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

Calcium binding site 1 out of 7 in 7xjo

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Calcium binding site 1 out of 7 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:7.4
occ:1.00
 OE2 A:GLU103 2.2 8.1 1.0
O A:GLY78 2.2 9.0 1.0
O A:LEU82 2.3 6.1 1.0
OD2 A:ASP100 2.3 7.9 1.0
OD1 A:ASP77 2.3 7.7 1.0
O A:ASP80 2.4 9.1 1.0
CD A:GLU103 3.4 8.6 1.0
CG A:ASP100 3.4 7.6 1.0
C A:ASP80 3.4 9.6 1.0
C A:LEU82 3.4 6.5 1.0
C A:GLY78 3.5 10.2 1.0
CG A:ASP77 3.5 8.2 1.0
N A:ASP80 3.7 10.5 1.0
N A:LEU82 3.9 7.2 1.0
C A:LYS79 4.0 12.3 1.0
OD2 A:ASP77 4.0 7.5 1.0
CB A:ASP100 4.0 7.6 1.0
CA A:ASP80 4.1 10.3 1.0
CA A:LEU82 4.1 7.0 1.0
N A:GLY78 4.2 8.2 1.0
OE1 A:GLU103 4.2 8.7 1.0
N A:ASP77 4.3 8.8 1.0
C A:ASP77 4.3 8.1 1.0
OD1 A:ASP100 4.3 7.8 1.0
C A:GLY81 4.4 7.8 1.0
CG A:GLU103 4.4 8.9 1.0
N A:LYS79 4.4 12.2 1.0
CA A:GLY78 4.4 8.9 1.0
O A:LYS79 4.4 13.2 1.0
N A:GLY81 4.5 9.1 1.0
CB A:LEU82 4.5 7.4 1.0
CA A:LYS79 4.5 13.1 1.0
N A:LEU83 4.5 6.1 1.0
CA A:ASP77 4.6 8.6 1.0
CB A:ASP77 4.7 8.2 1.0
O A:HOH388 4.7 21.4 1.0
CA A:GLY81 4.7 8.6 1.0
O A:ASP77 4.7 6.9 1.0
CA A:LEU83 4.7 6.2 1.0
CD2 A:LEU83 4.9 6.1 1.0
O A:GLY81 5.0 7.8 1.0

Calcium binding site 2 out of 7 in 7xjo

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Calcium binding site 2 out of 7 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:21.9
occ:1.00
 O A:HOH318 2.3 16.5 1.0
O A:GLY94 2.4 11.8 1.0
O A:ASP60 2.4 10.8 1.0
OD1 A:ASP96 2.5 12.3 1.0
O A:HOH337 2.6 16.4 1.0
O A:GLY92 2.6 14.4 1.0
C A:ASP60 3.5 12.5 1.0
CG A:ASP96 3.5 12.3 1.0
C A:GLY94 3.5 11.5 1.0
C A:GLY92 3.7 15.6 1.0
C A:VAL93 3.8 14.7 1.0
O A:VAL93 4.0 14.2 1.0
OD2 A:ASP96 4.0 11.2 1.0
N A:GLY94 4.0 13.5 1.0
O A:HOH331 4.0 18.9 1.0
O A:ALA59 4.0 17.5 1.0
N A:ASP96 4.2 9.2 1.0
CA A:ASP60 4.2 13.1 1.0
CA A:VAL93 4.2 16.1 1.0
CA A:GLY94 4.3 12.2 1.0
N A:VAL93 4.4 15.6 1.0
N A:ILE61 4.4 11.6 1.0
O A:GLY90 4.5 16.2 1.0
N A:GLY95 4.5 10.7 1.0
CA A:ILE61 4.6 12.6 1.0
CB A:ASP96 4.7 10.5 1.0
C A:GLY95 4.7 9.2 1.0
N A:MET62 4.7 12.0 1.0
CA A:GLY95 4.7 10.0 1.0
CA A:ASP96 4.7 9.4 1.0
O A:HOH348 4.8 12.1 1.0
CA A:GLY92 4.8 16.1 1.0
CH2 A:TRP11 4.9 18.6 1.0
N A:GLY92 4.9 15.8 1.0
C A:ALA59 4.9 16.3 1.0
CG A:MET62 5.0 14.7 1.0

Calcium binding site 3 out of 7 in 7xjo

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Calcium binding site 3 out of 7 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:23.5
occ:1.00
 O A:GLU103 2.2 9.0 1.0
O A:HOH424 2.4 25.7 1.0
O A:ASP101 2.4 7.8 1.0
OD2 A:ASP26 2.4 9.6 1.0
OD1 A:ASP101 2.5 9.6 1.0
O A:HOH344 2.5 18.2 1.0
C A:ASP101 3.3 8.6 1.0
CG A:ASP26 3.3 10.8 1.0
CG A:ASP101 3.3 10.3 1.0
C A:GLU103 3.4 9.6 1.0
OD1 A:ASP26 3.5 9.8 1.0
CA A:ASP101 3.7 8.8 1.0
O A:HOH423 4.0 37.6 1.0
OG1 A:THR24 4.0 11.2 1.0
CD1 A:TRP105 4.0 7.9 1.0
O A:HOH381 4.0 21.2 1.0
CB A:ASP101 4.0 9.6 1.0
OD2 A:ASP101 4.1 10.6 1.0
N A:LEU104 4.1 9.7 1.0
CA A:LEU104 4.1 11.4 1.0
N A:GLU103 4.2 8.8 1.0
N A:ASP102 4.3 8.4 1.0
C A:ASP102 4.4 8.5 1.0
CA A:GLU103 4.4 9.1 1.0
NH2 A:ARG67 4.5 14.0 1.0
NE1 A:TRP105 4.5 7.9 1.0
N A:TRP105 4.5 9.4 1.0
CA A:ASP102 4.7 8.4 1.0
CB A:ASP26 4.7 10.6 1.0
O A:HOH411 4.8 35.7 1.0
C A:LEU104 4.8 10.4 1.0
O A:ASP102 4.9 8.1 1.0

Calcium binding site 4 out of 7 in 7xjo

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Calcium binding site 4 out of 7 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:Ca207

b:26.4
occ:1.00
 O B:ARG67 2.3 10.8 1.0
O B:GLU69 2.4 10.6 1.0
O A:ARG67 2.4 8.8 1.0
O A:GLU69 2.4 8.6 1.0
CL A:CL208 2.7 9.8 1.0
C B:ARG67 3.4 13.2 1.0
C A:ARG67 3.4 9.3 1.0
C A:GLU69 3.4 9.0 1.0
C B:GLU69 3.5 11.2 1.0
N A:GLU69 3.9 9.5 1.0
N B:GLU69 3.9 12.5 1.0
N B:ARG67 4.0 13.8 1.0
C B:TRP68 4.1 13.1 1.0
N A:ARG67 4.1 8.8 1.0
C A:TRP68 4.2 9.3 1.0
CA B:ARG67 4.2 14.4 1.0
CA A:ARG67 4.2 9.2 1.0
N A:HIS70 4.2 8.9 1.0
N B:HIS70 4.3 10.6 1.0
CA B:HIS70 4.3 10.9 1.0
CA A:HIS70 4.3 9.0 1.0
CA A:GLU69 4.3 9.4 1.0
CA B:GLU69 4.3 12.0 1.0
N A:TRP68 4.3 9.2 1.0
CB A:TRP68 4.4 9.6 1.0
N B:TRP68 4.4 12.9 1.0
CB A:ARG67 4.4 9.8 1.0
CB B:HIS70 4.4 10.7 1.0
CB B:TRP68 4.5 13.9 1.0
CB B:ARG67 4.5 17.4 1.0
CB A:HIS70 4.5 8.3 1.0
CA A:TRP68 4.5 9.4 1.0
O B:TRP68 4.5 13.1 1.0
CA B:TRP68 4.5 13.0 1.0
O A:TRP68 4.7 9.5 1.0
O A:HOH428 5.0 16.6 1.0

Calcium binding site 5 out of 7 in 7xjo

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Calcium binding site 5 out of 7 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:13.0
occ:1.00
 OE2 B:GLU103 2.2 15.1 1.0
O B:LEU82 2.2 15.9 1.0
OD1 B:ASP77 2.3 15.6 1.0
O B:GLY78 2.3 12.1 1.0
O B:ASP80 2.3 17.3 1.0
OD2 B:ASP100 2.4 12.7 1.0
CD B:GLU103 3.4 16.2 1.0
C B:LEU82 3.4 17.0 1.0
CG B:ASP77 3.4 14.3 1.0
CG B:ASP100 3.5 13.3 1.0
C B:ASP80 3.5 18.0 1.0
C B:GLY78 3.5 13.0 1.0
N B:ASP80 3.9 17.7 1.0
N B:LEU82 4.0 16.2 1.0
OD2 B:ASP77 4.0 15.8 1.0
CL B:CL206 4.1 14.4 1.0
C B:LYS79 4.1 18.5 1.0
N B:GLY78 4.1 13.1 1.0
CB B:ASP100 4.1 14.1 1.0
C B:ASP77 4.2 13.3 1.0
CA B:ASP80 4.2 18.2 1.0
OE1 B:GLU103 4.2 17.9 1.0
CA B:LEU82 4.3 18.3 1.0
N B:ASP77 4.3 13.1 1.0
C B:GLY81 4.3 16.3 1.0
CG B:GLU103 4.4 15.5 1.0
CA B:GLY78 4.4 12.9 1.0
O B:LYS79 4.4 17.7 1.0
N B:LEU83 4.4 16.4 1.0
OD1 B:ASP100 4.4 12.1 1.0
N B:LYS79 4.5 14.7 1.0
N B:GLY81 4.5 17.0 1.0
CA B:LYS79 4.5 17.5 1.0
CA B:ASP77 4.6 13.4 1.0
O B:ASP77 4.6 13.2 1.0
CB B:ASP77 4.6 13.8 1.0
CA B:LEU83 4.6 16.7 1.0
CB B:LEU82 4.7 20.4 1.0
CA B:GLY81 4.7 16.4 1.0
O B:GLY81 4.8 13.8 1.0
CD2 B:LEU83 5.0 16.6 1.0

Calcium binding site 6 out of 7 in 7xjo

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Calcium binding site 6 out of 7 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:24.7
occ:1.00
 O B:ASP60 2.3 18.5 1.0
O B:HOH308 2.3 18.5 1.0
O B:GLY94 2.4 21.7 1.0
O B:HOH310 2.5 21.3 1.0
O B:GLY92 2.5 20.8 1.0
OD1 B:ASP96 2.6 21.1 1.0
C B:ASP60 3.4 19.5 1.0
C B:GLY94 3.5 18.3 1.0
CG B:ASP96 3.6 19.9 1.0
C B:GLY92 3.7 24.7 1.0
C B:VAL93 3.8 21.7 1.0
N B:GLY94 3.9 21.3 1.0
O B:ALA59 3.9 19.1 1.0
O B:VAL93 4.0 20.5 1.0
O B:HOH331 4.0 31.0 1.0
OD2 B:ASP96 4.0 21.1 1.0
CA B:ASP60 4.2 21.3 1.0
CA B:VAL93 4.2 24.5 1.0
CA B:GLY94 4.3 20.1 1.0
N B:ASP96 4.3 16.8 1.0
O B:GLY90 4.4 29.8 1.0
N B:VAL93 4.4 24.1 1.0
N B:ILE61 4.4 16.3 1.0
N B:GLY95 4.5 18.0 1.0
CA B:ILE61 4.7 17.0 1.0
CB B:ASP96 4.7 17.6 1.0
CA B:GLY95 4.7 17.8 1.0
N B:MET62 4.7 14.8 1.0
CA B:GLY92 4.7 26.1 1.0
C B:GLY95 4.8 17.2 1.0
CA B:ASP96 4.8 16.7 1.0
CH2 B:TRP11 4.8 29.3 1.0
N B:GLY92 4.8 26.7 1.0
C B:ALA59 4.9 20.9 1.0
CG B:MET62 4.9 17.7 1.0
OE1 B:GLU58 5.0 51.0 1.0

Calcium binding site 7 out of 7 in 7xjo

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Calcium binding site 7 out of 7 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:58.0
occ:1.00
 O B:GLU103 2.7 17.1 1.0
OD2 B:ASP26 2.8 31.2 1.0
O B:ASP101 2.9 15.8 1.0
OD1 B:ASP101 2.9 26.7 1.0
OG1 B:THR24 2.9 26.8 1.0
CD1 B:TRP105 3.5 15.0 1.0
C B:ASP101 3.6 15.8 1.0
CG B:ASP26 3.7 34.1 1.0
CB B:THR24 3.7 26.1 1.0
CA B:ASP101 3.7 16.4 1.0
CG B:ASP101 3.8 25.7 1.0
C B:GLU103 4.0 17.2 1.0
NE1 B:TRP105 4.0 14.3 1.0
OD1 B:ASP26 4.1 32.9 1.0
CB B:ASP101 4.3 20.2 1.0
CD B:PRO25 4.5 27.1 1.0
CA B:THR24 4.5 25.4 1.0
OD2 B:ASP101 4.5 36.0 1.0
N B:GLU103 4.6 14.9 1.0
CG B:TRP105 4.6 15.7 1.0
N B:TRP105 4.7 17.3 1.0
N B:ASP102 4.7 15.0 1.0
O B:ASP100 4.8 15.3 1.0
CA B:LEU104 4.8 20.4 1.0
N B:LEU104 4.8 20.4 1.0
CB B:ASP26 4.8 31.6 1.0
CG2 B:THR24 4.9 26.6 1.0
CA B:GLU103 4.9 15.8 1.0
N B:ASP101 5.0 14.6 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: Fri Jul 19 05:57:22 2024

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