Atomistry » Calcium » PDB 8jxa-8op8 » 8k5w
Atomistry »
  Calcium »
    PDB 8jxa-8op8 »
      8k5w »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy