Zinc in PDB 8h78: Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor

Enzymatic activity of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor:
3.4.24.24;

Protein crystallography data

The structure of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor, PDB code: 8h78 was solved by M.Kamitani, T.Takeuchi, M.Mima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.78 / 2.40
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 79.683, 79.683, 127.434, 90, 90, 90
R / Rfree (%) 26.5 / 31.9

Other elements in 8h78:

The structure of Crystal Structure of Human Mmp-2 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 Mmp-2 Catalytic Domain in Complex with Inhibitor (pdb code 8h78). 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 Mmp-2 Catalytic Domain in Complex with Inhibitor, PDB code: 8h78:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8h78

Go back to Zinc Binding Sites List in 8h78
Zinc binding site 1 out of 4 in the Crystal Structure of Human Mmp-2 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 Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:17.5
occ:1.00
 O1 A:L2U207 1.8 16.9 1.0
NE2 A:HIS121 1.8 13.5 1.0
NE2 A:HIS125 2.0 27.4 1.0
NE2 A:HIS131 2.1 20.1 1.0
C3 A:L2U207 2.7 16.6 1.0
CE1 A:HIS121 2.7 14.6 1.0
CD2 A:HIS121 2.9 14.3 1.0
O2 A:L2U207 3.0 16.1 1.0
CD2 A:HIS131 3.0 18.8 1.0
CE1 A:HIS125 3.0 29.3 1.0
CD2 A:HIS125 3.1 28.0 1.0
CE1 A:HIS131 3.2 21.2 1.0
ND1 A:HIS121 3.8 14.5 1.0
C7 A:L2U207 4.0 16.0 1.0
CG A:HIS121 4.0 14.7 1.0
C6 A:L2U207 4.0 16.2 1.0
C26 A:L2U207 4.1 16.4 1.0
ND1 A:HIS125 4.1 28.7 1.0
C34 A:L2U207 4.1 20.0 1.0
CG A:HIS131 4.2 20.3 1.0
CG A:HIS125 4.2 30.2 1.0
ND1 A:HIS131 4.2 20.6 1.0
C23 A:L2U207 4.4 16.3 1.0
C20 A:L2U207 4.4 15.0 1.0
N25 A:L2U207 4.6 16.3 1.0
CE A:MET139 4.7 17.3 1.0
N35 A:L2U207 4.7 19.5 1.0
O A:ALA140 4.8 20.7 1.0
C22 A:L2U207 4.8 16.4 1.0
C21 A:L2U207 4.9 15.3 1.0
C33 A:L2U207 4.9 19.2 1.0

Zinc binding site 2 out of 4 in 8h78

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Mmp-2 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 Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:24.2
occ:1.00
 ND1 A:HIS98 1.9 13.1 1.0
NE2 A:HIS70 2.0 24.2 1.0
OD2 A:ASP72 2.0 24.5 1.0
NE2 A:HIS85 2.1 24.7 1.0
CE1 A:HIS98 2.8 12.9 1.0
CD2 A:HIS70 2.8 23.4 1.0
CE1 A:HIS85 2.9 24.6 1.0
CG A:ASP72 2.9 26.3 1.0
CG A:HIS98 3.1 15.4 1.0
CE1 A:HIS70 3.1 23.3 1.0
OD1 A:ASP72 3.2 26.6 1.0
CD2 A:HIS85 3.3 23.4 1.0
CB A:HIS98 3.5 16.7 1.0
NE2 A:HIS98 4.0 13.3 1.0
CG A:HIS70 4.0 22.7 1.0
ND1 A:HIS85 4.1 23.6 1.0
ND1 A:HIS70 4.1 22.2 1.0
CD2 A:HIS98 4.1 13.9 1.0
CB A:ASP72 4.2 25.4 1.0
CG A:HIS85 4.3 22.4 1.0
O A:TYR74 4.5 21.1 1.0
CZ A:PHE76 4.5 19.2 1.0
CE1 A:PHE87 4.6 27.0 1.0
CE2 A:PHE76 4.7 19.7 1.0
CA A:HIS98 5.0 16.6 1.0
CZ A:PHE87 5.0 26.6 1.0

Zinc binding site 3 out of 4 in 8h78

Go back to Zinc Binding Sites List in 8h78
Zinc binding site 3 out of 4 in the Crystal Structure of Human Mmp-2 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 Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:49.4
occ:1.00
 NE2 B:HIS121 1.7 25.8 1.0
O1 B:L2U206 2.0 49.3 1.0
NE2 B:HIS125 2.1 64.8 1.0
NE2 B:HIS131 2.5 68.2 1.0
CE1 B:HIS121 2.7 31.6 1.0
C3 B:L2U206 2.8 50.9 1.0
CD2 B:HIS121 2.8 31.0 1.0
CD2 B:HIS125 2.9 63.7 1.0
O2 B:L2U206 3.0 49.1 1.0
CE1 B:HIS125 3.2 66.6 1.0
CD2 B:HIS131 3.3 69.6 1.0
CE1 B:HIS131 3.5 65.2 1.0
C21 B:L2U206 3.6 40.0 1.0
C22 B:L2U206 3.7 40.2 1.0
ND1 B:HIS121 3.8 31.2 1.0
CG B:HIS121 3.9 31.3 1.0
CG B:HIS125 4.1 62.3 1.0
C26 B:L2U206 4.2 48.9 1.0
ND1 B:HIS125 4.2 65.8 1.0
C20 B:L2U206 4.3 39.1 1.0
C23 B:L2U206 4.4 42.6 1.0
CG B:HIS131 4.4 67.2 1.0
ND1 B:HIS131 4.5 63.8 1.0
N25 B:L2U206 4.6 50.8 1.0
C34 B:L2U206 4.6 47.6 1.0
CE B:MET139 4.8 41.4 1.0
N19 B:L2U206 4.8 35.7 1.0
N35 B:L2U206 4.9 45.5 1.0
C28 B:L2U206 4.9 44.9 1.0
C27 B:L2U206 5.0 46.9 1.0
C7 B:L2U206 5.0 40.1 1.0

Zinc binding site 4 out of 4 in 8h78

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Mmp-2 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 Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:34.4
occ:1.00
 OD2 B:ASP72 1.8 17.2 1.0
ND1 B:HIS98 2.0 20.7 1.0
NE2 B:HIS70 2.0 34.9 1.0
NE2 B:HIS85 2.0 34.5 1.0
CG B:ASP72 2.8 23.7 1.0
CE1 B:HIS85 2.9 32.1 1.0
CE1 B:HIS98 2.9 19.6 1.0
CD2 B:HIS70 2.9 31.7 1.0
CG B:HIS98 3.0 21.4 1.0
CE1 B:HIS70 3.0 33.5 1.0
CD2 B:HIS85 3.1 34.0 1.0
CB B:HIS98 3.3 24.6 1.0
OD1 B:ASP72 3.3 30.4 1.0
ND1 B:HIS85 4.0 32.3 1.0
ND1 B:HIS70 4.0 30.6 1.0
NE2 B:HIS98 4.0 19.5 1.0
CG B:HIS70 4.1 32.7 1.0
CD2 B:HIS98 4.1 21.2 1.0
CB B:ASP72 4.1 24.6 1.0
CG B:HIS85 4.2 33.3 1.0
CZ B:PHE76 4.5 37.5 1.0
CE1 B:PHE87 4.6 32.0 1.0
O B:TYR74 4.6 29.7 1.0
CE2 B:PHE76 4.6 40.9 1.0
CA B:HIS98 4.7 27.5 1.0
O B:HOH305 4.9 26.5 1.0

Reference:

T.Takeuchi, Y.Nomura, T.Tamita, R.Nishikawa, H.Kakinuma, N.Kojima, K.Hitaka, Y.Tamura, M.Kamitani, M.Mima, A.Nozoe, M.Hayashi. Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with A Phenylbenzamide-Pentapeptide Hybrid Scaffold. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 36595440
DOI: 10.1021/ACS.JMEDCHEM.2C01698
Page generated: Sat Apr 8 09:15:16 2023

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