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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy