Zinc in PDB 7xgj: 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: 7xgj 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) 22.02 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.831, 41.305, 92.467, 90, 96.06, 90
R / Rfree (%) 22.4 / 28

Other elements in 7xgj:

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

Calcium (Ca) 9 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 7xgj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor, PDB code: 7xgj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7xgj

Go back to Zinc Binding Sites List in 7xgj
Zinc binding site 1 out of 6 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:9.2
occ:1.00
 OD1 D:ASP3 1.8 9.2 1.0
NE2 A:HIS121 2.0 6.2 1.0
NE2 A:HIS125 2.1 7.6 1.0
NE2 A:HIS131 2.2 10.8 1.0
CG D:ASP3 2.4 9.3 1.0
OD2 D:ASP3 2.5 9.3 1.0
CD2 A:HIS131 2.9 10.8 1.0
CE1 A:HIS121 3.0 6.2 1.0
CD2 A:HIS121 3.0 6.2 1.0
CD2 A:HIS125 3.1 7.5 1.0
CE1 A:HIS125 3.1 7.6 1.0
CE1 A:HIS131 3.3 10.8 1.0
CB D:ASP3 3.9 9.4 1.0
CG A:HIS131 4.1 10.8 1.0
ND1 A:HIS121 4.1 6.2 1.0
CG A:HIS121 4.2 6.3 1.0
ND1 A:HIS125 4.2 7.5 1.0
CG A:HIS125 4.2 7.5 1.0
ND1 A:HIS131 4.3 10.5 1.0
N47 D:GZS1 4.4 13.7 1.0
C50 D:GZS1 4.5 12.9 1.0
O A:HOH312 4.5 6.3 1.0
C51 D:GZS1 4.7 12.7 1.0
CA D:ASP3 4.8 9.7 1.0
C D:ASP3 4.8 9.6 1.0
CE A:MET139 4.8 11.2 1.0
C49 D:GZS1 5.0 13.3 1.0

Zinc binding site 2 out of 6 in 7xgj

Go back to Zinc Binding Sites List in 7xgj
Zinc binding site 2 out of 6 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:12.0
occ:1.00
 ND1 A:HIS98 1.9 8.4 1.0
NE2 A:HIS85 1.9 7.1 1.0
NE2 A:HIS70 2.0 14.2 1.0
OD2 A:ASP72 2.0 15.7 1.0
CE1 A:HIS98 2.8 8.5 1.0
CE1 A:HIS85 2.8 7.1 1.0
CG A:HIS98 2.9 8.2 1.0
CD2 A:HIS85 2.9 7.2 1.0
CG A:ASP72 2.9 16.3 1.0
CE1 A:HIS70 2.9 14.1 1.0
CD2 A:HIS70 3.0 14.5 1.0
OD1 A:ASP72 3.3 16.1 1.0
CB A:HIS98 3.3 7.8 1.0
NE2 A:HIS98 3.9 8.6 1.0
ND1 A:HIS85 3.9 7.2 1.0
CD2 A:HIS98 4.0 8.4 1.0
CG A:HIS85 4.0 7.3 1.0
ND1 A:HIS70 4.0 14.2 1.0
CG A:HIS70 4.1 14.4 1.0
CB A:ASP72 4.2 16.4 1.0
O A:TYR74 4.5 14.5 1.0
CE1 A:PHE87 4.6 9.2 1.0
CE2 A:PHE76 4.7 11.6 1.0
CZ A:PHE76 4.7 11.5 1.0
CA A:HIS98 4.7 7.5 1.0

Zinc binding site 3 out of 6 in 7xgj

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Zinc binding site 3 out of 6 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:31.8
occ:1.00
 NE2 B:HIS125 1.9 27.8 1.0
OD1 E:ASP3 2.1 28.7 1.0
NE2 B:HIS121 2.2 39.9 1.0
OD2 E:ASP3 2.4 31.6 1.0
CG E:ASP3 2.5 33.0 1.0
NE2 B:HIS131 2.6 56.1 1.0
CE1 B:HIS125 2.9 27.4 1.0
CD2 B:HIS125 2.9 27.6 1.0
CE1 B:HIS121 3.0 40.6 1.0
CD2 B:HIS121 3.2 38.3 1.0
CD2 B:HIS131 3.2 55.6 1.0
CE1 B:HIS131 3.5 57.2 1.0
CB E:ASP3 4.0 34.0 1.0
ND1 B:HIS125 4.0 27.3 1.0
C45 E:GZS1 4.0 49.1 1.0
CG B:HIS125 4.1 27.1 1.0
ND1 B:HIS121 4.1 39.1 1.0
CG B:HIS121 4.2 36.1 1.0
CG B:HIS131 4.2 56.7 1.0
ND1 B:HIS131 4.3 56.2 1.0
C46 E:GZS1 4.4 50.7 1.0
C50 E:GZS1 4.7 51.3 1.0
C44 E:GZS1 4.7 46.9 1.0
CE B:MET139 4.8 44.7 1.0
CA E:ASP3 4.9 34.3 1.0
N47 E:GZS1 4.9 51.8 1.0
O B:HIS121 4.9 28.1 1.0
C E:ASP3 5.0 32.5 1.0
C51 E:GZS1 5.0 49.0 1.0

Zinc binding site 4 out of 6 in 7xgj

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Zinc binding site 4 out of 6 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:12.9
occ:1.00
 NE2 B:HIS70 2.0 16.3 1.0
ND1 B:HIS98 2.0 15.2 1.0
NE2 B:HIS85 2.0 16.9 1.0
OD2 B:ASP72 2.0 16.7 1.0
CE1 B:HIS70 2.9 16.5 1.0
CD2 B:HIS70 2.9 16.8 1.0
CG B:ASP72 2.9 17.0 1.0
CE1 B:HIS98 3.0 15.2 1.0
CD2 B:HIS85 3.0 17.0 1.0
CE1 B:HIS85 3.0 17.1 1.0
CG B:HIS98 3.1 15.6 1.0
OD1 B:ASP72 3.3 16.8 1.0
CB B:HIS98 3.4 16.0 1.0
ND1 B:HIS70 4.0 16.6 1.0
CG B:HIS70 4.1 17.3 1.0
NE2 B:HIS98 4.1 15.2 1.0
ND1 B:HIS85 4.1 17.1 1.0
CD2 B:HIS98 4.1 15.5 1.0
CG B:HIS85 4.1 16.9 1.0
CB B:ASP72 4.2 17.3 1.0
O B:TYR74 4.2 21.3 1.0
CE2 B:PHE76 4.6 24.9 1.0
CZ B:PHE76 4.7 24.5 1.0
CA B:HIS98 4.8 16.4 1.0
CE1 B:PHE87 4.9 23.4 1.0

Zinc binding site 5 out of 6 in 7xgj

Go back to Zinc Binding Sites List in 7xgj
Zinc binding site 5 out of 6 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 5 of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:55.7
occ:1.00
 NE2 C:HIS131 2.1 49.5 1.0
OD2 F:ASP3 2.2 53.5 1.0
NE2 C:HIS125 2.2 43.8 1.0
NE2 C:HIS121 2.3 63.8 1.0
OD1 F:ASP3 2.8 58.1 1.0
CG F:ASP3 2.8 56.9 1.0
CD2 C:HIS131 2.9 50.3 1.0
CE1 C:HIS131 3.0 51.0 1.0
CE1 C:HIS125 3.2 43.6 1.0
CE1 C:HIS121 3.2 64.5 1.0
CD2 C:HIS121 3.2 63.2 1.0
CD2 C:HIS125 3.2 42.0 1.0
CG C:HIS131 3.9 53.3 1.0
ND1 C:HIS131 4.0 53.2 1.0
CB F:ASP3 4.3 55.6 1.0
ND1 C:HIS125 4.3 43.2 1.0
ND1 C:HIS121 4.3 63.7 1.0
CG C:HIS125 4.4 42.5 1.0
CG C:HIS121 4.4 61.7 1.0
C45 F:GZS1 4.8 69.8 1.0
O64 F:GZS1 4.9 68.8 1.0
O C:MET139 4.9 90.4 1.0
N47 F:GZS1 5.0 69.3 1.0

Zinc binding site 6 out of 6 in 7xgj

Go back to Zinc Binding Sites List in 7xgj
Zinc binding site 6 out of 6 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 6 of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:54.5
occ:1.00
 NE2 C:HIS85 2.2 45.2 1.0
NE2 C:HIS70 2.3 62.4 1.0
OD2 C:ASP72 2.4 59.9 1.0
ND1 C:HIS98 2.8 70.8 1.0
CD2 C:HIS85 2.8 45.9 1.0
CE1 C:HIS70 3.1 64.9 1.0
CE1 C:HIS85 3.3 44.9 1.0
CG C:HIS98 3.4 70.6 1.0
CB C:HIS98 3.4 69.0 1.0
CG C:ASP72 3.4 66.0 1.0
CD2 C:HIS70 3.4 64.7 1.0
OD1 C:ASP72 3.7 68.3 1.0
CE1 C:HIS98 3.8 72.9 1.0
CG C:HIS85 4.0 47.3 1.0
ND1 C:HIS85 4.2 43.3 1.0
ND1 C:HIS70 4.3 66.8 1.0
CG C:HIS70 4.5 65.9 1.0
CD2 C:HIS98 4.5 71.9 1.0
O C:TYR74 4.6 87.9 1.0
CE2 C:PHE76 4.6 79.2 1.0
CA C:HIS98 4.7 66.2 1.0
NE2 C:HIS98 4.7 74.3 1.0
CB C:ASP72 4.8 67.5 1.0
N C:HIS98 4.9 62.9 1.0
CZ C:PHE76 4.9 77.3 1.0
CE2 C:PHE87 4.9 49.6 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 15:04:41 2024

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