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Calcium in PDB 8k5y: Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor

Enzymatic activity of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor, PDB code: 8k5y was solved by M.Kamitani, M.Mima, R.Nishikawa-Shimono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.01 / 1.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.53, 73.99, 77.13, 90, 103.36, 90
R / Rfree (%) 17.6 / 19.8

Other elements in 8k5y:

The structure of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor (pdb code 8k5y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor, PDB code: 8k5y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8k5y

Go back to Calcium Binding Sites List in 8k5y
Calcium binding site 1 out of 6 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:20.7
occ:1.00
 OE2 A:GLU208 2.2 24.6 1.0
O A:GLY183 2.3 23.0 1.0
O A:LEU187 2.3 19.8 1.0
OD2 A:ASP205 2.3 19.2 1.0
OD1 A:ASP182 2.4 19.8 1.0
O A:ASP185 2.4 22.1 1.0
CG A:ASP205 3.4 18.7 1.0
CD A:GLU208 3.5 23.5 1.0
CG A:ASP182 3.5 23.9 1.0
C A:GLY183 3.5 25.6 1.0
C A:LEU187 3.6 18.5 1.0
C A:ASP185 3.6 24.0 1.0
N A:ASP185 3.9 24.5 1.0
OD2 A:ASP182 4.0 24.7 1.0
N A:LEU187 4.0 21.6 1.0
C A:LYS184 4.1 26.0 1.0
N A:GLY183 4.1 25.0 1.0
CB A:ASP205 4.2 17.0 1.0
CA A:ASP185 4.3 25.6 1.0
OD1 A:ASP205 4.3 19.2 1.0
OE1 A:GLU208 4.3 25.2 1.0
C A:ASP182 4.4 23.9 1.0
N A:ASP182 4.4 22.6 1.0
CG A:GLU208 4.4 22.8 1.0
CA A:LEU187 4.4 21.0 1.0
C A:GLY186 4.4 19.9 1.0
CA A:GLY183 4.4 25.0 1.0
N A:LYS184 4.4 25.1 1.0
O A:LYS184 4.5 28.4 1.0
CA A:LYS184 4.5 25.0 1.0
N A:LEU188 4.6 17.7 1.0
N A:GLY186 4.6 22.0 1.0
CB A:ASP182 4.7 22.5 1.0
CD1 A:LEU187 4.7 31.2 1.0
CA A:LEU188 4.7 17.8 1.0
CA A:ASP182 4.7 22.9 1.0
CA A:GLY186 4.8 20.2 1.0
CG A:LEU187 4.8 27.3 1.0
O A:ASP182 4.9 26.5 1.0

Calcium binding site 2 out of 6 in 8k5y

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Calcium binding site 2 out of 6 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:32.0
occ:1.00
 O A:GLU208 2.3 23.0 1.0
OD2 A:ASP131 2.4 27.3 1.0
OD1 A:ASP206 2.4 19.6 1.0
O A:ASP206 2.5 23.1 1.0
O A:HOH442 2.5 34.2 1.0
CG A:ASP131 3.2 29.1 1.0
CG A:ASP206 3.3 21.6 1.0
C A:ASP206 3.4 22.5 1.0
OD1 A:ASP131 3.4 30.9 1.0
C A:GLU208 3.5 21.8 1.0
CA A:ASP206 3.7 20.9 1.0
OG A:SER129 3.9 20.7 1.0
CB A:ASP206 4.0 22.7 1.0
OD2 A:ASP206 4.2 23.8 1.0
CD1 A:TRP210 4.2 21.1 1.0
N A:GLU208 4.3 21.4 1.0
CA A:LEU209 4.3 22.3 1.0
N A:LEU209 4.3 21.2 1.0
N A:ASP207 4.4 21.9 1.0
C A:ASP207 4.5 22.3 1.0
O A:HOH470 4.5 27.1 1.0
CA A:GLU208 4.5 19.9 1.0
CB A:ASP131 4.6 24.7 1.0
N A:TRP210 4.7 21.0 1.0
CA A:ASP207 4.7 23.8 1.0
NE1 A:TRP210 4.8 22.5 1.0
O A:ASP207 5.0 24.4 1.0
C A:LEU209 5.0 23.3 1.0

Calcium binding site 3 out of 6 in 8k5y

Go back to Calcium Binding Sites List in 8k5y
Calcium binding site 3 out of 6 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:19.5
occ:1.00
 O A:GLY197 2.3 21.2 1.0
O A:ASP165 2.3 17.8 1.0
OD1 A:ASP201 2.3 17.4 1.0
O A:GLN199 2.3 18.5 1.0
O A:HOH412 2.4 20.2 1.0
O A:HOH406 2.4 21.4 1.0
CG A:ASP201 3.4 20.0 1.0
C A:ASP165 3.5 18.2 1.0
C A:GLY197 3.5 23.5 1.0
C A:GLN199 3.6 18.1 1.0
OD2 A:ASP201 3.9 20.3 1.0
C A:ILE198 4.1 20.6 1.0
O A:ALA164 4.2 25.9 1.0
O A:ILE198 4.2 20.8 1.0
N A:GLN199 4.2 20.3 1.0
N A:ASP201 4.2 17.6 1.0
O A:HOH445 4.3 32.6 1.0
O A:GLY195 4.3 20.9 1.0
CA A:ASP165 4.3 18.6 1.0
N A:GLY200 4.4 17.8 1.0
N A:GLY197 4.4 23.6 1.0
C A:GLY200 4.4 16.6 1.0
CA A:GLY197 4.4 25.2 1.0
N A:ILE198 4.4 23.2 1.0
CA A:GLY200 4.5 17.4 1.0
N A:ILE166 4.5 17.7 1.0
CA A:ILE198 4.5 23.3 1.0
CA A:GLN199 4.5 19.6 1.0
N A:VAL167 4.5 17.5 1.0
CB A:ASP201 4.6 18.5 1.0
CA A:ILE166 4.7 17.7 1.0
CA A:ASP201 4.7 16.6 1.0
C A:PRO196 4.8 23.8 1.0
O A:HOH421 4.8 23.4 1.0
CG2 A:VAL167 4.9 20.9 1.0

Calcium binding site 4 out of 6 in 8k5y

Go back to Calcium Binding Sites List in 8k5y
Calcium binding site 4 out of 6 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:18.5
occ:1.00
 OE2 B:GLU208 2.3 22.7 1.0
O B:GLY183 2.3 19.5 1.0
O B:LEU187 2.3 19.3 1.0
OD1 B:ASP182 2.3 19.2 1.0
OD2 B:ASP205 2.3 18.2 1.0
O B:ASP185 2.3 20.4 1.0
CD B:GLU208 3.5 21.6 1.0
CG B:ASP205 3.5 18.3 1.0
C B:LEU187 3.5 18.7 1.0
CG B:ASP182 3.5 19.4 1.0
C B:GLY183 3.5 21.4 1.0
C B:ASP185 3.5 21.6 1.0
N B:LEU187 3.9 20.8 1.0
N B:ASP185 3.9 21.9 1.0
OD2 B:ASP182 4.0 22.2 1.0
C B:LYS184 4.1 21.9 1.0
N B:GLY183 4.1 21.2 1.0
CB B:ASP205 4.2 17.2 1.0
CA B:LEU187 4.2 22.4 1.0
CA B:ASP185 4.3 21.5 1.0
OE1 B:GLU208 4.3 21.7 1.0
C B:ASP182 4.3 20.3 1.0
C B:GLY186 4.4 19.9 1.0
OD1 B:ASP205 4.4 18.7 1.0
CG B:GLU208 4.4 20.8 1.0
N B:ASP182 4.4 20.1 1.0
CA B:GLY183 4.4 21.2 1.0
N B:LYS184 4.4 21.2 1.0
CB B:LEU187 4.4 27.7 1.0
CA B:LYS184 4.5 22.2 1.0
O B:LYS184 4.5 22.6 1.0
N B:LEU188 4.5 17.2 1.0
N B:GLY186 4.5 21.1 1.0
CB B:ASP182 4.7 21.5 1.0
CA B:LEU188 4.7 16.4 1.0
CA B:ASP182 4.7 20.4 1.0
CA B:GLY186 4.7 20.5 1.0
O B:ASP182 4.8 24.1 1.0

Calcium binding site 5 out of 6 in 8k5y

Go back to Calcium Binding Sites List in 8k5y
Calcium binding site 5 out of 6 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:31.0
occ:1.00
 O B:GLU208 2.3 22.4 1.0
O B:ASP206 2.4 20.9 1.0
OD2 B:ASP131 2.4 24.1 1.0
OD1 B:ASP206 2.4 21.2 1.0
CG B:ASP131 3.2 27.2 1.0
OD1 B:ASP131 3.3 31.3 1.0
C B:ASP206 3.3 20.4 1.0
CG B:ASP206 3.3 21.4 1.0
C B:GLU208 3.5 21.5 1.0
CA B:ASP206 3.7 19.4 1.0
OG B:SER129 4.0 20.4 1.0
CB B:ASP206 4.0 20.2 1.0
OD2 B:ASP206 4.2 25.1 1.0
CD1 B:TRP210 4.3 19.6 1.0
N B:GLU208 4.3 20.7 1.0
N B:LEU209 4.3 20.8 1.0
N B:ASP207 4.4 19.8 1.0
CA B:LEU209 4.4 22.0 1.0
C B:ASP207 4.5 22.8 1.0
CA B:GLU208 4.5 20.6 1.0
CB B:ASP131 4.6 25.3 1.0
O B:HOH423 4.6 28.4 1.0
CA B:ASP207 4.7 22.3 1.0
N B:TRP210 4.7 20.7 1.0
NE1 B:TRP210 4.9 19.2 1.0
O B:ASP207 5.0 24.7 1.0

Calcium binding site 6 out of 6 in 8k5y

Go back to Calcium Binding Sites List in 8k5y
Calcium binding site 6 out of 6 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:18.6
occ:1.00
 O B:GLN199 2.3 18.6 1.0
O B:ASP165 2.3 16.0 1.0
O B:GLY197 2.3 19.6 1.0
OD1 B:ASP201 2.3 17.6 1.0
O B:HOH424 2.4 19.3 1.0
O B:HOH418 2.4 17.2 1.0
CG B:ASP201 3.4 18.3 1.0
C B:GLN199 3.5 18.7 1.0
C B:GLY197 3.5 22.5 1.0
C B:ASP165 3.5 15.2 1.0
OD2 B:ASP201 3.9 18.7 1.0
C B:ILE198 4.1 19.9 1.0
N B:GLN199 4.1 18.6 1.0
N B:ASP201 4.2 16.3 1.0
O B:ILE198 4.2 19.4 1.0
N B:GLY200 4.3 18.5 1.0
CA B:GLY200 4.3 17.2 1.0
N B:GLY197 4.4 22.1 1.0
C B:GLY200 4.4 17.0 1.0
O B:GLY195 4.4 20.8 1.0
CA B:ASP165 4.4 16.2 1.0
O B:ALA164 4.4 20.2 1.0
CA B:GLY197 4.4 23.1 1.0
N B:ILE198 4.4 22.8 1.0
N B:ILE166 4.5 15.5 1.0
CA B:ILE198 4.5 21.5 1.0
CA B:GLN199 4.5 18.1 1.0
O B:HOH525 4.5 22.7 1.0
CB B:ASP201 4.6 17.4 1.0
N B:VAL167 4.6 15.0 1.0
CA B:ILE166 4.6 15.4 1.0
O B:HOH410 4.6 26.7 1.0
C B:PRO196 4.7 21.4 1.0
CA B:ASP201 4.8 16.1 1.0
O B:HOH428 4.9 21.2 1.0
CG2 B:VAL167 4.9 18.7 1.0

Reference:

R.Nishikawa-Shimono, M.Kuwabara, S.Fujisaki, D.Matsuda, M.Endo, M.Kamitani, A.Futamura, Y.Nomura, T.Yamaguchi-Sasaki, T.Yabuuchi, C.Yamaguchi, N.Tanaka-Yamamoto, S.Satake, K.Abe-Sato, K.Funayama, M.Sakata, S.Takahashi, K.Hirano, T.Fukunaga, Y.Uozumi, S.Kato, Y.Tamura, T.Nakamori, M.Mima, C.Mishima-Tsumagari, D.Nozawa, Y.Imai, T.Asami. Discovery of Novel Indole Derivatives As Potent and Selective Inhibitors of Prommp-9 Activation. Bioorg.Med.Chem.Lett. V. 97 29541 2023.
ISSN: ESSN 1464-3405
PubMed: 37952596
DOI: 10.1016/J.BMCL.2023.129541
Page generated: Thu Jul 10 06:12:21 2025

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