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Calcium in PDB 8k5v: 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: 8k5v 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) 49.17 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.04, 73.82, 77.68, 90, 104.21, 90
R / Rfree (%) 17.8 / 21.7

Other elements in 8k5v:

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

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 8k5v). 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: 8k5v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8k5v

Go back to Calcium Binding Sites List in 8k5v
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:31.6
occ:1.00
 OE2 A:GLU208 2.1 34.9 1.0
OD2 A:ASP205 2.3 31.8 1.0
O A:GLY183 2.3 38.5 1.0
OD1 A:ASP182 2.3 33.9 1.0
O A:LEU187 2.3 35.4 1.0
O A:ASP185 2.4 35.8 1.0
CD A:GLU208 3.4 35.7 1.0
CG A:ASP205 3.4 37.8 1.0
CG A:ASP182 3.4 37.1 1.0
C A:LEU187 3.5 32.4 1.0
C A:GLY183 3.6 39.3 1.0
C A:ASP185 3.6 35.7 1.0
N A:ASP185 3.9 38.1 1.0
OD2 A:ASP182 3.9 37.3 1.0
N A:LEU187 4.0 33.7 1.0
C A:LYS184 4.1 40.2 1.0
N A:GLY183 4.1 37.5 1.0
CB A:ASP205 4.1 35.3 1.0
CG A:GLU208 4.3 35.6 1.0
CA A:ASP185 4.3 36.9 1.0
OE1 A:GLU208 4.3 37.7 1.0
OD1 A:ASP205 4.3 35.7 1.0
CA A:LEU187 4.4 33.1 1.0
N A:ASP182 4.4 33.4 1.0
C A:ASP182 4.4 38.7 1.0
N A:LYS184 4.4 36.0 1.0
CA A:LYS184 4.4 38.2 1.0
C A:GLY186 4.4 35.3 1.0
O A:LYS184 4.5 37.5 1.0
CA A:GLY183 4.5 38.1 1.0
N A:LEU188 4.5 30.3 1.0
CD1 A:LEU187 4.6 47.0 1.0
N A:GLY186 4.6 37.7 1.0
CB A:ASP182 4.7 39.8 1.0
CA A:LEU188 4.7 30.0 1.0
CA A:ASP182 4.7 39.6 1.0
CG A:LEU187 4.8 44.7 1.0
CA A:GLY186 4.8 37.6 1.0
O A:ASP182 4.9 39.7 1.0

Calcium binding site 2 out of 6 in 8k5v

Go back to Calcium Binding Sites List in 8k5v
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:46.0
occ:1.00
 OD2 A:ASP131 2.3 38.6 1.0
O A:ASP206 2.4 38.7 1.0
O A:GLU208 2.4 34.6 1.0
OD1 A:ASP206 2.5 33.8 1.0
O A:HOH402 2.6 40.9 1.0
CG A:ASP131 3.2 46.0 1.0
C A:ASP206 3.3 35.6 1.0
CG A:ASP206 3.3 35.1 1.0
OD1 A:ASP131 3.4 47.0 1.0
C A:GLU208 3.6 32.2 1.0
CA A:ASP206 3.7 33.9 1.0
CB A:ASP206 4.0 35.3 1.0
OG A:SER129 4.1 35.6 1.0
OD2 A:ASP206 4.2 39.0 1.0
N A:GLU208 4.2 32.7 1.0
CD1 A:TRP210 4.3 30.0 1.0
CA A:LEU209 4.3 35.2 1.0
N A:LEU209 4.3 33.5 1.0
N A:ASP207 4.4 34.0 1.0
C A:ASP207 4.4 36.6 1.0
O A:HOH476 4.5 59.2 1.0
O A:HOH441 4.5 35.1 1.0
CA A:GLU208 4.6 31.4 1.0
CB A:ASP131 4.6 41.3 1.0
CA A:ASP207 4.7 36.8 1.0
N A:TRP210 4.7 33.6 1.0
NE1 A:TRP210 4.9 32.9 1.0
O A:ASP207 5.0 37.7 1.0

Calcium binding site 3 out of 6 in 8k5v

Go back to Calcium Binding Sites List in 8k5v
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:33.9
occ:1.00
 O A:GLY197 2.3 32.7 1.0
O A:ASP165 2.3 30.3 1.0
O A:HOH404 2.4 32.1 1.0
O A:HOH438 2.4 33.5 1.0
OD1 A:ASP201 2.4 34.4 1.0
O A:GLN199 2.5 32.0 1.0
C A:ASP165 3.4 31.4 1.0
CG A:ASP201 3.4 38.6 1.0
C A:GLY197 3.5 37.7 1.0
C A:GLN199 3.7 34.9 1.0
OD2 A:ASP201 3.9 34.0 1.0
N A:ASP201 4.2 27.8 1.0
C A:ILE198 4.2 35.1 1.0
O A:ALA164 4.2 39.8 1.0
CA A:ASP165 4.3 32.4 1.0
N A:GLN199 4.3 35.3 1.0
O A:ILE198 4.3 32.4 1.0
C A:GLY200 4.3 26.7 1.0
N A:ILE166 4.4 32.3 1.0
CA A:GLY197 4.4 42.6 1.0
CA A:GLY200 4.4 27.6 1.0
N A:GLY197 4.4 42.6 1.0
O A:HOH409 4.4 43.9 1.0
O A:GLY195 4.5 34.4 1.0
N A:GLY200 4.5 30.2 1.0
N A:ILE198 4.5 36.4 1.0
CA A:ILE198 4.6 38.0 1.0
N A:VAL167 4.6 30.7 1.0
CA A:GLN199 4.6 33.3 1.0
CB A:ASP201 4.6 34.4 1.0
CA A:ILE166 4.7 33.0 1.0
CA A:ASP201 4.7 30.8 1.0
C A:PRO196 4.8 43.3 1.0
O A:HOH413 4.8 38.8 1.0
CG2 A:VAL167 4.9 35.1 1.0
CH2 A:TRP116 4.9 30.9 1.0
O A:PRO196 5.0 40.4 1.0

Calcium binding site 4 out of 6 in 8k5v

Go back to Calcium Binding Sites List in 8k5v
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:30.3
occ:1.00
 OE2 B:GLU208 2.2 39.8 1.0
O B:GLY183 2.3 33.0 1.0
O B:ASP185 2.3 34.3 1.0
OD2 B:ASP205 2.3 31.3 1.0
O B:LEU187 2.3 31.2 1.0
OD1 B:ASP182 2.4 33.6 1.0
CG B:ASP205 3.4 31.2 1.0
CD B:GLU208 3.5 39.2 1.0
C B:ASP185 3.5 33.8 1.0
C B:LEU187 3.5 30.9 1.0
CG B:ASP182 3.5 34.9 1.0
C B:GLY183 3.5 37.0 1.0
N B:LEU187 3.8 31.3 1.0
N B:ASP185 3.9 34.9 1.0
OD2 B:ASP182 4.0 33.2 1.0
C B:LYS184 4.1 37.5 1.0
N B:GLY183 4.1 33.0 1.0
CA B:LEU187 4.2 35.2 1.0
CB B:ASP205 4.2 26.2 1.0
CA B:ASP185 4.2 33.7 1.0
OE1 B:GLU208 4.3 37.5 1.0
CG B:GLU208 4.3 33.1 1.0
C B:GLY186 4.3 34.0 1.0
OD1 B:ASP205 4.3 32.5 1.0
C B:ASP182 4.4 33.9 1.0
N B:ASP182 4.4 34.6 1.0
CB B:LEU187 4.4 41.3 1.0
CA B:GLY183 4.4 34.8 1.0
N B:LYS184 4.5 35.1 1.0
N B:GLY186 4.5 30.4 1.0
O B:LYS184 4.5 36.0 1.0
N B:LEU188 4.5 28.6 1.0
CA B:LYS184 4.6 39.9 1.0
CB B:ASP182 4.7 33.8 1.0
CA B:GLY186 4.7 33.3 1.0
CA B:LEU188 4.7 25.2 1.0
CA B:ASP182 4.7 34.1 1.0
O B:ASP182 4.8 38.0 1.0
O B:GLY186 5.0 32.5 1.0

Calcium binding site 5 out of 6 in 8k5v

Go back to Calcium Binding Sites List in 8k5v
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:43.2
occ:1.00
 O B:HOH477 2.2 50.1 1.0
O B:GLU208 2.3 32.3 1.0
O B:ASP206 2.4 31.7 1.0
OD2 B:ASP131 2.4 34.5 1.0
O B:HOH443 2.5 54.7 1.0
OD1 B:ASP206 2.5 32.1 1.0
CG B:ASP131 3.2 39.4 1.0
OD1 B:ASP131 3.2 44.3 1.0
C B:ASP206 3.4 27.6 1.0
CG B:ASP206 3.4 31.5 1.0
C B:GLU208 3.5 33.3 1.0
CA B:ASP206 3.8 29.6 1.0
OG B:SER129 4.0 29.7 1.0
CB B:ASP206 4.1 30.4 1.0
OD2 B:ASP206 4.3 37.0 1.0
N B:LEU209 4.3 32.1 1.0
N B:GLU208 4.3 30.6 1.0
CA B:LEU209 4.4 35.2 1.0
N B:ASP207 4.4 27.6 1.0
CD1 B:TRP210 4.4 29.1 1.0
C B:ASP207 4.5 35.9 1.0
CA B:GLU208 4.6 31.6 1.0
O B:HOH413 4.6 40.6 1.0
CB B:ASP131 4.6 34.1 1.0
CA B:ASP207 4.7 32.5 1.0
N B:TRP210 4.7 31.4 1.0
NE1 B:TRP210 5.0 29.6 1.0
O B:ASP207 5.0 35.6 1.0

Calcium binding site 6 out of 6 in 8k5v

Go back to Calcium Binding Sites List in 8k5v
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:31.9
occ:1.00
 O B:GLN199 2.3 29.6 1.0
O B:GLY197 2.3 30.8 1.0
O B:ASP165 2.4 27.6 1.0
OD1 B:ASP201 2.4 27.9 1.0
O B:HOH427 2.4 30.4 1.0
O B:HOH404 2.4 27.9 1.0
CG B:ASP201 3.4 30.5 1.0
C B:GLN199 3.5 27.8 1.0
C B:ASP165 3.6 27.6 1.0
C B:GLY197 3.6 37.2 1.0
OD2 B:ASP201 3.9 29.4 1.0
C B:ILE198 4.1 32.5 1.0
N B:GLN199 4.2 28.3 1.0
N B:ASP201 4.2 26.3 1.0
O B:GLY195 4.3 35.9 1.0
O B:ILE198 4.3 32.1 1.0
N B:GLY197 4.4 35.8 1.0
N B:GLY200 4.4 28.9 1.0
C B:GLY200 4.4 28.1 1.0
CA B:GLY200 4.4 29.4 1.0
O B:ALA164 4.4 32.4 1.0
CA B:ASP165 4.4 29.0 1.0
O B:HOH426 4.4 34.4 1.0
CA B:GLY197 4.4 36.8 1.0
CA B:GLN199 4.5 28.5 1.0
N B:ILE198 4.5 36.6 1.0
O B:HOH507 4.5 37.7 1.0
N B:ILE166 4.5 28.2 1.0
CA B:ILE198 4.6 31.8 1.0
N B:VAL167 4.6 25.0 1.0
CB B:ASP201 4.6 27.6 1.0
CA B:ILE166 4.7 26.7 1.0
C B:PRO196 4.7 36.4 1.0
CA B:ASP201 4.8 27.3 1.0
O B:HOH455 4.9 33.9 1.0
CG2 B:VAL167 5.0 27.7 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: Fri Jul 19 10:51:03 2024

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