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Calcium 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:

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 8h78). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor, PDB code: 8h78:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8h78

Go back to Calcium Binding Sites List in 8h78
Calcium 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 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:23.6
occ:1.00
 O A:GLY78 2.0 18.1 1.0
OE2 A:GLU103 2.2 21.7 1.0
O A:ASP80 2.2 14.7 1.0
OD2 A:ASP100 2.3 18.2 1.0
O A:LEU82 2.3 18.1 1.0
OD1 A:ASP77 2.7 13.6 1.0
C A:GLY78 3.3 19.5 1.0
CG A:ASP100 3.3 18.5 1.0
CD A:GLU103 3.5 23.5 1.0
C A:ASP80 3.5 16.4 1.0
C A:LEU82 3.5 17.2 1.0
CG A:ASP77 3.7 13.5 1.0
N A:ASP80 3.8 17.3 1.0
N A:GLY78 3.9 16.1 1.0
CB A:ASP100 3.9 18.3 1.0
N A:LEU82 4.0 17.9 1.0
C A:ASP77 4.0 15.4 1.0
C A:LYS79 4.1 20.4 1.0
N A:ASP77 4.1 17.1 1.0
CA A:GLY78 4.2 17.3 1.0
OD1 A:ASP100 4.2 16.9 1.0
N A:LYS79 4.2 21.9 1.0
CA A:LEU82 4.2 17.7 1.0
OD2 A:ASP77 4.2 11.6 1.0
CA A:ASP80 4.2 16.4 1.0
OE1 A:GLU103 4.2 24.0 1.0
C A:GLY81 4.4 16.9 1.0
O A:ASP77 4.4 15.2 1.0
CA A:LYS79 4.4 22.1 1.0
CG A:GLU103 4.4 23.2 1.0
CA A:ASP77 4.5 15.2 1.0
N A:GLY81 4.5 17.0 1.0
N A:LEU83 4.5 15.6 1.0
O A:LYS79 4.5 20.7 1.0
CB A:LEU82 4.6 17.8 1.0
CB A:ASP77 4.7 14.4 1.0
CA A:GLY81 4.8 16.8 1.0
CA A:LEU83 4.8 15.2 1.0
O A:HOH310 4.9 7.3 1.0

Calcium binding site 2 out of 6 in 8h78

Go back to Calcium Binding Sites List in 8h78
Calcium 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 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:39.4
occ:1.00
 O A:GLY92 1.8 27.8 1.0
O A:ASP60 2.2 19.8 1.0
OD1 A:ASP96 2.6 21.6 1.0
C A:GLY92 3.0 34.5 1.0
O A:GLY94 3.1 37.2 1.0
CG A:ASP96 3.4 19.1 1.0
C A:ASP60 3.4 24.0 1.0
O A:ALA59 3.7 26.0 1.0
OD2 A:ASP96 3.7 18.2 1.0
N A:GLY94 3.7 36.6 1.0
C A:GLY94 3.8 35.3 1.0
CA A:GLY92 3.9 39.3 1.0
C A:VAL93 3.9 38.4 1.0
N A:GLY92 4.0 40.6 1.0
N A:VAL93 4.0 33.2 1.0
CA A:ASP60 4.2 26.9 1.0
CA A:GLY94 4.3 37.0 1.0
CA A:VAL93 4.3 36.5 1.0
O A:VAL93 4.3 43.3 1.0
N A:ILE61 4.5 24.0 1.0
O A:GLY90 4.5 42.2 1.0
N A:ASP96 4.5 22.4 1.0
C A:THR91 4.6 40.6 1.0
CB A:ASP96 4.6 19.9 1.0
C A:ALA59 4.7 29.2 1.0
N A:GLY95 4.8 30.3 1.0
N A:MET62 4.9 23.1 1.0
CA A:ILE61 4.9 23.2 1.0
N A:ASP60 4.9 28.3 1.0
CG A:MET62 4.9 25.9 1.0
OE2 A:GLU58 4.9 68.5 1.0
O A:THR91 4.9 37.1 1.0
CA A:ASP96 4.9 20.6 1.0

Calcium binding site 3 out of 6 in 8h78

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Calcium 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 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:45.9
occ:1.00
 OD2 A:ASP26 2.3 20.6 1.0
O A:GLU103 2.4 20.6 1.0
O A:ASP101 2.5 21.3 1.0
OD1 A:ASP101 2.7 22.1 1.0
CG A:ASP26 3.1 21.1 1.0
O A:HOH321 3.1 22.3 1.0
OD1 A:ASP26 3.2 22.3 1.0
C A:ASP101 3.4 20.0 1.0
C A:GLU103 3.6 19.2 1.0
CG A:ASP101 3.6 22.2 1.0
OG1 A:THR24 3.6 18.8 1.0
CA A:ASP101 3.8 19.9 1.0
CD1 A:TRP105 4.0 12.3 1.0
CB A:ASP101 4.2 20.8 1.0
N A:GLU103 4.2 22.3 1.0
N A:ASP102 4.4 20.6 1.0
N A:LEU104 4.4 17.6 1.0
CA A:LEU104 4.5 15.8 1.0
CB A:ASP26 4.5 21.0 1.0
C A:ASP102 4.5 21.4 1.0
OD2 A:ASP101 4.5 24.9 1.0
CA A:GLU103 4.6 21.5 1.0
NE1 A:TRP105 4.6 12.2 1.0
N A:TRP105 4.7 13.2 1.0
CA A:ASP102 4.7 20.6 1.0
NH2 A:ARG67 4.8 23.8 1.0
CB A:THR24 4.9 22.4 1.0
O A:ASP100 5.0 20.0 1.0

Calcium binding site 4 out of 6 in 8h78

Go back to Calcium Binding Sites List in 8h78
Calcium 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 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
B:Ca203

b:48.8
occ:1.00
 OE2 B:GLU103 2.1 24.7 1.0
O B:GLY78 2.2 53.1 1.0
O B:ASP80 2.2 60.3 1.0
O B:LEU82 2.3 67.1 1.0
OD1 B:ASP77 2.5 25.5 1.0
OD2 B:ASP100 2.6 44.0 1.0
CD B:GLU103 3.4 32.8 1.0
C B:ASP80 3.4 53.7 1.0
C B:GLY78 3.4 48.8 1.0
C B:LEU82 3.5 55.8 1.0
CG B:ASP100 3.5 50.0 1.0
CG B:ASP77 3.7 29.2 1.0
N B:GLY78 3.9 40.5 1.0
CB B:ASP100 4.0 51.7 1.0
N B:ASP80 4.0 60.4 1.0
C B:LYS79 4.0 59.7 1.0
N B:LEU82 4.0 56.3 1.0
C B:ASP77 4.1 35.8 1.0
OE1 B:GLU103 4.2 38.5 1.0
CA B:ASP80 4.2 54.0 1.0
C B:GLY81 4.2 59.2 1.0
CA B:LEU82 4.2 54.1 1.0
N B:ASP77 4.3 38.3 1.0
CA B:GLY78 4.3 45.5 1.0
O B:LYS79 4.3 50.0 1.0
CG B:GLU103 4.3 32.9 1.0
N B:LYS79 4.3 54.9 1.0
N B:GLY81 4.4 53.8 1.0
OD1 B:ASP100 4.4 48.2 1.0
OD2 B:ASP77 4.5 29.7 1.0
O B:ASP77 4.5 37.9 1.0
N B:LEU83 4.5 55.3 1.0
CA B:GLY81 4.5 55.1 1.0
CA B:LYS79 4.5 57.6 1.0
CB B:LEU82 4.6 53.5 1.0
CA B:ASP77 4.6 36.3 1.0
O B:GLY81 4.7 61.2 1.0
CA B:LEU83 4.7 51.2 1.0
CB B:ASP77 4.8 32.5 1.0

Calcium binding site 5 out of 6 in 8h78

Go back to Calcium Binding Sites List in 8h78
Calcium 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 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:Ca204

b:15.9
occ:1.00
 O B:ASP60 2.1 16.6 1.0
O B:GLY92 2.3 18.4 1.0
OD1 B:ASP96 2.4 24.9 1.0
O B:HOH302 2.4 10.0 1.0
O B:HOH304 2.5 11.6 1.0
O B:GLY94 2.6 21.5 1.0
CG B:ASP96 3.3 26.4 1.0
C B:ASP60 3.3 17.4 1.0
C B:GLY94 3.5 20.9 1.0
C B:GLY92 3.5 20.0 1.0
OD2 B:ASP96 3.8 26.7 1.0
N B:GLY94 3.8 22.6 1.0
C B:VAL93 3.9 22.3 1.0
O B:VAL93 4.2 23.4 1.0
CA B:ASP60 4.2 18.8 1.0
O B:ALA59 4.2 18.5 1.0
CA B:GLY94 4.2 21.7 1.0
N B:ASP96 4.2 24.5 1.0
N B:ILE61 4.3 15.8 1.0
CA B:VAL93 4.3 22.8 1.0
N B:VAL93 4.4 21.7 1.0
CA B:ILE61 4.4 16.8 1.0
O B:GLY90 4.4 21.8 1.0
N B:GLY95 4.5 22.6 1.0
CB B:ASP96 4.5 26.4 1.0
O B:HOH310 4.5 18.4 1.0
CA B:GLY92 4.5 19.8 1.0
N B:MET62 4.5 18.1 1.0
N B:GLY92 4.7 20.7 1.0
CA B:ASP96 4.7 25.3 1.0
C B:GLY95 4.7 24.8 1.0
CA B:GLY95 4.7 24.0 1.0
C B:THR91 4.8 22.6 1.0
O B:THR91 4.8 26.1 1.0
CG B:MET62 4.9 19.8 1.0
CH2 B:TRP11 4.9 25.9 1.0
C B:ALA59 5.0 20.3 1.0

Calcium binding site 6 out of 6 in 8h78

Go back to Calcium Binding Sites List in 8h78
Calcium 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 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:Ca205

b:48.8
occ:1.00
 OD2 B:ASP26 2.2 43.6 1.0
OD1 B:ASP101 2.5 40.0 1.0
O B:ASP101 2.8 40.1 1.0
CG B:ASP26 2.8 42.5 1.0
O B:GLU103 2.9 40.5 1.0
OD1 B:ASP26 3.0 43.7 1.0
OG1 B:THR24 3.2 53.5 1.0
CG B:ASP101 3.5 39.8 1.0
C B:ASP101 3.8 40.0 1.0
CD1 B:TRP105 3.9 33.4 1.0
CA B:ASP101 4.1 39.9 1.0
C B:GLU103 4.1 41.5 1.0
CB B:ASP26 4.1 44.6 1.0
CB B:ASP101 4.3 39.7 1.0
OD2 B:ASP101 4.4 42.9 1.0
NE1 B:TRP105 4.5 32.0 1.0
CB B:THR24 4.5 57.0 1.0
CA B:LEU104 4.6 44.5 1.0
N B:TRP105 4.6 52.5 1.0
N B:LEU104 4.8 43.2 1.0
CG B:TRP105 4.9 36.1 1.0
N B:ASP102 4.9 39.1 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: Fri Jul 19 09:22:02 2024

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