Atomistry » Zinc » PDB 8jsz-8k81 » 8k5w
Atomistry »
  Zinc »
    PDB 8jsz-8k81 »
      8k5w »

Zinc 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:

Fluorine (F) 2 atoms
Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor, PDB code: 8k5w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8k5w

Go back to Zinc Binding Sites List in 8k5w
Zinc binding site 1 out of 4 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn301

b:23.0
occ:1.00
 NE2 A:HIS230 2.0 21.3 1.0
NE2 A:HIS236 2.1 22.0 1.0
NE2 A:HIS226 2.1 17.9 1.0
SG A:CYS99 2.2 24.7 1.0
CB A:CYS99 2.9 23.1 1.0
CD2 A:HIS230 3.0 23.0 1.0
CD2 A:HIS236 3.0 23.3 1.0
CD2 A:HIS226 3.0 22.2 1.0
CE1 A:HIS230 3.0 22.9 1.0
CE1 A:HIS226 3.1 21.2 1.0
CE1 A:HIS236 3.1 21.6 1.0
CB A:VAL101 4.0 24.8 1.0
ND1 A:HIS230 4.1 20.0 1.0
CG A:HIS230 4.1 21.3 1.0
CG A:HIS236 4.1 22.7 1.0
ND1 A:HIS236 4.2 20.6 1.0
CG A:HIS226 4.2 21.7 1.0
ND1 A:HIS226 4.2 20.6 1.0
CG2 A:VAL101 4.2 25.1 1.0
OE2 A:GLU227 4.3 23.7 1.0
CA A:CYS99 4.3 24.6 1.0
OE1 A:GLU227 4.4 22.4 1.0
CD A:GLU227 4.7 21.8 1.0
CE A:MET244 4.7 17.5 1.0
CG1 A:VAL101 4.8 27.2 1.0
N A:VAL101 4.9 23.7 1.0
CA A:PRO246 4.9 23.1 1.0
C A:CYS99 4.9 23.2 1.0
CA A:VAL101 5.0 26.3 1.0

Zinc binding site 2 out of 4 in 8k5w

Go back to Zinc Binding Sites List in 8k5w
Zinc binding site 2 out of 4 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn302

b:34.3
occ:1.00
 OD2 A:ASP177 1.8 48.6 1.0
ND1 A:HIS203 2.0 27.5 1.0
NE2 A:HIS190 2.1 29.9 1.0
NE2 A:HIS175 2.1 35.9 1.0
CG A:ASP177 2.8 40.5 1.0
CD2 A:HIS175 2.9 35.5 1.0
CE1 A:HIS203 3.0 26.9 1.0
CG A:HIS203 3.0 28.8 1.0
CE1 A:HIS190 3.0 31.7 1.0
CD2 A:HIS190 3.1 31.3 1.0
OD1 A:ASP177 3.2 35.7 1.0
CE1 A:HIS175 3.2 36.3 1.0
CB A:HIS203 3.3 27.2 1.0
NE2 A:HIS203 4.1 29.2 1.0
CB A:ASP177 4.1 41.9 1.0
CG A:HIS175 4.1 37.4 1.0
CD2 A:HIS203 4.1 28.6 1.0
ND1 A:HIS190 4.2 33.5 1.0
CZ A:PHE192 4.2 34.4 1.0
CE2 A:PHE192 4.2 34.9 1.0
ND1 A:HIS175 4.2 37.4 1.0
CG A:HIS190 4.2 33.2 1.0
O A:TYR179 4.4 41.1 1.0
CZ A:PHE181 4.4 33.0 1.0
CA A:HIS203 4.8 29.8 1.0
CE2 A:PHE181 4.8 33.6 1.0
O A:HOH436 4.9 34.2 1.0
CE1 A:PHE181 4.9 37.9 1.0

Zinc binding site 3 out of 4 in 8k5w

Go back to Zinc Binding Sites List in 8k5w
Zinc binding site 3 out of 4 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn301

b:30.0
occ:1.00
 NE2 B:HIS236 1.8 26.9 1.0
NE2 B:HIS226 2.1 24.1 1.0
NE2 B:HIS230 2.1 26.1 1.0
SG B:CYS99 2.1 33.0 1.0
CE1 B:HIS236 2.8 31.8 1.0
CB B:CYS99 2.9 34.6 1.0
CD2 B:HIS236 2.9 33.0 1.0
CD2 B:HIS226 3.0 26.0 1.0
CD2 B:HIS230 3.0 26.6 1.0
CE1 B:HIS230 3.1 26.6 1.0
CE1 B:HIS226 3.1 27.1 1.0
CB B:VAL101 3.9 40.9 1.0
ND1 B:HIS236 3.9 31.4 1.0
CG B:HIS236 4.0 31.2 1.0
OE2 B:GLU227 4.0 30.1 1.0
CG B:HIS226 4.1 24.8 1.0
CG B:HIS230 4.1 27.0 1.0
CG2 B:VAL101 4.2 36.7 1.0
ND1 B:HIS230 4.2 28.4 1.0
ND1 B:HIS226 4.2 24.3 1.0
CA B:CYS99 4.3 33.7 1.0
OE1 B:GLU227 4.4 29.6 1.0
CD B:GLU227 4.6 32.2 1.0
CG1 B:VAL101 4.7 41.2 1.0
CE B:MET244 4.7 29.3 1.0
N B:VAL101 4.8 40.6 1.0
CA B:PRO246 4.8 31.1 1.0
C B:CYS99 4.9 35.2 1.0
CA B:VAL101 4.9 40.2 1.0
O B:VAL101 5.0 38.6 1.0

Zinc binding site 4 out of 4 in 8k5w

Go back to Zinc Binding Sites List in 8k5w
Zinc binding site 4 out of 4 in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn302

b:42.4
occ:1.00
 OD2 B:ASP177 2.0 57.7 1.0
NE2 B:HIS190 2.0 37.3 1.0
NE2 B:HIS175 2.0 45.0 1.0
ND1 B:HIS203 2.1 39.0 1.0
CG B:ASP177 2.9 53.7 1.0
CE1 B:HIS190 3.0 37.0 1.0
CD2 B:HIS190 3.0 38.5 1.0
CG B:HIS203 3.0 37.4 1.0
CE1 B:HIS203 3.0 38.9 1.0
CD2 B:HIS175 3.0 51.4 1.0
CE1 B:HIS175 3.0 53.2 1.0
OD1 B:ASP177 3.3 49.9 1.0
CB B:HIS203 3.3 36.0 1.0
CZ B:PHE192 4.1 42.9 1.0
ND1 B:HIS190 4.1 36.4 1.0
NE2 B:HIS203 4.1 38.6 1.0
CG B:HIS190 4.1 34.4 1.0
ND1 B:HIS175 4.1 51.4 1.0
CD2 B:HIS203 4.1 42.7 1.0
CG B:HIS175 4.2 52.5 1.0
CE2 B:PHE192 4.2 40.5 1.0
CB B:ASP177 4.2 53.5 1.0
O B:TYR179 4.2 61.8 1.0
CZ B:PHE181 4.6 41.9 1.0
CB B:TYR179 4.8 69.7 1.0
CA B:HIS203 4.8 33.9 1.0
CE2 B:PHE181 4.9 43.9 1.0
NE2 B:GLN169 4.9 55.5 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 Aug 22 11:40:44 2025

Last articles

Zn in 8XV6
Zn in 8XV4
Zn in 8XPT
Zn in 8XSO
Zn in 8XUF
Zn in 8XRM
Zn in 8XU6
Zn in 8XRJ
Zn in 8XSJ
Zn in 8XSF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy