Zinc in PDB 8k5y: 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: 8k5y 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) 49.01 / 1.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.53, 73.99, 77.13, 90, 103.36, 90
R / Rfree (%) 17.6 / 19.8

Other elements in 8k5y:

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 8k5y). 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: 8k5y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8k5y

Go back to Zinc Binding Sites List in 8k5y
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:16.3
occ:1.00
 NE2 A:HIS236 2.0 15.2 1.0
NE2 A:HIS226 2.0 14.7 1.0
NE2 A:HIS230 2.1 15.3 1.0
SG A:CYS99 2.3 16.8 1.0
CD2 A:HIS226 3.0 16.1 1.0
CD2 A:HIS236 3.0 15.6 1.0
CB A:CYS99 3.0 17.4 1.0
CD2 A:HIS230 3.0 17.0 1.0
CE1 A:HIS236 3.0 16.4 1.0
CE1 A:HIS230 3.1 17.3 1.0
CE1 A:HIS226 3.1 17.0 1.0
CB A:VAL101 4.1 16.6 1.0
CG A:HIS236 4.1 15.9 1.0
ND1 A:HIS236 4.1 17.1 1.0
CG A:HIS226 4.2 15.8 1.0
ND1 A:HIS230 4.2 16.3 1.0
CG A:HIS230 4.2 15.5 1.0
ND1 A:HIS226 4.2 17.2 1.0
CG2 A:VAL101 4.3 17.6 1.0
OE2 A:GLU227 4.4 18.1 1.0
CA A:CYS99 4.5 18.2 1.0
OE1 A:GLU227 4.5 16.7 1.0
CE A:MET244 4.7 18.0 1.0
CG1 A:VAL101 4.8 17.5 1.0
CD A:GLU227 4.8 18.3 1.0
N A:VAL101 4.9 16.6 1.0

Zinc binding site 2 out of 4 in 8k5y

Go back to Zinc Binding Sites List in 8k5y
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:20.3
occ:1.00
 OD2 A:ASP177 2.0 24.5 1.0
ND1 A:HIS203 2.0 19.3 1.0
NE2 A:HIS175 2.1 19.5 1.0
NE2 A:HIS190 2.1 19.2 1.0
CG A:ASP177 2.9 22.6 1.0
CE1 A:HIS203 2.9 22.0 1.0
CD2 A:HIS175 3.0 18.9 1.0
CE1 A:HIS190 3.1 19.2 1.0
CE1 A:HIS175 3.1 21.3 1.0
CG A:HIS203 3.1 19.5 1.0
CD2 A:HIS190 3.1 19.1 1.0
OD1 A:ASP177 3.3 22.8 1.0
CB A:HIS203 3.5 17.1 1.0
NE2 A:HIS203 4.1 21.1 1.0
CG A:HIS175 4.2 21.9 1.0
ND1 A:HIS190 4.2 17.8 1.0
ND1 A:HIS175 4.2 20.8 1.0
CD2 A:HIS203 4.2 19.9 1.0
CB A:ASP177 4.2 21.8 1.0
CE1 A:PHE192 4.2 26.7 1.0
CG A:HIS190 4.3 17.2 1.0
O A:TYR179 4.4 21.6 1.0
CZ A:PHE181 4.5 21.7 1.0
CZ A:PHE192 4.5 27.7 1.0
O A:HOH424 4.8 30.7 1.0
CE1 A:PHE181 4.8 21.8 1.0
O A:HOH453 4.9 21.9 1.0

Zinc binding site 3 out of 4 in 8k5y

Go back to Zinc Binding Sites List in 8k5y
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:16.1
occ:1.00
 NE2 B:HIS230 2.0 13.8 1.0
NE2 B:HIS226 2.1 14.8 1.0
NE2 B:HIS236 2.1 16.0 1.0
SG B:CYS99 2.3 16.4 1.0
CD2 B:HIS236 3.0 15.2 1.0
CD2 B:HIS226 3.0 16.8 1.0
CD2 B:HIS230 3.0 15.3 1.0
CB B:CYS99 3.0 15.5 1.0
CE1 B:HIS230 3.0 14.4 1.0
CE1 B:HIS226 3.1 16.1 1.0
CE1 B:HIS236 3.2 16.8 1.0
CB B:VAL101 4.1 16.0 1.0
ND1 B:HIS230 4.1 15.5 1.0
CG B:HIS226 4.2 14.7 1.0
CG B:HIS230 4.2 14.2 1.0
CG B:HIS236 4.2 15.3 1.0
ND1 B:HIS226 4.2 15.7 1.0
ND1 B:HIS236 4.2 16.1 1.0
CG2 B:VAL101 4.3 16.4 1.0
OE2 B:GLU227 4.4 16.7 1.0
CA B:CYS99 4.5 16.7 1.0
OE1 B:GLU227 4.5 16.8 1.0
CE B:MET244 4.8 16.1 1.0
CD B:GLU227 4.8 17.9 1.0
CG1 B:VAL101 4.8 16.9 1.0
N B:VAL101 4.9 17.0 1.0
CA B:PRO246 5.0 17.1 1.0

Zinc binding site 4 out of 4 in 8k5y

Go back to Zinc Binding Sites List in 8k5y
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:17.9
occ:1.00
 NE2 B:HIS175 2.0 17.6 1.0
ND1 B:HIS203 2.0 18.4 1.0
OD2 B:ASP177 2.0 17.6 1.0
NE2 B:HIS190 2.1 18.5 1.0
CE1 B:HIS203 2.9 18.6 1.0
CG B:ASP177 3.0 20.7 1.0
CD2 B:HIS175 3.0 19.1 1.0
CE1 B:HIS190 3.0 15.8 1.0
CE1 B:HIS175 3.0 16.6 1.0
CD2 B:HIS190 3.1 16.9 1.0
CG B:HIS203 3.2 16.2 1.0
OD1 B:ASP177 3.3 19.6 1.0
CB B:HIS203 3.5 15.1 1.0
ND1 B:HIS175 4.1 18.4 1.0
NE2 B:HIS203 4.2 19.2 1.0
CG B:HIS175 4.2 19.1 1.0
ND1 B:HIS190 4.2 15.6 1.0
CD2 B:HIS203 4.2 20.8 1.0
CG B:HIS190 4.3 16.0 1.0
CB B:ASP177 4.3 20.3 1.0
O B:TYR179 4.3 18.6 1.0
CE1 B:PHE192 4.4 24.7 1.0
CZ B:PHE181 4.5 19.8 1.0
CZ B:PHE192 4.7 22.8 1.0
O B:HOH427 4.8 27.4 1.0
CE2 B:PHE181 4.9 19.9 1.0
CE1 B:PHE181 5.0 19.5 1.0
CB B:TYR179 5.0 19.0 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: Thu Oct 31 08:35:17 2024

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