Atomistry » Zinc » PDB 8aop-8b9n » 8b2n
Atomistry »
  Zinc »
    PDB 8aop-8b9n »
      8b2n »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy