Zinc 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:

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 8k5v). 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: 8k5v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8k5v

Go back to Zinc Binding Sites List in 8k5v
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:27.1
occ:1.00
 NE2 A:HIS230 2.0 26.0 1.0
NE2 A:HIS226 2.0 25.9 1.0
NE2 A:HIS236 2.1 30.1 1.0
SG A:CYS99 2.3 28.5 1.0
CD2 A:HIS226 3.0 27.3 1.0
CD2 A:HIS236 3.0 29.6 1.0
CB A:CYS99 3.0 29.9 1.0
CE1 A:HIS230 3.0 26.9 1.0
CD2 A:HIS230 3.1 28.9 1.0
CE1 A:HIS236 3.1 29.1 1.0
CE1 A:HIS226 3.1 29.0 1.0
CB A:VAL101 4.1 27.7 1.0
CG A:HIS236 4.1 31.9 1.0
CG A:HIS226 4.1 26.8 1.0
ND1 A:HIS230 4.2 26.4 1.0
ND1 A:HIS236 4.2 29.5 1.0
ND1 A:HIS226 4.2 27.9 1.0
CG A:HIS230 4.2 25.8 1.0
CG2 A:VAL101 4.2 28.0 1.0
OE2 A:GLU227 4.4 30.7 1.0
CA A:CYS99 4.5 29.5 1.0
OE1 A:GLU227 4.6 30.4 1.0
CE A:MET244 4.8 25.7 1.0
CD A:GLU227 4.8 28.6 1.0
N A:VAL101 4.9 26.4 1.0
CG1 A:VAL101 4.9 28.4 1.0

Zinc binding site 2 out of 4 in 8k5v

Go back to Zinc Binding Sites List in 8k5v
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:36.2
occ:1.00
 OD2 A:ASP177 2.0 48.3 1.0
ND1 A:HIS203 2.0 30.1 1.0
NE2 A:HIS175 2.1 37.5 1.0
NE2 A:HIS190 2.2 34.2 1.0
CD2 A:HIS175 2.9 40.0 1.0
CG A:ASP177 2.9 43.8 1.0
CE1 A:HIS203 2.9 32.8 1.0
CE1 A:HIS190 3.1 35.8 1.0
CG A:HIS203 3.1 32.5 1.0
CD2 A:HIS190 3.2 32.7 1.0
CE1 A:HIS175 3.2 44.0 1.0
OD1 A:ASP177 3.3 42.0 1.0
CB A:HIS203 3.5 31.1 1.0
NE2 A:HIS203 4.1 34.4 1.0
CG A:HIS175 4.1 46.3 1.0
CD2 A:HIS203 4.2 34.2 1.0
ND1 A:HIS175 4.2 42.3 1.0
ND1 A:HIS190 4.3 31.9 1.0
CB A:ASP177 4.3 47.4 1.0
CG A:HIS190 4.3 33.7 1.0
CZ A:PHE192 4.3 39.8 1.0
CE1 A:PHE192 4.4 42.1 1.0
O A:TYR179 4.4 39.5 1.0
CZ A:PHE181 4.4 34.6 1.0
CE1 A:PHE181 4.8 36.1 1.0
CE2 A:PHE181 4.9 32.9 1.0

Zinc binding site 3 out of 4 in 8k5v

Go back to Zinc Binding Sites List in 8k5v
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:27.6
occ:1.00
 NE2 B:HIS230 2.0 24.8 1.0
NE2 B:HIS236 2.0 28.6 1.0
NE2 B:HIS226 2.2 26.7 1.0
SG B:CYS99 2.3 28.6 1.0
CD2 B:HIS236 2.9 32.6 1.0
CB B:CYS99 2.9 31.1 1.0
CD2 B:HIS230 3.0 24.8 1.0
CE1 B:HIS230 3.0 28.4 1.0
CD2 B:HIS226 3.0 27.9 1.0
CE1 B:HIS236 3.1 31.4 1.0
CE1 B:HIS226 3.2 30.0 1.0
CB B:VAL101 4.0 30.0 1.0
CG B:HIS236 4.1 33.2 1.0
ND1 B:HIS230 4.1 26.9 1.0
CG B:HIS230 4.1 28.2 1.0
ND1 B:HIS236 4.1 28.7 1.0
CG B:HIS226 4.2 26.5 1.0
CG2 B:VAL101 4.2 28.7 1.0
ND1 B:HIS226 4.3 25.7 1.0
OE2 B:GLU227 4.3 30.3 1.0
OE1 B:GLU227 4.4 28.6 1.0
CA B:CYS99 4.4 28.3 1.0
CD B:GLU227 4.7 29.2 1.0
CE B:MET244 4.8 27.6 1.0
CG1 B:VAL101 4.8 29.8 1.0
N B:VAL101 4.9 28.1 1.0
CA B:PRO246 4.9 27.8 1.0
C B:CYS99 5.0 29.5 1.0

Zinc binding site 4 out of 4 in 8k5v

Go back to Zinc Binding Sites List in 8k5v
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:30.2
occ:1.00
 ND1 B:HIS203 2.0 28.2 1.0
OD2 B:ASP177 2.0 32.7 1.0
NE2 B:HIS175 2.0 29.4 1.0
NE2 B:HIS190 2.1 27.6 1.0
CE1 B:HIS203 2.9 31.6 1.0
CG B:ASP177 2.9 28.9 1.0
CD2 B:HIS175 3.0 29.8 1.0
CG B:HIS203 3.1 31.1 1.0
CE1 B:HIS190 3.1 29.1 1.0
CE1 B:HIS175 3.1 31.9 1.0
CD2 B:HIS190 3.2 29.9 1.0
OD1 B:ASP177 3.3 32.0 1.0
CB B:HIS203 3.5 28.6 1.0
NE2 B:HIS203 4.1 30.1 1.0
CG B:HIS175 4.1 28.4 1.0
CD2 B:HIS203 4.1 35.6 1.0
ND1 B:HIS175 4.2 28.6 1.0
ND1 B:HIS190 4.2 27.1 1.0
O B:TYR179 4.2 35.0 1.0
CB B:ASP177 4.2 32.8 1.0
CZ B:PHE192 4.3 36.4 1.0
CG B:HIS190 4.3 27.5 1.0
CE1 B:PHE192 4.4 34.3 1.0
CZ B:PHE181 4.4 32.5 1.0
CE2 B:PHE181 4.8 28.9 1.0
O B:HOH437 4.9 38.2 1.0
CE1 B:PHE181 4.9 33.9 1.0
CB B:TYR179 4.9 31.2 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 08:34:21 2024

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