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Calcium in PDB 8k5x: 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: 8k5x 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) 22.01 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.388, 73.176, 76.163, 90, 103.66, 90
R / Rfree (%) 17.3 / 20.6

Other elements in 8k5x:

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
Chlorine (Cl) 1 atom

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 8k5x). 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: 8k5x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8k5x

Go back to Calcium Binding Sites List in 8k5x
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:17.0
occ:1.00
 OE2 A:GLU208 2.2 15.4 1.0
O A:GLY183 2.3 21.1 1.0
O A:LEU187 2.3 14.4 1.0
OD2 A:ASP205 2.3 14.1 1.0
OD1 A:ASP182 2.4 14.6 1.0
O A:ASP185 2.4 17.4 1.0
CD A:GLU208 3.4 17.9 1.0
CG A:ASP182 3.4 16.5 1.0
CG A:ASP205 3.5 16.0 1.0
C A:GLY183 3.5 22.3 1.0
C A:LEU187 3.5 14.7 1.0
C A:ASP185 3.6 17.6 1.0
N A:LEU187 3.9 16.3 1.0
OD2 A:ASP182 3.9 16.0 1.0
N A:ASP185 3.9 20.3 1.0
C A:LYS184 4.1 22.1 1.0
CB A:ASP205 4.2 15.0 1.0
N A:GLY183 4.2 20.9 1.0
CA A:ASP185 4.2 20.4 1.0
CG A:GLU208 4.3 16.7 1.0
CA A:LEU187 4.3 16.6 1.0
OE1 A:GLU208 4.3 15.8 1.0
OD1 A:ASP205 4.3 17.5 1.0
N A:ASP182 4.4 17.5 1.0
C A:GLY186 4.4 15.8 1.0
N A:LYS184 4.4 21.8 1.0
CA A:LYS184 4.4 22.9 1.0
C A:ASP182 4.4 19.5 1.0
CA A:GLY183 4.5 21.8 1.0
N A:LEU188 4.5 13.2 1.0
CD1 A:LEU187 4.6 19.5 1.0
N A:GLY186 4.6 18.2 1.0
O A:LYS184 4.6 21.9 1.0
CB A:ASP182 4.7 17.1 1.0
CA A:LEU188 4.7 12.8 1.0
CG A:LEU187 4.7 18.6 1.0
CA A:ASP182 4.7 19.1 1.0
O A:HOH507 4.8 34.8 1.0
CA A:GLY186 4.8 15.9 1.0
O A:ASP182 4.9 19.5 1.0

Calcium binding site 2 out of 6 in 8k5x

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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:32.8
occ:1.00
 O A:ASP206 2.3 16.9 1.0
O A:GLU208 2.4 18.7 1.0
OD2 A:ASP131 2.4 20.2 1.0
OD1 A:ASP206 2.5 15.2 1.0
O A:HOH411 2.6 23.7 1.0
O A:HOH517 2.7 34.6 1.0
C A:ASP206 3.2 16.5 1.0
CG A:ASP131 3.3 25.0 1.0
CG A:ASP206 3.3 16.9 1.0
OD1 A:ASP131 3.5 23.3 1.0
C A:GLU208 3.5 19.2 1.0
CA A:ASP206 3.6 16.5 1.0
CB A:ASP206 3.9 17.4 1.0
OG A:SER129 4.0 18.4 1.0
OD2 A:ASP206 4.2 18.4 1.0
N A:GLU208 4.2 18.3 1.0
CD1 A:TRP210 4.2 14.4 1.0
N A:ASP207 4.3 18.1 1.0
CA A:LEU209 4.3 19.7 1.0
N A:LEU209 4.3 19.8 1.0
C A:ASP207 4.4 17.4 1.0
O A:HOH473 4.5 22.3 1.0
CA A:GLU208 4.5 17.1 1.0
CA A:ASP207 4.6 18.5 1.0
N A:TRP210 4.6 18.9 1.0
CB A:ASP131 4.7 22.7 1.0
NE1 A:TRP210 4.8 15.5 1.0
O A:ASP207 4.9 18.3 1.0
C A:LEU209 5.0 19.2 1.0

Calcium binding site 3 out of 6 in 8k5x

Go back to Calcium Binding Sites List in 8k5x
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:16.3
occ:1.00
 O A:GLN199 2.3 13.0 1.0
O A:ASP165 2.3 12.8 1.0
O A:GLY197 2.3 16.1 1.0
O A:HOH418 2.3 16.1 1.0
O A:HOH449 2.3 13.4 1.0
OD1 A:ASP201 2.4 12.9 1.0
CG A:ASP201 3.4 13.2 1.0
C A:ASP165 3.5 13.4 1.0
C A:GLN199 3.5 13.8 1.0
C A:GLY197 3.5 16.8 1.0
OD2 A:ASP201 3.9 13.7 1.0
C A:ILE198 4.0 15.0 1.0
O A:ALA164 4.1 19.4 1.0
N A:GLN199 4.1 14.6 1.0
N A:ASP201 4.1 11.5 1.0
O A:HOH472 4.2 23.7 1.0
O A:ILE198 4.2 12.7 1.0
C A:GLY200 4.3 12.2 1.0
CA A:ASP165 4.3 14.3 1.0
N A:GLY200 4.3 12.2 1.0
N A:GLY197 4.4 18.2 1.0
O A:GLY195 4.4 15.5 1.0
CA A:GLY197 4.4 18.0 1.0
N A:ILE166 4.4 13.6 1.0
CA A:GLY200 4.4 11.8 1.0
N A:ILE198 4.4 16.1 1.0
CA A:GLN199 4.4 14.6 1.0
CA A:ILE198 4.5 16.9 1.0
N A:VAL167 4.5 13.9 1.0
CB A:ASP201 4.6 12.4 1.0
CA A:ILE166 4.6 14.5 1.0
C A:PRO196 4.7 18.1 1.0
CA A:ASP201 4.7 11.7 1.0
O A:HOH426 4.8 14.4 1.0
CG2 A:VAL167 4.9 15.5 1.0
CH2 A:TRP116 5.0 14.2 1.0
O A:PRO196 5.0 16.2 1.0

Calcium binding site 4 out of 6 in 8k5x

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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:12.0
occ:1.00
 O B:LEU187 2.2 12.1 1.0
OE2 B:GLU208 2.2 16.9 1.0
O B:GLY183 2.3 14.6 1.0
O B:ASP185 2.3 16.3 1.0
OD1 B:ASP182 2.4 13.5 1.0
OD2 B:ASP205 2.4 13.0 1.0
C B:LEU187 3.4 13.3 1.0
CG B:ASP205 3.4 12.2 1.0
CD B:GLU208 3.4 15.9 1.0
CG B:ASP182 3.5 13.2 1.0
C B:ASP185 3.5 16.4 1.0
C B:GLY183 3.5 15.1 1.0
N B:LEU187 3.8 15.4 1.0
N B:ASP185 3.9 15.9 1.0
OD2 B:ASP182 4.0 12.2 1.0
C B:LYS184 4.1 17.2 1.0
CA B:LEU187 4.1 15.6 1.0
CB B:ASP205 4.1 11.7 1.0
N B:GLY183 4.2 13.2 1.0
CA B:ASP185 4.2 16.4 1.0
OE1 B:GLU208 4.2 15.5 1.0
C B:GLY186 4.3 15.5 1.0
OD1 B:ASP205 4.3 12.6 1.0
C B:ASP182 4.4 13.6 1.0
N B:ASP182 4.4 13.4 1.0
CG B:GLU208 4.4 15.0 1.0
CB B:LEU187 4.4 19.1 1.0
N B:LYS184 4.4 15.5 1.0
N B:LEU188 4.4 11.6 1.0
O B:LYS184 4.4 16.2 1.0
CA B:GLY183 4.5 14.2 1.0
CA B:LYS184 4.5 17.6 1.0
N B:GLY186 4.5 15.3 1.0
O B:HOH408 4.6 24.4 1.0
CA B:LEU188 4.6 10.8 1.0
CB B:ASP182 4.7 13.3 1.0
CA B:GLY186 4.7 15.5 1.0
CA B:ASP182 4.7 14.1 1.0
O B:ASP182 4.8 13.8 1.0
O B:GLY186 4.9 16.1 1.0

Calcium binding site 5 out of 6 in 8k5x

Go back to Calcium Binding Sites List in 8k5x
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:28.3
occ:1.00
 O B:GLU208 2.3 13.0 1.0
O B:HOH512 2.4 23.1 1.0
OD1 B:ASP206 2.4 13.4 1.0
OD2 B:ASP131 2.4 18.9 1.0
O B:ASP206 2.4 12.7 1.0
CG B:ASP131 3.2 19.4 1.0
OD1 B:ASP131 3.3 21.0 1.0
CG B:ASP206 3.3 13.1 1.0
C B:ASP206 3.3 12.8 1.0
C B:GLU208 3.5 13.7 1.0
CA B:ASP206 3.7 12.7 1.0
OG B:SER129 3.9 13.0 1.0
CB B:ASP206 4.0 12.5 1.0
OD2 B:ASP206 4.2 15.9 1.0
CD1 B:TRP210 4.2 13.8 1.0
N B:GLU208 4.3 13.5 1.0
N B:LEU209 4.3 13.4 1.0
CA B:LEU209 4.4 15.2 1.0
N B:ASP207 4.4 11.8 1.0
C B:ASP207 4.5 14.0 1.0
CB B:ASP131 4.6 18.4 1.0
CA B:GLU208 4.6 14.0 1.0
O B:HOH413 4.6 18.6 1.0
N B:TRP210 4.6 15.4 1.0
CA B:ASP207 4.7 14.0 1.0
NE1 B:TRP210 4.8 13.6 1.0
CB B:SER129 5.0 15.1 1.0
C B:LEU209 5.0 14.7 1.0

Calcium binding site 6 out of 6 in 8k5x

Go back to Calcium Binding Sites List in 8k5x
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:13.7
occ:1.00
 O B:GLY197 2.2 14.3 1.0
O B:GLN199 2.3 12.0 1.0
O B:HOH423 2.3 11.3 1.0
OD1 B:ASP201 2.4 9.3 1.0
O B:ASP165 2.4 9.7 1.0
O B:HOH421 2.4 10.2 1.0
CG B:ASP201 3.4 9.9 1.0
C B:GLY197 3.4 18.3 1.0
C B:GLN199 3.5 12.7 1.0
C B:ASP165 3.5 10.1 1.0
OD2 B:ASP201 3.9 10.2 1.0
C B:ILE198 4.1 16.0 1.0
N B:GLN199 4.2 13.6 1.0
N B:ASP201 4.2 9.0 1.0
O B:ILE198 4.2 17.3 1.0
N B:GLY200 4.3 10.6 1.0
O B:HOH543 4.3 17.9 1.0
N B:GLY197 4.4 15.8 1.0
CA B:GLY200 4.4 10.5 1.0
CA B:GLY197 4.4 17.1 1.0
O B:ALA164 4.4 11.4 1.0
N B:ILE198 4.4 17.6 1.0
CA B:ASP165 4.4 10.7 1.0
O B:GLY195 4.4 15.1 1.0
C B:GLY200 4.4 9.6 1.0
CA B:ILE198 4.4 17.0 1.0
N B:ILE166 4.5 10.3 1.0
CA B:GLN199 4.5 13.3 1.0
O B:HOH434 4.5 17.0 1.0
N B:VAL167 4.6 10.4 1.0
CB B:ASP201 4.6 9.4 1.0
CA B:ILE166 4.6 10.8 1.0
C B:PRO196 4.7 16.0 1.0
CG2 B:VAL167 4.8 11.4 1.0
CA B:ASP201 4.8 9.4 1.0
O B:HOH446 4.9 12.4 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 06:11:51 2025

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