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

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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: Thu Oct 31 08:34:46 2024

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