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Zinc 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:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8b2n

Go back to Zinc Binding Sites List in 8b2n
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn304

b:35.5
occ:1.00
 OD1 A:ASP170 2.1 41.0 1.0
NE2 A:HIS168 2.1 35.8 1.0
ND1 A:HIS196 2.1 31.7 1.0
NE2 A:HIS183 2.1 33.2 1.0
CG A:ASP170 2.9 43.9 1.0
CE1 A:HIS183 3.0 34.0 1.0
CD2 A:HIS168 3.0 37.6 1.0
CE1 A:HIS196 3.0 31.3 1.0
OD2 A:ASP170 3.1 48.1 1.0
CE1 A:HIS168 3.1 36.9 1.0
CG A:HIS196 3.1 29.8 1.0
CD2 A:HIS183 3.2 31.5 1.0
CB A:HIS196 3.5 26.6 1.0
O A:HIS172 4.1 45.4 1.0
ND1 A:HIS183 4.1 34.6 1.0
CG A:HIS168 4.2 38.4 1.0
NE2 A:HIS196 4.2 31.0 1.0
CG A:HIS183 4.2 31.1 1.0
ND1 A:HIS168 4.2 39.8 1.0
CD2 A:HIS196 4.3 30.7 1.0
CB A:ASP170 4.3 42.1 1.0
CE1 A:PHE185 4.4 33.0 1.0
CZ A:PHE174 4.6 32.7 1.0
CE2 A:PHE174 4.6 37.8 1.0
O A:HOH483 4.8 41.7 0.5
CZ A:PHE185 4.9 32.0 1.0

Zinc binding site 2 out of 4 in 8b2n

Go back to Zinc Binding Sites List in 8b2n
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn305

b:24.2
occ:1.00
 NE2 A:HIS218 2.1 22.4 1.0
NE2 A:HIS222 2.1 24.1 1.0
NE2 A:HIS228 2.1 26.4 1.0
OD1 B:ASP64 2.1 25.6 1.0
OD2 B:ASP64 2.4 18.4 1.0
CG B:ASP64 2.6 24.3 1.0
CD2 A:HIS228 3.0 25.6 1.0
CD2 A:HIS218 3.0 22.5 1.0
CE1 A:HIS222 3.1 23.1 1.0
CD2 A:HIS222 3.1 24.8 1.0
CE1 A:HIS218 3.1 22.5 1.0
CE1 A:HIS228 3.1 26.2 1.0
O B:HOH216 3.6 30.8 1.0
CB B:ASP64 4.1 24.3 1.0
CG A:HIS218 4.2 22.0 1.0
CG A:HIS228 4.2 24.6 1.0
ND1 A:HIS218 4.2 23.6 1.0
CG A:HIS222 4.2 22.8 1.0
ND1 A:HIS222 4.2 23.5 1.0
ND1 A:HIS228 4.2 26.3 1.0
CB B:TYR63 4.4 24.4 1.0
N B:ASP64 4.6 24.2 1.0
OE2 A:GLU219 4.6 26.5 1.0
O B:HOH201 4.6 34.7 1.0
CA B:ASP64 4.8 23.7 1.0
O B:ALA102 4.9 30.1 1.0
CA B:GLY103 4.9 26.2 1.0
CE A:MET236 5.0 23.3 1.0
OD1 B:ASN65 5.0 30.7 1.0

Zinc binding site 3 out of 4 in 8b2n

Go back to Zinc Binding Sites List in 8b2n
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
C:Zn304

b:29.4
occ:1.00
 NE2 C:HIS183 2.1 29.9 1.0
OD1 C:ASP170 2.1 25.7 1.0
ND1 C:HIS196 2.1 28.1 1.0
NE2 C:HIS168 2.1 29.9 1.0
CG C:ASP170 2.9 32.9 1.0
CE1 C:HIS183 3.0 29.6 1.0
CD2 C:HIS168 3.0 31.8 1.0
CE1 C:HIS196 3.0 27.7 1.0
CG C:HIS196 3.1 26.4 1.0
CD2 C:HIS183 3.1 29.0 1.0
OD2 C:ASP170 3.1 33.6 1.0
CE1 C:HIS168 3.2 30.5 1.0
CB C:HIS196 3.4 23.0 1.0
O C:HIS172 4.1 33.3 1.0
ND1 C:HIS183 4.1 28.2 1.0
CG C:HIS168 4.2 32.8 1.0
NE2 C:HIS196 4.2 28.6 1.0
CG C:HIS183 4.2 26.6 1.0
CD2 C:HIS196 4.2 29.0 1.0
ND1 C:HIS168 4.3 33.0 1.0
CB C:ASP170 4.3 33.5 1.0
CE1 C:PHE185 4.4 28.8 1.0
CZ C:PHE174 4.7 24.1 1.0
CE2 C:PHE174 4.7 27.6 1.0
CZ C:PHE185 4.9 28.1 1.0
CA C:HIS196 5.0 22.0 1.0

Zinc binding site 4 out of 4 in 8b2n

Go back to Zinc Binding Sites List in 8b2n
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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:Zn305

b:21.8
occ:1.00
 NE2 C:HIS218 2.1 21.4 1.0
NE2 C:HIS228 2.1 20.2 1.0
NE2 C:HIS222 2.1 22.7 1.0
OD1 D:ASP64 2.1 23.6 1.0
OD2 D:ASP64 2.4 24.6 1.0
CG D:ASP64 2.5 24.9 1.0
CD2 C:HIS228 3.0 19.8 1.0
CD2 C:HIS218 3.0 22.2 1.0
CD2 C:HIS222 3.1 23.1 1.0
CE1 C:HIS222 3.1 23.0 1.0
CE1 C:HIS218 3.1 20.8 1.0
CE1 C:HIS228 3.1 20.5 1.0
O D:HOH218 3.6 24.8 1.0
CB D:ASP64 4.1 21.3 1.0
CG C:HIS228 4.2 18.8 1.0
CG C:HIS218 4.2 21.3 1.0
CG C:HIS222 4.2 21.3 1.0
ND1 C:HIS218 4.2 22.6 1.0
ND1 C:HIS222 4.2 23.3 1.0
ND1 C:HIS228 4.2 21.8 1.0
CB D:TYR63 4.4 26.2 1.0
OE2 C:GLU219 4.5 22.9 1.0
O D:HOH213 4.6 23.1 1.0
N D:ASP64 4.6 21.2 1.0
CA D:ASP64 4.8 19.3 1.0
O D:ALA102 5.0 26.6 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: Wed Oct 30 18:08:27 2024

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