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Calcium in PDB 7uaf: Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)

Enzymatic activity of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)

All present enzymatic activity of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide):
3.4.24.18;

Other elements in 7uaf:

The structure of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) (pdb code 7uaf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide), PDB code: 7uaf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7uaf

Go back to Calcium Binding Sites List in 7uaf
Calcium binding site 1 out of 8 in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:32.0
occ:1.00
 OD1 B:ASP285 1.9 36.8 1.0
OD1 B:ASP288 2.3 33.5 1.0
CG B:ASP285 2.4 36.8 1.0
O B:THR287 2.5 35.9 1.0
OD2 B:ASP285 2.5 36.8 1.0
O B:GLY282 2.6 36.6 1.0
C B:THR287 3.5 35.9 1.0
CG B:ASP288 3.6 33.5 1.0
C B:GLY282 3.7 36.6 1.0
CB B:ASP285 3.8 36.8 1.0
CA B:ASP288 4.1 33.5 1.0
N B:ASP288 4.2 33.5 1.0
N B:GLY282 4.4 36.6 1.0
CB B:ASP288 4.4 33.5 1.0
OD2 B:ASP288 4.4 33.5 1.0
CB B:GLN281 4.5 30.6 1.0
OE1 B:GLN281 4.5 30.6 1.0
N B:THR287 4.5 35.9 1.0
CA B:THR287 4.6 35.9 1.0
N B:THR283 4.6 39.1 1.0
C B:GLN281 4.6 30.6 1.0
CA B:GLY282 4.6 36.6 1.0
CA B:ASP285 4.7 36.8 1.0
C B:ASP285 4.7 36.8 1.0
CA B:THR283 4.7 39.1 1.0
O B:ASP285 4.7 36.8 1.0
O B:LEU329 4.7 27.6 1.0
N B:LEU329 4.8 27.6 1.0
N B:ASP285 4.9 36.8 1.0
CA B:ALA328 4.9 29.2 1.0
O B:GLN281 5.0 30.6 1.0

Calcium binding site 2 out of 8 in 7uaf

Go back to Calcium Binding Sites List in 7uaf
Calcium binding site 2 out of 8 in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:23.9
occ:1.00
 O B:THR270 2.3 29.8 1.0
OD1 B:ASP422 2.3 27.9 1.0
OE2 B:GLU272 2.3 31.4 1.0
O B:TYR313 2.3 31.8 1.0
OG1 B:THR303 2.4 29.4 1.0
OD2 B:ASP422 2.5 27.9 1.0
CG B:ASP422 2.8 27.9 1.0
OD2 B:ASP301 3.0 31.5 1.0
CD B:GLU272 3.3 31.4 1.0
CB B:THR303 3.3 29.4 1.0
C B:TYR313 3.5 31.8 1.0
C B:THR270 3.5 29.8 1.0
N B:TYR313 3.9 31.8 1.0
OE1 B:GLU272 3.9 31.4 1.0
CG B:ASP301 4.0 31.5 1.0
CB B:THR270 4.1 29.8 1.0
CA B:THR270 4.1 29.8 1.0
CA B:TYR313 4.2 31.8 1.0
CG2 B:THR303 4.3 29.4 1.0
CB B:ASP301 4.3 31.5 1.0
N B:THR303 4.3 29.4 1.0
CB B:ASP422 4.3 27.9 1.0
CG B:GLU272 4.3 31.4 1.0
CA B:THR303 4.4 29.4 1.0
N B:PHE314 4.5 28.9 1.0
OG1 B:THR270 4.6 29.8 1.0
N B:PHE271 4.6 29.1 1.0
OD1 B:ASP423 4.7 29.3 1.0
CB B:PHE271 4.7 29.1 1.0
C B:GLY312 4.8 32.9 1.0
C B:PHE271 4.8 29.1 1.0
CA B:PHE314 4.8 28.9 1.0
CB B:TYR313 4.9 31.8 1.0
CA B:PHE271 4.9 29.1 1.0
N B:GLU272 5.0 31.4 1.0

Calcium binding site 3 out of 8 in 7uaf

Go back to Calcium Binding Sites List in 7uaf
Calcium binding site 3 out of 8 in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:30.9
occ:1.00
 OD1 A:ASP288 2.3 31.9 1.0
OD1 A:ASP285 2.3 35.3 1.0
OD2 A:ASP285 2.4 35.3 1.0
O A:THR287 2.5 33.4 1.0
O A:GLY282 2.5 36.2 1.0
CG A:ASP285 2.7 35.3 1.0
C A:THR287 3.5 33.4 1.0
CG A:ASP288 3.5 31.9 1.0
C A:GLY282 3.7 36.2 1.0
N A:ASP288 4.1 31.9 1.0
CA A:ASP288 4.1 31.9 1.0
CB A:ASP285 4.2 35.3 1.0
N A:GLY282 4.4 36.2 1.0
N A:THR287 4.4 33.4 1.0
OD2 A:ASP288 4.4 31.9 1.0
CB A:GLN281 4.4 30.2 1.0
CB A:ASP288 4.4 31.9 1.0
CA A:THR287 4.5 33.4 1.0
N A:THR283 4.5 39.0 1.0
CA A:THR283 4.5 39.0 1.0
C A:GLN281 4.6 30.2 1.0
CA A:GLY282 4.6 36.2 1.0
OE1 A:GLN281 4.6 30.2 1.0
O A:LEU329 4.8 26.4 1.0
N A:LEU329 4.9 26.4 1.0
O A:GLN281 4.9 30.2 1.0
CA A:GLN281 5.0 30.2 1.0

Calcium binding site 4 out of 8 in 7uaf

Go back to Calcium Binding Sites List in 7uaf
Calcium binding site 4 out of 8 in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:22.9
occ:1.00
 O A:TYR313 2.3 31.1 1.0
OE2 A:GLU272 2.3 31.7 1.0
OD1 A:ASP422 2.4 28.4 1.0
O A:THR270 2.4 30.1 1.0
OG1 A:THR303 2.4 30.5 1.0
OD2 A:ASP422 2.6 28.4 1.0
CG A:ASP422 2.9 28.4 1.0
OD2 A:ASP301 3.0 32.1 1.0
CD A:GLU272 3.3 31.7 1.0
CB A:THR303 3.3 30.5 1.0
C A:TYR313 3.4 31.1 1.0
C A:THR270 3.6 30.1 1.0
OE1 A:GLU272 3.8 31.7 1.0
N A:TYR313 3.8 31.1 1.0
CG A:ASP301 4.0 32.1 1.0
CB A:ASP301 4.0 32.1 1.0
CA A:TYR313 4.1 31.1 1.0
CG2 A:THR303 4.3 30.5 1.0
N A:THR303 4.3 30.5 1.0
CA A:THR270 4.3 30.1 1.0
CB A:ASP422 4.4 28.4 1.0
N A:PHE314 4.4 30.2 1.0
CB A:THR270 4.4 30.1 1.0
CA A:THR303 4.4 30.5 1.0
CG A:GLU272 4.5 31.7 1.0
CB A:PHE271 4.6 29.4 1.0
N A:PHE271 4.6 29.4 1.0
C A:GLY312 4.7 32.7 1.0
CA A:PHE314 4.7 30.2 1.0
OD1 A:ASP423 4.8 29.9 1.0
CB A:TYR313 4.8 31.1 1.0
C A:PHE271 4.8 29.4 1.0
CA A:PHE271 4.9 29.4 1.0
N A:GLU272 5.0 31.7 1.0

Calcium binding site 5 out of 8 in 7uaf

Go back to Calcium Binding Sites List in 7uaf
Calcium binding site 5 out of 8 in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:42.3
occ:1.00
 OD1 C:ASP285 2.3 46.7 1.0
OD1 C:ASP288 2.4 46.7 1.0
O C:GLY282 2.5 51.9 1.0
OD2 C:ASP285 2.5 46.7 1.0
O C:THR287 2.6 44.9 1.0
CG C:ASP285 2.8 46.7 1.0
C C:THR287 3.6 44.9 1.0
CG C:ASP288 3.6 46.7 1.0
C C:GLY282 3.7 51.9 1.0
N C:GLY282 4.3 51.9 1.0
N C:ASP288 4.3 46.7 1.0
CA C:ASP288 4.3 46.7 1.0
CB C:ASP285 4.3 46.7 1.0
CB C:GLN281 4.3 50.3 1.0
OD2 C:ASP288 4.5 46.7 1.0
CA C:GLY282 4.5 51.9 1.0
C C:GLN281 4.5 50.3 1.0
CB C:ASP288 4.5 46.7 1.0
OE1 C:GLN281 4.6 50.3 1.0
N C:THR287 4.6 44.9 1.0
CA C:THR287 4.6 44.9 1.0
N C:THR283 4.6 53.0 1.0
CA C:THR283 4.8 53.0 1.0
O C:LEU329 4.8 41.0 1.0
N C:LEU329 4.9 41.0 1.0
O C:GLN281 5.0 50.3 1.0
CA C:GLN281 5.0 50.3 1.0

Calcium binding site 6 out of 8 in 7uaf

Go back to Calcium Binding Sites List in 7uaf
Calcium binding site 6 out of 8 in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:39.7
occ:1.00
 O C:TYR313 2.3 52.6 1.0
OE2 C:GLU272 2.3 53.6 1.0
OG1 C:THR303 2.3 48.0 1.0
OD1 C:ASP422 2.4 43.5 1.0
O C:THR270 2.4 48.3 1.0
OD2 C:ASP422 2.5 43.5 1.0
OD2 C:ASP301 2.7 49.0 1.0
CG C:ASP422 2.7 43.5 1.0
CB C:THR303 3.3 48.0 1.0
CD C:GLU272 3.3 53.6 1.0
C C:TYR313 3.5 52.6 1.0
C C:THR270 3.5 48.3 1.0
CG C:ASP301 3.7 49.0 1.0
OE1 C:GLU272 3.7 53.6 1.0
N C:TYR313 3.8 52.6 1.0
N C:THR303 3.9 48.0 1.0
CB C:THR270 4.0 48.3 1.0
CA C:THR270 4.0 48.3 1.0
CB C:ASP301 4.0 49.0 1.0
CA C:THR303 4.2 48.0 1.0
CA C:TYR313 4.2 52.6 1.0
CB C:ASP422 4.3 43.5 1.0
OD1 C:ASP423 4.3 44.0 1.0
CG2 C:THR303 4.4 48.0 1.0
N C:PHE314 4.5 46.8 1.0
OG1 C:THR270 4.6 48.3 1.0
CG C:GLU272 4.6 53.6 1.0
N C:PHE271 4.6 48.6 1.0
C C:GLY312 4.7 57.5 1.0
OD1 C:ASP301 4.8 49.0 1.0
CB C:PHE271 4.8 48.6 1.0
CA C:PHE314 4.8 46.8 1.0
CA C:GLY312 4.9 57.5 1.0
N C:HIS302 4.9 45.2 1.0
N C:ASP423 4.9 44.0 1.0
CB C:TYR313 4.9 52.6 1.0

Calcium binding site 7 out of 8 in 7uaf

Go back to Calcium Binding Sites List in 7uaf
Calcium binding site 7 out of 8 in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:42.6
occ:1.00
 OD1 D:ASP288 2.3 42.7 1.0
OD2 D:ASP285 2.4 45.8 1.0
O D:GLY282 2.5 47.4 1.0
O D:THR287 2.9 43.4 1.0
CG D:ASP285 3.4 45.8 1.0
C D:GLY282 3.5 47.4 1.0
CG D:ASP288 3.6 42.7 1.0
C D:THR287 3.8 43.4 1.0
OD1 D:ASP285 4.0 45.8 1.0
O D:ASP285 4.1 45.8 1.0
N D:GLY282 4.2 47.4 1.0
CA D:ASP288 4.3 42.7 1.0
CB D:GLN281 4.3 44.7 1.0
N D:THR283 4.3 48.7 1.0
N D:ASP288 4.4 42.7 1.0
CA D:THR283 4.4 48.7 1.0
CA D:GLY282 4.4 47.4 1.0
OD2 D:ASP288 4.4 42.7 1.0
CB D:ASP285 4.5 45.8 1.0
CB D:ASP288 4.5 42.7 1.0
OE1 D:GLN281 4.6 44.7 1.0
C D:GLN281 4.6 44.7 1.0
N D:THR287 4.6 43.4 1.0
C D:ASP285 4.7 45.8 1.0
CA D:THR287 4.7 43.4 1.0
O D:LEU329 4.9 38.4 1.0

Calcium binding site 8 out of 8 in 7uaf

Go back to Calcium Binding Sites List in 7uaf
Calcium binding site 8 out of 8 in the Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human Meprin Alpha Inhibitory Complex with Compound 10D (N~3~,N~3~- Bis[(2H-1,3-Benzodioxol-5-Yl)Methyl]-N-Hydroxy-Beta-Alaninamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca704

b:34.7
occ:1.00
 O D:TYR313 2.3 48.2 1.0
OD1 D:ASP422 2.3 39.7 1.0
O D:THR270 2.3 43.6 1.0
OG1 D:THR303 2.4 44.5 1.0
OE2 D:GLU272 2.4 48.1 1.0
OD2 D:ASP422 2.6 39.7 1.0
CG D:ASP422 2.8 39.7 1.0
CD D:GLU272 3.3 48.1 1.0
CB D:THR303 3.4 44.5 1.0
C D:TYR313 3.4 48.2 1.0
OE1 D:GLU272 3.4 48.1 1.0
C D:THR270 3.5 43.6 1.0
OD2 D:ASP301 3.5 47.2 1.0
N D:TYR313 3.7 48.2 1.0
CB D:ASP301 4.0 47.2 1.0
CA D:TYR313 4.1 48.2 1.0
CA D:THR270 4.2 43.6 1.0
N D:THR303 4.2 44.5 1.0
CB D:THR270 4.2 43.6 1.0
CG D:ASP301 4.3 47.2 1.0
CB D:ASP422 4.3 39.7 1.0
CA D:THR303 4.4 44.5 1.0
CG2 D:THR303 4.4 44.5 1.0
N D:PHE314 4.5 43.7 1.0
C D:GLY312 4.5 52.1 1.0
N D:PHE271 4.6 44.1 1.0
CB D:PHE271 4.6 44.1 1.0
OD1 D:ASP423 4.6 40.3 1.0
OG1 D:THR270 4.6 43.6 1.0
CG D:GLU272 4.7 48.1 1.0
CB D:TYR313 4.8 48.2 1.0
CA D:GLY312 4.8 52.1 1.0
CA D:PHE314 4.9 43.7 1.0
CA D:PHE271 4.9 44.1 1.0
C D:PHE271 4.9 44.1 1.0
N D:ASP423 5.0 40.3 1.0

Reference:

C.Bayly-Jones, C.J.Lupton, C.Fritz, H.Venugopal, D.Ramsbeck, M.Wermann, C.Jager, A.De Marco, S.Schilling, D.Schlenzig, J.C.Whisstock. Helical Ultrastructure of the Metalloprotease Meprin Alpha in Complex with A Small Molecule Inhibitor. Nat Commun V. 13 6178 2022.
ISSN: ESSN 2041-1723
PubMed: 36261433
DOI: 10.1038/S41467-022-33893-7
Page generated: Fri Jul 19 04:45:33 2024

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