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Calcium in PDB 8b2n: Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12

Enzymatic activity of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12

All present enzymatic activity of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12:
3.4.24.65;

Protein crystallography data

The structure of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12, PDB code: 8b2n was solved by J.Potempa, M.Ksiazek, T.Goulas, A.Cuppari, A.Rodriguez-Banqueri, J.L.Arolas, M.Lopez-Pelegrin, I.Garcia-Ferrer, T.Guevara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.69 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.41, 63, 135.37, 90, 90, 90
R / Rfree (%) 19 / 22.8

Other elements in 8b2n:

The structure of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12 (pdb code 8b2n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12, PDB code: 8b2n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8b2n

Go back to Calcium Binding Sites List in 8b2n
Calcium binding site 1 out of 6 in the Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:47.8
occ:1.00
 OE2 A:GLU199 2.4 41.5 1.0
O A:GLU199 2.4 41.3 1.0
OD1 A:ASP124 2.4 43.0 1.0
O A:HOH475 2.4 46.7 1.0
O A:HOH479 2.4 52.1 1.0
O A:GLU201 2.4 39.9 1.0
OD2 A:ASP124 2.7 53.1 1.0
CG A:ASP124 2.9 45.7 1.0
C A:GLU199 3.5 40.7 1.0
CD A:GLU199 3.5 58.5 1.0
C A:GLU201 3.6 42.0 1.0
OG1 A:THR122 4.1 46.8 1.0
CG A:GLU199 4.1 51.0 1.0
CA A:GLU199 4.2 37.0 1.0
CD1 A:TRP203 4.2 34.0 1.0
CA A:PHE202 4.3 41.5 1.0
N A:PHE202 4.4 40.1 1.0
CB A:ASP124 4.4 42.9 1.0
N A:GLU201 4.4 38.2 1.0
C A:ASP200 4.5 43.9 1.0
N A:ASP200 4.5 37.7 1.0
OE1 A:GLU199 4.6 42.8 1.0
NH2 A:ARG165 4.6 73.2 1.0
CA A:GLU201 4.7 37.0 1.0
NE1 A:TRP203 4.7 31.8 1.0
CA A:ASP200 4.7 39.4 1.0
CB A:GLU199 4.8 39.6 1.0
N A:TRP203 4.8 37.7 1.0
CD1 A:PHE202 5.0 55.7 1.0

Calcium binding site 2 out of 6 in 8b2n

Go back to Calcium Binding Sites List in 8b2n
Calcium binding site 2 out of 6 in the Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:32.7
occ:1.00
 O A:GLY192 2.4 32.8 1.0
O A:HOH413 2.4 34.0 1.0
O A:ASP158 2.4 30.6 1.0
O A:GLY190 2.4 36.6 1.0
OD2 A:ASP194 2.4 29.1 1.0
O A:HOH427 2.4 33.2 1.0
CG A:ASP194 3.4 32.4 1.0
C A:ASP158 3.5 31.3 1.0
C A:GLY192 3.6 30.9 1.0
C A:GLY190 3.6 37.9 1.0
OD1 A:ASP194 3.9 29.5 1.0
O A:HOH436 4.0 57.0 1.0
C A:ILE191 4.0 32.9 1.0
N A:GLY192 4.1 29.7 1.0
O A:ILE191 4.2 30.7 1.0
N A:ASP194 4.2 26.0 1.0
O A:ALA157 4.2 35.5 1.0
O A:GLY188 4.3 32.6 1.0
CA A:ASP158 4.4 27.0 1.0
CA A:GLY192 4.4 27.7 1.0
N A:ILE159 4.4 27.0 1.0
N A:ILE191 4.5 32.1 1.0
CA A:ILE191 4.5 30.7 1.0
N A:GLY193 4.5 26.7 1.0
N A:GLY190 4.5 35.0 1.0
CA A:ILE159 4.5 26.4 1.0
CA A:GLY190 4.6 35.1 1.0
CA A:GLY193 4.6 24.9 1.0
C A:GLY193 4.6 28.0 1.0
CB A:ASP194 4.6 29.1 1.0
O A:HOH420 4.7 32.6 1.0
N A:LEU160 4.7 25.4 1.0
CA A:ASP194 4.8 25.5 1.0
C A:SER189 4.8 35.9 1.0
CH2 A:TRP109 4.9 33.5 1.0

Calcium binding site 3 out of 6 in 8b2n

Go back to Calcium Binding Sites List in 8b2n
Calcium binding site 3 out of 6 in the Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:38.0
occ:1.00
 O A:GLY176 2.4 36.4 1.0
O A:GLY178 2.4 39.2 1.0
OE2 A:GLU201 2.4 38.0 1.0
OD1 A:ASP198 2.4 40.5 1.0
O A:ILE180 2.4 34.1 1.0
OD2 A:ASP175 2.4 43.4 1.0
CG A:ASP198 3.4 39.2 1.0
CD A:GLU201 3.6 45.1 1.0
CG A:ASP175 3.6 44.5 1.0
C A:GLY178 3.6 41.7 1.0
C A:GLY176 3.6 41.6 1.0
C A:ILE180 3.6 32.9 1.0
N A:GLY178 3.9 42.1 1.0
N A:ILE180 4.0 32.5 1.0
CG A:GLU201 4.1 39.6 1.0
CB A:ASP198 4.1 33.6 1.0
N A:GLY176 4.2 40.9 1.0
OD1 A:ASP175 4.2 41.2 1.0
C A:ASP175 4.3 46.2 1.0
OD2 A:ASP198 4.3 36.2 1.0
C A:GLY179 4.3 38.4 1.0
C A:LYS177 4.4 45.6 1.0
CA A:GLY178 4.4 40.5 1.0
CA A:ILE180 4.5 29.3 1.0
N A:ASP175 4.5 40.4 1.0
CA A:GLY176 4.5 41.9 1.0
N A:LYS177 4.5 39.5 1.0
CA A:LYS177 4.5 39.7 1.0
N A:GLY179 4.6 38.1 1.0
OE1 A:GLU201 4.6 37.4 1.0
N A:LEU181 4.6 27.6 1.0
CA A:GLY179 4.6 36.9 1.0
CB A:ASP175 4.7 39.2 1.0
O A:ASP175 4.7 48.5 1.0
CA A:ASP175 4.7 40.4 1.0
CA A:LEU181 4.7 28.1 1.0
O A:GLY179 4.9 36.7 1.0
CD1 A:ILE180 4.9 37.7 1.0

Calcium binding site 4 out of 6 in 8b2n

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Calcium binding site 4 out of 6 in the Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:40.6
occ:1.00
 OD1 C:ASP124 2.4 43.0 1.0
O C:GLU199 2.4 39.2 1.0
OE2 C:GLU199 2.4 32.8 1.0
O C:HOH450 2.4 39.5 1.0
O C:HOH463 2.4 43.1 1.0
O C:GLU201 2.4 37.6 1.0
OD2 C:ASP124 2.7 44.9 1.0
CG C:ASP124 2.9 44.1 1.0
C C:GLU199 3.5 37.3 1.0
CD C:GLU199 3.5 49.6 1.0
C C:GLU201 3.6 39.0 1.0
OG1 C:THR122 4.1 38.9 1.0
CG C:GLU199 4.1 42.3 1.0
CA C:GLU199 4.2 32.0 1.0
CA C:PHE202 4.2 41.5 1.0
CD1 C:TRP203 4.3 36.0 1.0
N C:PHE202 4.3 39.9 1.0
N C:GLU201 4.4 34.9 1.0
CB C:ASP124 4.4 42.6 1.0
C C:ASP200 4.5 37.6 1.0
N C:ASP200 4.6 32.7 1.0
OE1 C:GLU199 4.6 44.3 1.0
CA C:GLU201 4.6 34.3 1.0
CA C:ASP200 4.7 33.6 1.0
NE1 C:TRP203 4.7 33.9 1.0
O C:HOH437 4.8 47.2 1.0
CB C:GLU199 4.8 33.9 1.0
N C:TRP203 4.8 39.3 1.0
NH2 C:ARG165 4.8 49.1 1.0
O C:HOH469 4.8 47.4 1.0
CD1 C:PHE202 4.9 55.1 1.0

Calcium binding site 5 out of 6 in 8b2n

Go back to Calcium Binding Sites List in 8b2n
Calcium binding site 5 out of 6 in the Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:33.9
occ:1.00
 O C:GLY190 2.4 35.5 1.0
O C:ASP158 2.4 32.5 1.0
O C:HOH406 2.4 36.0 1.0
O C:HOH419 2.4 36.9 1.0
OD2 C:ASP194 2.4 28.0 1.0
O C:GLY192 2.4 34.3 1.0
CG C:ASP194 3.4 30.5 1.0
C C:ASP158 3.5 34.3 1.0
C C:GLY192 3.6 32.2 1.0
C C:GLY190 3.6 38.0 1.0
OD1 C:ASP194 3.8 32.3 1.0
O C:HOH410 3.9 53.7 1.0
C C:ILE191 4.0 32.9 1.0
N C:GLY192 4.0 30.1 1.0
O C:ILE191 4.2 31.1 1.0
N C:ASP194 4.2 23.4 1.0
O C:ALA157 4.2 39.1 1.0
CA C:ASP158 4.3 33.2 1.0
O C:GLY188 4.3 37.6 1.0
CA C:GLY192 4.4 29.3 1.0
N C:ILE159 4.4 30.9 1.0
CA C:ILE191 4.4 32.1 1.0
N C:ILE191 4.4 34.2 1.0
N C:GLY190 4.5 37.9 1.0
CA C:ILE159 4.5 27.7 1.0
CA C:GLY190 4.5 36.9 1.0
N C:GLY193 4.5 25.2 1.0
CA C:GLY193 4.6 24.8 1.0
CB C:ASP194 4.6 24.1 1.0
C C:GLY193 4.6 26.4 1.0
N C:LEU160 4.7 30.3 1.0
C C:SER189 4.8 40.0 1.0
CA C:ASP194 4.8 22.3 1.0
O C:HOH430 4.8 36.2 1.0
CH2 C:TRP109 4.9 33.2 1.0

Calcium binding site 6 out of 6 in 8b2n

Go back to Calcium Binding Sites List in 8b2n
Calcium binding site 6 out of 6 in the Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Potempin A (Pota) From Tannerella Forsythia in Complex with the Catalytic Domain of Human Mmp-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:33.3
occ:1.00
 OD1 C:ASP198 2.4 34.0 1.0
O C:ILE180 2.4 23.8 1.0
OE2 C:GLU201 2.4 37.5 1.0
O C:GLY178 2.4 31.1 1.0
O C:GLY176 2.4 36.5 1.0
OD2 C:ASP175 2.4 34.0 1.0
CG C:ASP198 3.4 35.2 1.0
CD C:GLU201 3.6 38.9 1.0
CG C:ASP175 3.6 35.2 1.0
C C:GLY178 3.6 35.7 1.0
C C:ILE180 3.6 25.1 1.0
C C:GLY176 3.6 41.0 1.0
N C:GLY178 3.9 37.5 1.0
N C:ILE180 4.0 26.6 1.0
CG C:GLU201 4.1 39.5 1.0
CB C:ASP198 4.1 24.9 1.0
N C:GLY176 4.2 38.5 1.0
OD1 C:ASP175 4.2 34.4 1.0
C C:ASP175 4.3 42.0 1.0
OD2 C:ASP198 4.3 36.8 1.0
C C:GLY179 4.4 34.5 1.0
C C:LYS177 4.4 42.3 1.0
CA C:GLY178 4.4 36.8 1.0
N C:ASP175 4.5 34.6 1.0
CA C:ILE180 4.5 25.1 1.0
CA C:GLY176 4.5 39.3 1.0
N C:LYS177 4.5 41.0 1.0
CA C:LYS177 4.5 40.5 1.0
N C:LEU181 4.6 22.0 1.0
N C:GLY179 4.6 33.5 1.0
OE1 C:GLU201 4.6 42.1 1.0
CA C:GLY179 4.6 32.0 1.0
O C:ASP175 4.7 42.7 1.0
CB C:ASP175 4.7 37.0 1.0
CA C:LEU181 4.7 20.5 1.0
CA C:ASP175 4.7 36.4 1.0
O C:GLY179 4.9 33.0 1.0
CD1 C:ILE180 4.9 34.5 1.0

Reference:

M.Ksiazek, T.Goulas, D.Mizgalska, A.Rodriguez-Banqueri, U.Eckhard, F.Veillard, I.Waligorska, M.Benedyk-Machaczka, A.M.Sochaj-Gregorczyk, M.Madej, I.B.Thogersen, J.J.Enghild, A.Cuppari, J.L.Arolas, I.De Diego, M.Lopez-Pelegrin, I.Garcia-Ferrer, T.Guevara, V.Dive, M.L.Zani, T.Moreau, J.Potempa, F.X.Gomis-Ruth. A Unique Network of Attack, Defence and Competence on the Outer Membrane of the Periodontitis Pathogen Tannerella Forsythia Chem Sci 2023.
ISSN: ESSN 2041-6539
Page generated: Fri Jul 19 07:07:10 2024

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