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Calcium in PDB 8k5w: 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: 8k5w 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) 21.57 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.319, 73.002, 75.994, 90, 102.57, 90
R / Rfree (%) 22.5 / 27.3

Other elements in 8k5w:

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 8k5w). 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: 8k5w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8k5w

Go back to Calcium Binding Sites List in 8k5w
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:29.1
occ:1.00
 O A:ASP185 2.2 29.4 1.0
OE2 A:GLU208 2.2 28.7 1.0
OD2 A:ASP205 2.3 31.5 1.0
O A:LEU187 2.3 30.9 1.0
OD1 A:ASP182 2.3 30.1 1.0
O A:GLY183 2.4 31.4 1.0
C A:ASP185 3.4 29.7 1.0
CG A:ASP205 3.4 31.1 1.0
CG A:ASP182 3.4 29.5 1.0
C A:LEU187 3.5 29.6 1.0
CD A:GLU208 3.5 29.0 1.0
C A:GLY183 3.6 33.5 1.0
N A:ASP185 3.8 31.0 1.0
N A:LEU187 3.9 30.6 1.0
OD2 A:ASP182 4.0 26.6 1.0
C A:LYS184 4.0 35.0 1.0
CA A:ASP185 4.1 31.9 1.0
CB A:ASP205 4.1 29.6 1.0
CA A:LEU187 4.1 33.0 1.0
N A:GLY183 4.3 31.6 1.0
C A:GLY186 4.3 31.5 1.0
CB A:LEU187 4.3 36.9 1.0
OE1 A:GLU208 4.3 29.4 1.0
CG A:GLU208 4.3 29.1 1.0
O A:LYS184 4.4 33.0 1.0
N A:ASP182 4.4 30.9 1.0
OD1 A:ASP205 4.4 30.5 1.0
C A:ASP182 4.4 29.3 1.0
N A:GLY186 4.4 29.6 1.0
CA A:LYS184 4.5 38.7 1.0
N A:LYS184 4.5 34.7 1.0
N A:LEU188 4.5 26.0 1.0
CA A:GLY183 4.6 33.6 1.0
CB A:ASP182 4.7 31.2 1.0
CA A:GLY186 4.7 32.0 1.0
CA A:ASP182 4.7 31.3 1.0
CA A:LEU188 4.7 25.1 1.0
O A:ASP182 4.8 31.0 1.0
O A:GLY186 4.9 29.5 1.0

Calcium binding site 2 out of 6 in 8k5w

Go back to Calcium Binding Sites List in 8k5w
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:42.0
occ:1.00
 O A:ASP206 2.2 33.5 1.0
OD2 A:ASP131 2.3 30.0 1.0
OD1 A:ASP206 2.3 28.9 1.0
O A:GLU208 2.4 29.4 1.0
CG A:ASP131 3.1 33.0 1.0
C A:ASP206 3.1 32.1 1.0
OD1 A:ASP131 3.3 33.6 1.0
CG A:ASP206 3.3 31.4 1.0
C A:GLU208 3.5 30.2 1.0
CA A:ASP206 3.6 32.0 1.0
CB A:ASP206 3.9 31.5 1.0
OG A:SER129 4.0 30.2 1.0
CD1 A:TRP210 4.2 27.6 1.0
N A:ASP207 4.2 31.2 1.0
N A:GLU208 4.3 29.6 1.0
OD2 A:ASP206 4.3 39.0 1.0
N A:LEU209 4.3 30.4 1.0
CA A:LEU209 4.3 31.4 1.0
CB A:ASP131 4.5 29.1 1.0
C A:ASP207 4.5 30.8 1.0
N A:TRP210 4.5 30.6 1.0
CA A:GLU208 4.6 30.2 1.0
CA A:ASP207 4.7 29.7 1.0
NE1 A:TRP210 4.8 28.7 1.0
C A:LEU209 4.9 32.3 1.0
N A:ASP206 5.0 32.1 1.0
CB A:SER129 5.0 31.7 1.0

Calcium binding site 3 out of 6 in 8k5w

Go back to Calcium Binding Sites List in 8k5w
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:31.5
occ:1.00
 O A:GLY197 2.1 27.8 1.0
O A:ASP165 2.2 26.0 1.0
O A:GLN199 2.3 25.3 1.0
OD1 A:ASP201 2.5 29.2 1.0
C A:GLY197 3.4 34.1 1.0
C A:ASP165 3.4 30.1 1.0
CG A:ASP201 3.5 32.9 1.0
C A:GLN199 3.5 31.5 1.0
OD2 A:ASP201 4.0 28.9 1.0
C A:ILE198 4.1 32.1 1.0
N A:GLY197 4.1 38.7 1.0
N A:ASP201 4.1 27.6 1.0
CA A:GLY197 4.2 37.2 1.0
O A:ALA164 4.2 37.4 1.0
N A:GLN199 4.2 32.5 1.0
CA A:ASP165 4.2 31.9 1.0
O A:ILE198 4.2 30.2 1.0
C A:GLY200 4.3 30.4 1.0
O A:GLY195 4.3 31.3 1.0
N A:GLY200 4.3 32.2 1.0
CA A:GLY200 4.4 33.5 1.0
N A:ILE198 4.4 31.4 1.0
N A:ILE166 4.4 27.9 1.0
CA A:GLN199 4.5 30.5 1.0
CA A:ILE198 4.5 34.4 1.0
CA A:ILE166 4.6 32.4 1.0
C A:PRO196 4.6 39.6 1.0
N A:VAL167 4.6 29.6 1.0
CB A:ASP201 4.6 34.5 1.0
O A:HOH416 4.7 24.8 1.0
CA A:ASP201 4.7 29.7 1.0
CH2 A:TRP116 4.7 32.0 1.0
O A:PRO196 4.9 40.1 1.0

Calcium binding site 4 out of 6 in 8k5w

Go back to Calcium Binding Sites List in 8k5w
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:42.7
occ:1.00
 OD2 B:ASP205 2.2 39.8 1.0
O B:LEU187 2.2 35.0 1.0
O B:ASP185 2.2 42.7 1.0
OD1 B:ASP182 2.2 43.8 1.0
O B:GLY183 2.3 49.9 1.0
OE2 B:GLU208 2.3 48.4 1.0
CG B:ASP182 3.3 44.5 1.0
C B:LEU187 3.4 39.9 1.0
CG B:ASP205 3.4 39.0 1.0
C B:ASP185 3.4 40.4 1.0
CD B:GLU208 3.5 50.7 1.0
C B:GLY183 3.6 48.5 1.0
OD2 B:ASP182 3.7 41.7 1.0
N B:LEU187 3.8 43.3 1.0
N B:ASP185 4.0 40.9 1.0
C B:LYS184 4.0 52.6 1.0
CA B:LEU187 4.1 44.7 1.0
CB B:ASP205 4.1 37.8 1.0
N B:GLY183 4.1 39.5 1.0
C B:GLY186 4.2 44.6 1.0
O B:LYS184 4.2 47.8 1.0
C B:ASP182 4.2 40.8 1.0
CA B:ASP185 4.3 39.6 1.0
CB B:LEU187 4.3 48.2 1.0
N B:ASP182 4.3 45.8 1.0
OD1 B:ASP205 4.3 38.7 1.0
CG B:GLU208 4.4 47.6 1.0
N B:LEU188 4.4 40.2 1.0
OE1 B:GLU208 4.4 49.3 1.0
N B:GLY186 4.4 37.8 1.0
CA B:GLY183 4.5 43.3 1.0
N B:LYS184 4.5 51.2 1.0
CA B:GLY186 4.5 39.2 1.0
CB B:ASP182 4.5 43.7 1.0
CA B:LYS184 4.6 54.6 1.0
O B:ASP182 4.6 45.0 1.0
CA B:ASP182 4.6 42.6 1.0
CA B:LEU188 4.6 34.8 1.0
O B:GLY186 4.8 42.4 1.0

Calcium binding site 5 out of 6 in 8k5w

Go back to Calcium Binding Sites List in 8k5w
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:65.9
occ:1.00
 O B:GLU208 2.3 37.3 1.0
O B:ASP206 2.4 41.5 1.0
OD2 B:ASP131 2.4 48.8 1.0
OD1 B:ASP206 2.6 41.9 1.0
CG B:ASP131 3.2 48.6 1.0
OD1 B:ASP131 3.2 59.3 1.0
C B:ASP206 3.3 39.2 1.0
C B:GLU208 3.4 41.4 1.0
CG B:ASP206 3.6 39.0 1.0
CA B:ASP206 3.9 40.8 1.0
OG B:SER129 3.9 46.1 1.0
CA B:LEU209 4.1 42.7 1.0
N B:LEU209 4.1 44.3 1.0
CD1 B:TRP210 4.2 31.1 1.0
N B:GLU208 4.3 47.0 1.0
CB B:ASP206 4.3 39.2 1.0
OD2 B:ASP206 4.3 43.1 1.0
N B:ASP207 4.4 42.8 1.0
C B:ASP207 4.4 44.0 1.0
N B:TRP210 4.5 40.7 1.0
CA B:GLU208 4.5 45.2 1.0
CB B:ASP131 4.6 43.9 1.0
CA B:ASP207 4.7 44.1 1.0
NE1 B:TRP210 4.7 29.4 1.0
C B:LEU209 4.8 40.2 1.0
O B:ASP207 5.0 46.5 1.0

Calcium binding site 6 out of 6 in 8k5w

Go back to Calcium Binding Sites List in 8k5w
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:34.7
occ:1.00
 O B:HOH430 2.1 30.4 1.0
O B:GLN199 2.1 32.4 1.0
O B:HOH413 2.2 36.5 1.0
O B:ASP165 2.3 28.7 1.0
O B:GLY197 2.4 37.5 1.0
OD1 B:ASP201 2.4 32.4 1.0
C B:GLN199 3.4 34.7 1.0
CG B:ASP201 3.4 34.3 1.0
C B:ASP165 3.5 33.7 1.0
C B:GLY197 3.6 42.5 1.0
OD2 B:ASP201 3.9 31.6 1.0
C B:ILE198 4.0 40.5 1.0
N B:GLN199 4.0 36.5 1.0
N B:ASP201 4.2 33.2 1.0
O B:GLY195 4.2 40.3 1.0
O B:ILE198 4.2 39.9 1.0
O B:ALA164 4.2 34.9 1.0
N B:GLY200 4.3 33.9 1.0
CA B:GLN199 4.3 38.7 1.0
C B:GLY200 4.3 35.1 1.0
CA B:ASP165 4.4 34.3 1.0
N B:GLY197 4.4 40.0 1.0
CA B:GLY200 4.4 36.1 1.0
N B:ILE198 4.5 39.7 1.0
N B:ILE166 4.5 30.3 1.0
CA B:GLY197 4.5 40.7 1.0
CA B:ILE198 4.6 39.5 1.0
N B:VAL167 4.6 32.3 1.0
CB B:ASP201 4.6 32.9 1.0
C B:PRO196 4.6 40.4 1.0
CA B:ILE166 4.6 31.2 1.0
CG2 B:VAL167 4.7 34.0 1.0
CA B:ASP201 4.8 33.1 1.0
CH2 B:TRP116 4.9 39.5 1.0
O B:PRO196 4.9 43.2 1.0
O B:GLY200 5.0 35.0 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: Fri Jul 19 10:51:26 2024

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