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Calcium 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:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor, PDB code: 7xgj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7xgj

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Calcium binding site 1 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca203

b:17.1
occ:1.00
 O A:ASP80 2.2 19.9 1.0
OD2 A:ASP100 2.3 8.4 1.0
O A:GLY78 2.3 15.3 1.0
OE2 A:GLU103 2.3 8.5 1.0
O A:LEU82 2.3 12.1 1.0
OD1 A:ASP77 2.4 12.4 1.0
CG A:ASP100 3.3 8.1 1.0
C A:ASP80 3.4 19.0 1.0
C A:GLY78 3.5 15.4 1.0
C A:LEU82 3.5 12.5 1.0
CD A:GLU103 3.5 8.4 1.0
CG A:ASP77 3.6 12.8 1.0
N A:ASP80 3.8 19.1 1.0
CB A:ASP100 3.9 8.0 1.0
C A:LYS79 4.1 19.1 1.0
N A:LEU82 4.1 13.5 1.0
N A:GLY78 4.1 14.0 1.0
CA A:ASP80 4.2 19.1 1.0
OD2 A:ASP77 4.2 13.2 1.0
OD1 A:ASP100 4.3 8.0 1.0
C A:ASP77 4.3 13.6 1.0
N A:ASP77 4.3 12.5 1.0
CA A:LEU82 4.3 13.3 1.0
CG A:GLU103 4.3 8.3 1.0
C A:GLY81 4.4 14.1 1.0
CA A:GLY78 4.4 14.3 1.0
N A:GLY81 4.4 17.3 1.0
N A:LYS79 4.4 17.1 1.0
O A:LYS79 4.4 19.8 1.0
OE1 A:GLU103 4.4 8.6 1.0
CA A:LYS79 4.5 18.4 1.0
N A:LEU83 4.5 11.6 1.0
CA A:GLY81 4.6 15.4 1.0
CA A:ASP77 4.6 12.8 1.0
CB A:LEU82 4.6 13.9 1.0
CB A:ASP77 4.7 12.8 1.0
O A:ASP77 4.7 14.0 1.0
CA A:LEU83 4.8 10.8 1.0
O A:GLY81 5.0 13.4 1.0

Calcium binding site 2 out of 9 in 7xgj

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Calcium binding site 2 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca204

b:15.2
occ:1.00
 O A:ASP60 2.2 10.1 1.0
O A:HOH301 2.3 3.7 1.0
O A:GLY92 2.4 8.0 1.0
O A:GLY94 2.4 7.0 1.0
OD1 A:ASP96 2.6 6.6 1.0
C A:ASP60 3.3 10.7 1.0
C A:GLY92 3.6 8.1 1.0
C A:GLY94 3.6 7.0 1.0
CG A:ASP96 3.6 6.5 1.0
O A:HOH303 3.6 18.2 1.0
O A:ALA59 3.8 12.6 1.0
CA A:ASP60 3.9 11.3 1.0
OD2 A:ASP96 4.0 6.1 1.0
N A:GLY94 4.1 7.4 1.0
C A:VAL93 4.2 7.8 1.0
O A:GLY90 4.2 9.0 1.0
N A:ASP96 4.3 6.8 1.0
N A:ILE61 4.4 10.7 1.0
CA A:GLY94 4.4 7.2 1.0
N A:GLY92 4.4 8.5 1.0
CA A:GLY92 4.4 8.3 1.0
O A:VAL93 4.5 8.0 1.0
N A:GLY95 4.5 6.9 1.0
N A:VAL93 4.5 7.9 1.0
OE2 A:GLU58 4.5 19.2 1.0
O A:HOH308 4.5 7.0 1.0
CA A:VAL93 4.6 7.9 1.0
CA A:GLY95 4.6 7.0 1.0
CA A:ILE61 4.7 10.6 1.0
C A:ALA59 4.7 12.6 1.0
C A:GLY95 4.7 7.0 1.0
CB A:ASP96 4.7 6.6 1.0
N A:MET62 4.7 9.6 1.0
CA A:ASP96 4.8 6.6 1.0
N A:ASP60 4.8 11.6 1.0
CG A:MET62 4.9 9.5 1.0
C A:THR91 4.9 8.6 1.0

Calcium binding site 3 out of 9 in 7xgj

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Calcium binding site 3 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca205

b:25.4
occ:1.00
 O A:GLU103 2.4 7.5 1.0
OD2 A:ASP26 2.4 9.6 1.0
O A:ASP101 2.5 8.8 1.0
OD1 A:ASP101 2.7 8.7 1.0
CG A:ASP26 3.1 9.5 1.0
OD1 A:ASP26 3.1 9.7 1.0
C A:ASP101 3.5 8.5 1.0
C A:GLU103 3.5 7.8 1.0
CG A:ASP101 3.7 8.7 1.0
CA A:ASP101 4.0 8.5 1.0
OG1 A:THR24 4.2 7.2 1.0
CA A:LEU104 4.2 7.6 1.0
N A:LEU104 4.3 7.7 1.0
CB A:ASP101 4.4 8.5 1.0
N A:GLU103 4.4 8.1 1.0
C A:ASP102 4.4 8.2 1.0
CB A:ASP26 4.5 9.3 1.0
N A:ASP102 4.5 8.4 1.0
NH2 A:ARG67 4.5 18.1 1.0
OD2 A:ASP101 4.6 8.9 1.0
CD1 A:TRP105 4.6 7.5 1.0
CA A:GLU103 4.6 8.0 1.0
O A:ASP102 4.7 8.5 1.0
CA A:ASP102 4.7 8.4 1.0
N A:TRP105 4.8 7.3 1.0

Calcium binding site 4 out of 9 in 7xgj

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Calcium binding site 4 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca206

b:25.0
occ:1.00
 O A:ARG67 2.2 15.6 1.0
O B:GLU69 2.2 19.1 1.0
O B:ARG67 2.4 21.1 1.0
O A:GLU69 2.5 14.6 1.0
O B:HOH313 2.7 1.4 1.0
C B:GLU69 3.3 20.9 1.0
C A:GLU69 3.4 15.8 1.0
C A:ARG67 3.4 15.4 1.0
C B:ARG67 3.6 21.5 1.0
N B:GLU69 3.9 21.9 1.0
N A:GLU69 3.9 16.2 1.0
C A:TRP68 4.1 15.9 1.0
N A:HIS70 4.1 14.8 1.0
N A:ARG67 4.1 15.0 1.0
N B:HIS70 4.1 18.8 1.0
CA B:HIS70 4.2 17.9 1.0
C B:TRP68 4.2 20.9 1.0
CA A:GLU69 4.2 17.1 1.0
CA B:GLU69 4.2 22.6 1.0
CB A:TRP68 4.2 15.9 1.0
CA A:ARG67 4.3 15.7 1.0
CA A:HIS70 4.3 15.0 1.0
N A:TRP68 4.3 15.4 1.0
CB B:HIS70 4.3 17.8 1.0
CB B:TRP68 4.4 20.4 1.0
CA A:TRP68 4.4 15.8 1.0
N B:ARG67 4.4 22.2 1.0
N B:TRP68 4.5 20.9 1.0
CG A:ARG67 4.5 16.4 1.0
CG B:ARG67 4.5 23.9 1.0
CB A:HIS70 4.5 14.8 1.0
O A:TRP68 4.5 16.2 1.0
CA B:ARG67 4.5 22.5 1.0
CA B:TRP68 4.5 20.6 1.0
O B:TRP68 4.7 21.0 1.0
CB B:GLU69 4.9 24.5 1.0
CB A:ARG67 4.9 16.4 1.0
CB A:GLU69 5.0 18.7 1.0

Calcium binding site 5 out of 9 in 7xgj

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Calcium binding site 5 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca203

b:33.2
occ:1.00
 O B:ASP80 2.1 32.9 1.0
O B:LEU82 2.2 25.5 1.0
O B:GLY78 2.4 25.7 1.0
OE2 B:GLU103 2.4 25.5 1.0
OD1 B:ASP77 2.4 28.2 1.0
OD2 B:ASP100 2.5 21.5 1.0
C B:ASP80 3.3 30.9 1.0
C B:LEU82 3.4 27.0 1.0
C B:GLY78 3.5 27.2 1.0
CD B:GLU103 3.6 27.3 1.0
CG B:ASP77 3.6 28.4 1.0
CG B:ASP100 3.6 21.2 1.0
N B:LEU82 3.7 32.4 1.0
C B:ASP77 3.8 27.7 1.0
O B:ASP77 3.9 29.9 1.0
N B:GLY78 3.9 27.4 1.0
C B:GLY81 4.0 32.4 1.0
CA B:LEU82 4.0 30.4 1.0
N B:ASP80 4.1 29.8 1.0
N B:ASP77 4.1 25.0 1.0
N B:GLY81 4.2 31.1 1.0
CA B:ASP80 4.2 29.8 1.0
CA B:GLY81 4.2 31.0 1.0
CB B:ASP100 4.3 20.8 1.0
C B:LYS79 4.3 29.6 1.0
CA B:GLY78 4.3 26.9 1.0
CA B:ASP77 4.3 26.4 1.0
OE1 B:GLU103 4.3 29.2 1.0
CB B:LEU82 4.4 32.8 1.0
OD2 B:ASP77 4.4 29.8 1.0
N B:LEU83 4.4 24.5 1.0
CB B:ASP77 4.6 27.2 1.0
O B:LYS79 4.6 30.3 1.0
N B:LYS79 4.6 28.4 1.0
O B:GLY81 4.6 35.3 1.0
CG B:GLU103 4.6 27.3 1.0
OD1 B:ASP100 4.6 22.0 1.0
CA B:LYS79 4.8 29.4 1.0
CA B:LEU83 4.8 22.4 1.0

Calcium binding site 6 out of 9 in 7xgj

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Calcium binding site 6 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca204

b:15.9
occ:1.00
 O B:HOH301 2.2 10.7 1.0
O B:GLY92 2.2 17.4 1.0
O B:ASP60 2.3 14.5 1.0
OD1 B:ASP96 2.4 15.4 1.0
O B:GLY94 2.4 16.1 1.0
C B:ASP60 3.3 15.4 1.0
CG B:ASP96 3.4 15.0 1.0
C B:GLY92 3.5 17.2 1.0
C B:GLY94 3.5 15.2 1.0
O B:ALA59 3.7 16.3 1.0
OD2 B:ASP96 3.9 14.6 1.0
CA B:ASP60 4.0 16.0 1.0
C B:VAL93 4.0 15.5 1.0
N B:GLY94 4.1 15.2 1.0
O B:VAL93 4.3 14.7 1.0
N B:ASP96 4.3 15.1 1.0
O B:GLY90 4.3 21.9 1.0
CA B:GLY94 4.3 15.1 1.0
N B:VAL93 4.4 16.4 1.0
N B:ILE61 4.4 15.2 1.0
CA B:GLY92 4.4 17.8 1.0
CA B:VAL93 4.5 15.9 1.0
N B:GLY95 4.5 15.1 1.0
OE2 B:GLU58 4.5 29.8 1.0
N B:GLY92 4.6 18.3 1.0
CA B:GLY95 4.6 15.4 1.0
C B:GLY95 4.6 15.5 1.0
C B:ALA59 4.6 17.3 1.0
CA B:ILE61 4.7 15.1 1.0
CH2 B:TRP11 4.7 30.4 1.0
CB B:ASP96 4.7 14.8 1.0
N B:MET62 4.7 13.7 1.0
CG B:MET62 4.8 13.2 1.0
N B:ASP60 4.8 16.7 1.0
CA B:ASP96 4.9 15.2 1.0
C B:THR91 4.9 19.6 1.0

Calcium binding site 7 out of 9 in 7xgj

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Calcium binding site 7 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 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:Ca205

b:69.8
occ:1.00
 O B:GLU103 2.5 26.3 1.0
O B:ASP101 2.7 25.4 1.0
OD1 B:ASP26 2.9 36.9 1.0
OG1 B:THR24 3.3 23.6 1.0
CG B:ASP26 3.4 33.2 1.0
C B:ASP101 3.5 26.2 1.0
OD2 B:ASP26 3.5 34.1 1.0
OD1 B:ASP101 3.6 31.9 1.0
C B:GLU103 3.7 28.9 1.0
CD1 B:TRP105 3.8 25.4 1.0
CA B:ASP101 4.1 26.1 1.0
N B:GLU103 4.3 29.2 1.0
CG B:ASP101 4.4 29.4 1.0
NE1 B:TRP105 4.4 25.9 1.0
N B:ASP102 4.5 26.0 1.0
CB B:ASP26 4.5 32.0 1.0
CA B:LEU104 4.5 33.5 1.0
N B:LEU104 4.5 32.5 1.0
N B:TRP105 4.6 30.6 1.0
CB B:THR24 4.6 23.6 1.0
C B:ASP102 4.6 28.1 1.0
CA B:GLU103 4.6 28.6 1.0
CA B:ASP102 4.7 26.9 1.0
CB B:ASP101 4.8 28.1 1.0
CG B:TRP105 4.9 26.4 1.0
O B:ASP100 5.0 20.3 1.0

Calcium binding site 8 out of 9 in 7xgj

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Calcium binding site 8 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 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:Ca203

b:60.5
occ:1.00
 O C:LEU82 1.9 72.1 1.0
O C:GLY78 1.9 91.2 1.0
OD2 C:ASP100 2.1 45.9 1.0
O C:ASP80 2.9 66.3 1.0
OE2 C:GLU103 3.1 86.3 1.0
C C:LEU82 3.1 76.3 1.0
C C:GLY78 3.1 84.5 1.0
CG C:ASP100 3.3 53.1 1.0
OD1 C:ASP77 3.6 66.0 1.0
CD C:GLU103 3.7 85.6 1.0
CG C:GLU103 3.7 87.9 1.0
CB C:ASP100 3.8 56.1 1.0
N C:GLY78 3.9 84.6 1.0
N C:ASP80 3.9 78.7 1.0
C C:LYS79 3.9 80.9 1.0
C C:ASP80 4.0 73.9 1.0
CA C:GLY78 4.0 85.5 1.0
C C:ASP77 4.0 81.9 1.0
N C:LYS79 4.1 80.0 1.0
N C:LEU83 4.1 71.9 1.0
N C:LEU82 4.1 80.9 1.0
CA C:LEU82 4.1 81.8 1.0
CA C:LYS79 4.2 79.0 1.0
N C:ASP77 4.3 79.3 1.0
O C:ASP77 4.3 79.1 1.0
CA C:LEU83 4.3 65.8 1.0
OD1 C:ASP100 4.3 53.4 1.0
O C:LYS79 4.4 82.7 1.0
CA C:ASP80 4.5 75.3 1.0
CG C:ASP77 4.6 70.8 1.0
CB C:LEU82 4.6 85.9 1.0
CA C:ASP77 4.7 78.7 1.0
OE1 C:GLU103 4.8 87.2 1.0
CD1 C:PHE76 4.9 77.8 1.0
CB C:PHE76 5.0 83.5 1.0
C C:GLY81 5.0 76.1 1.0

Calcium binding site 9 out of 9 in 7xgj

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Calcium binding site 9 out of 9 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 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:Ca204

b:55.6
occ:1.00
 O C:GLY94 2.4 46.5 1.0
O C:ASP60 2.6 63.5 1.0
O C:GLY92 2.8 47.0 1.0
OD1 C:ASP96 2.9 45.1 1.0
C C:GLY92 3.5 49.2 1.0
C C:GLY94 3.5 47.4 1.0
C C:ASP60 3.7 62.9 1.0
C C:VAL93 3.8 47.4 1.0
N C:GLY94 3.8 47.0 1.0
CG C:ASP96 3.9 45.8 1.0
CA C:VAL93 4.0 48.1 1.0
N C:VAL93 4.0 48.8 1.0
O C:GLY90 4.1 47.9 1.0
O C:ALA59 4.1 63.4 1.0
N C:GLY92 4.2 50.6 1.0
CA C:GLY94 4.3 47.5 1.0
N C:ASP96 4.3 48.9 1.0
O C:VAL93 4.3 46.9 1.0
CA C:ASP60 4.3 61.7 1.0
CA C:GLY92 4.4 50.8 1.0
OD2 C:ASP96 4.5 43.8 1.0
N C:GLY95 4.5 47.0 1.0
C C:THR91 4.6 50.5 1.0
CA C:GLY95 4.7 49.5 1.0
C C:GLY95 4.7 49.6 1.0
N C:ILE61 4.8 61.8 1.0
O C:THR91 4.9 48.4 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: Fri Jul 19 05:56:57 2024

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