Zinc in PDB 7xjo: 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: 7xjo was solved by M.Kamitani, M.Mima, T.Takeuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.10 / 2.00
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.977, 128.977, 91.027, 90, 90, 120
R / Rfree (%) 19.9 / 24.3

Other elements in 7xjo:

The structure of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Calcium (Ca) 7 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 7xjo). 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: 7xjo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7xjo

Go back to Zinc Binding Sites List in 7xjo
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:7.8
occ:1.00
 OD2 C:ASP10 2.0 7.3 1.0
NE2 A:HIS131 2.0 9.9 1.0
NE2 A:HIS121 2.0 6.1 1.0
NE2 A:HIS125 2.1 7.6 1.0
OD1 C:ASP10 2.7 7.6 1.0
CG C:ASP10 2.7 8.1 1.0
O A:HOH365 2.8 8.0 1.0
CD2 A:HIS131 3.0 9.9 1.0
CD2 A:HIS121 3.0 6.6 1.0
CE1 A:HIS131 3.0 10.1 1.0
CE1 A:HIS121 3.0 6.5 1.0
CE1 A:HIS125 3.1 7.5 1.0
CD2 A:HIS125 3.1 7.8 1.0
ND1 A:HIS131 4.1 9.7 1.0
CG A:HIS131 4.1 9.8 1.0
O C:HOH107 4.1 11.0 1.0
CG A:HIS121 4.2 6.5 1.0
ND1 A:HIS121 4.2 6.2 1.0
ND1 A:HIS125 4.2 7.6 1.0
CB C:ASP10 4.2 8.5 1.0
CG A:HIS125 4.2 8.1 1.0
O C:HOH105 4.6 12.0 1.0
CG C:DAB11 4.7 12.2 1.0
CAS C:OUL7 4.9 7.2 1.0
CA A:PRO141 5.0 8.6 1.0
CE A:MET139 5.0 7.4 1.0
C C:ASP10 5.0 10.1 1.0
O A:PRO141 5.0 9.3 1.0

Zinc binding site 2 out of 4 in 7xjo

Go back to Zinc Binding Sites List in 7xjo
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:8.7
occ:1.00
 OD2 A:ASP72 1.9 12.5 1.0
NE2 A:HIS85 2.0 7.8 1.0
NE2 A:HIS70 2.0 7.9 1.0
ND1 A:HIS98 2.0 7.3 1.0
CG A:ASP72 2.9 11.5 1.0
CE1 A:HIS85 2.9 7.2 1.0
CE1 A:HIS98 2.9 7.3 1.0
CE1 A:HIS70 3.0 8.2 1.0
CD2 A:HIS70 3.0 8.0 1.0
CD2 A:HIS85 3.0 7.3 1.0
CG A:HIS98 3.0 7.6 1.0
OD1 A:ASP72 3.2 10.8 1.0
CB A:HIS98 3.4 7.6 1.0
ND1 A:HIS85 4.0 7.7 1.0
NE2 A:HIS98 4.1 7.3 1.0
ND1 A:HIS70 4.1 8.0 1.0
CG A:HIS70 4.1 8.2 1.0
CG A:HIS85 4.1 7.3 1.0
CD2 A:HIS98 4.1 7.5 1.0
CB A:ASP72 4.2 11.7 1.0
O A:TYR74 4.4 10.5 1.0
CZ A:PHE76 4.6 8.6 1.0
O A:HOH387 4.7 7.6 1.0
CE1 A:PHE87 4.7 12.2 1.0
CE2 A:PHE76 4.8 8.7 1.0
CA A:HIS98 4.9 7.7 1.0

Zinc binding site 3 out of 4 in 7xjo

Go back to Zinc Binding Sites List in 7xjo
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:21.4
occ:1.00
 NE2 B:HIS125 2.0 16.6 1.0
OD1 D:ASP10 2.0 16.6 1.0
NE2 B:HIS121 2.1 22.0 1.0
NE2 B:HIS131 2.1 30.8 1.0
O D:HOH101 2.6 22.6 1.0
OD2 D:ASP10 2.7 17.3 1.0
CG D:ASP10 2.7 18.9 1.0
CD2 B:HIS125 2.9 18.6 1.0
CD2 B:HIS121 2.9 24.0 1.0
CD2 B:HIS131 3.0 30.4 1.0
CE1 B:HIS131 3.1 30.3 1.0
CE1 B:HIS125 3.1 20.0 1.0
CE1 B:HIS121 3.2 25.8 1.0
CG B:HIS131 4.0 33.1 1.0
ND1 B:HIS131 4.0 32.0 1.0
O D:HOH104 4.1 28.1 1.0
CG B:HIS125 4.1 19.5 1.0
CG B:HIS121 4.1 22.9 1.0
CB D:ASP10 4.1 19.8 1.0
ND1 B:HIS125 4.2 20.2 1.0
ND1 B:HIS121 4.2 23.9 1.0
O D:HOH102 4.5 32.9 1.0
CB D:DAB11 4.6 25.2 1.0
O D:ASP10 4.8 20.0 1.0
CE B:MET139 4.8 27.5 1.0
C D:ASP10 4.9 21.1 1.0

Zinc binding site 4 out of 4 in 7xjo

Go back to Zinc Binding Sites List in 7xjo
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:15.0
occ:1.00
 OD2 B:ASP72 1.8 13.5 1.0
NE2 B:HIS85 1.9 16.5 1.0
NE2 B:HIS70 2.0 10.3 1.0
ND1 B:HIS98 2.0 14.8 1.0
CE1 B:HIS85 2.8 17.5 1.0
CG B:ASP72 2.8 13.7 1.0
CD2 B:HIS70 2.9 10.7 1.0
CE1 B:HIS98 3.0 14.4 1.0
CD2 B:HIS85 3.0 17.2 1.0
CG B:HIS98 3.1 14.3 1.0
CE1 B:HIS70 3.1 11.2 1.0
OD1 B:ASP72 3.3 14.8 1.0
CB B:HIS98 3.4 14.8 1.0
ND1 B:HIS85 4.0 18.8 1.0
CG B:HIS70 4.1 10.8 1.0
CG B:HIS85 4.1 17.3 1.0
CB B:ASP72 4.1 14.1 1.0
NE2 B:HIS98 4.1 13.5 1.0
ND1 B:HIS70 4.2 11.7 1.0
CD2 B:HIS98 4.2 13.8 1.0
O B:TYR74 4.5 17.3 1.0
CZ B:PHE76 4.6 14.2 1.0
CE1 B:PHE87 4.6 23.1 1.0
CE2 B:PHE76 4.7 13.7 1.0
O B:HOH338 4.8 13.3 1.0
CA B:HIS98 4.9 14.5 1.0

Reference:

T.Takeuchi, M.Hayashi, T.Tamita, Y.Nomura, N.Kojima, A.Mitani, T.Takeda, K.Hitaka, Y.Kato, M.Kamitani, M.Mima, H.Toki, M.Ohkubo, A.Nozoe, H.Kakinuma. Discovery of Aryloxyphenyl-Heptapeptide Hybrids As Potent and Selective Matrix Metalloproteinase-2 Inhibitors For the Treatment of Idiopathic Pulmonary Fibrosis. J.Med.Chem. V. 65 8493 2022.
ISSN: ISSN 0022-2623
PubMed: 35687819
DOI: 10.1021/ACS.JMEDCHEM.2C00613
Page generated: Wed Oct 30 15:07:29 2024

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