Atomistry » Calcium » PDB 8gq9-8hb5 » 8h78
Atomistry »
  Calcium »
    PDB 8gq9-8hb5 »
      8h78 »

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

Go back to Calcium Binding Sites List in 8h78
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: Thu Jul 10 05:00:39 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy