103.8 1.0
CB B:CYS53 3.6 116.8 1.0
CB B:HIS84 3.7 87.8 1.0
ND1 B:HIS90 3.8 92.7 1.0
O B:SER86 4.0 81.8 1.0
NE2 B:HIS84 4.0 81.5 1.0
CG B:HIS90 4.1 95.0 1.0
CD2 B:HIS84 4.2 82.5 1.0
CA B:HIS84 4.5 86.3 1.0
CA B:CYS58 4.7 106.6 1.0
C B:SER86 4.8 79.1 1.0
CA B:CYS87 4.8 86.1 1.0
CB B:ALA60 4.9 107.9 1.0
CA B:CYS53 4.9 119.7 1.0
CB B:LYS55 5.0 106.9 1.0

Zinc binding site 6 out of 6 in 7xe3

Go back to Zinc Binding Sites List in 7xe3
Zinc binding site 6 out of 6 in the Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)


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-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn903

b:130.7
occ:1.00
 SG B:CYS92 2.3 109.2 1.0
SG B:CYS95 2.3 114.4 1.0
SG B:CYS65 2.3 120.9 1.0
SG B:CYS73 2.3 151.4 1.0
CB B:CYS65 3.2 114.2 1.0
CB B:CYS95 3.2 114.4 1.0
CB B:CYS73 3.5 146.0 1.0
N B:SER68 3.9 127.3 1.0
CA B:CYS73 3.9 145.2 1.0
CB B:CYS92 4.0 116.1 1.0
CA B:SER68 4.1 130.3 1.0
N B:ALA74 4.2 127.2 1.0
N B:CYS92 4.2 110.0 1.0
N B:CYS95 4.3 117.7 1.0
CA B:CYS95 4.3 118.0 1.0
C B:CYS73 4.5 144.4 1.0
OG B:SER68 4.5 126.3 1.0
CA B:CYS92 4.6 115.2 1.0
CA B:CYS65 4.7 107.8 1.0
O B:CYS92 4.8 113.2 1.0
N B:LYS75 4.9 127.8 1.0
CB B:SER68 4.9 127.5 1.0
N B:ALA69 5.0 132.5 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: Sat Apr 8 05:51:17 2023

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