Zinc in PDB 5m11: Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.

The structure of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis., PDB code: 5m11 was solved by A.M.Lasica, T.Goulas, D.Mizgalska, X.Zhou, M.Ksiazek, M.Madej, Y.Guo, T.Guevara, M.Nowak, B.Potempa, A.Goel, M.Sztukowska, A.T.Prabhakar, M.Bzowska, M.Widziolek, I.B.Thogersen, J.J.Enghild, M.Simonian, A.W.Kulczyk, K.-A.Nguyen, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.46 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	115.520, 115.520, 139.880, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.8

The structure of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. also contains other interesting chemical elements:

Arsenic	(As)	1 atom
Calcium	(Ca)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. (pdb code 5m11). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis., PDB code: 5m11:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:0.7 occ:1.00 NE2 A:HIS475 2.1 84.6 1.0 CD2 A:HIS475 2.9 82.4 1.0 CE1 A:HIS475 3.2 85.9 1.0 CG A:HIS475 4.1 80.9 1.0 OG1 A:THR473 4.1 92.5 1.0 ND1 A:HIS475 4.2 85.5 1.0 CB A:THR473 4.5 91.2 1.0 OE1 A:GLU525 4.7 97.7 1.0 CG A:PRO524 4.9 81.2 1.0

Zinc binding site 2 out of 8 in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:0.3 occ:1.00 NZ A:LYS417 2.1 0.5 1.0 OD2 A:ASP402 2.1 0.7 1.0 OD1 A:ASP400 2.2 92.7 1.0 OD2 A:ASP400 2.2 93.1 1.0 CG A:ASP400 2.5 89.1 1.0 CE A:LYS417 3.2 0.3 1.0 CG A:ASP402 3.3 97.8 1.0 OD1 A:ASP418 3.5 97.2 1.0 CD A:LYS417 3.9 1.0 1.0 OD1 A:ASP402 4.0 99.3 1.0 CB A:ASP400 4.0 74.8 1.0 CG A:ASP418 4.2 95.3 1.0 CB A:HIS403 4.4 71.8 1.0 CB A:ASP402 4.4 76.2 1.0 OD2 A:ASP418 4.4 0.1 1.0 N A:HIS403 4.5 68.8 1.0 C A:ASP402 4.6 73.2 1.0 CG A:LYS417 4.7 88.6 1.0 O A:HOH913 4.7 60.8 1.0 CA A:ASP402 4.8 70.9 1.0 CA A:ASP400 4.9 72.0 1.0 N A:ASP402 4.9 69.7 1.0 CA A:HIS403 4.9 68.9 1.0 N A:ASP418 5.0 72.3 1.0

Zinc binding site 3 out of 8 in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:88.9 occ:1.00 O1 A:GOL818 2.1 80.9 1.0 NE2 A:HIS618 2.2 81.2 1.0 O A:HOH934 2.4 62.8 1.0 O2 A:GOL818 2.7 84.5 1.0 CD2 A:HIS618 3.1 78.7 1.0 C1 A:GOL818 3.2 81.6 1.0 CE1 A:HIS618 3.2 80.0 1.0 C2 A:GOL818 3.3 84.1 1.0 C3 A:GOL818 3.6 85.4 1.0 CG A:HIS618 4.3 74.1 1.0 N A:GLU633 4.3 72.0 1.0 ND1 A:HIS618 4.3 77.3 1.0 CB A:SER632 4.4 78.3 1.0 CA A:SER632 4.6 72.0 1.0 CG A:GLU633 4.7 90.0 1.0 O3 A:GOL818 4.8 86.1 1.0 CD1 A:LEU639 4.9 73.7 1.0 CB A:GLU633 4.9 75.8 1.0

Zinc binding site 4 out of 8 in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:88.9 occ:1.00 O1 A:GOL817 2.1 88.1 1.0 O A:HOH911 2.3 96.9 1.0 OE1 A:GLU336 2.3 87.0 1.0 O2 A:GOL817 2.7 94.3 1.0 CD A:GLU336 2.7 95.8 1.0 OE2 A:GLU336 2.7 98.4 1.0 C1 A:GOL817 3.1 88.6 1.0 C2 A:GOL817 3.1 91.1 1.0 OD2 A:ASP610 3.7 69.4 1.0 O A:MET337 3.8 56.6 1.0 CG A:GLU336 4.0 66.3 1.0 OD1 A:ASP610 4.1 72.5 1.0 CG A:ASP610 4.2 70.0 1.0 N A:MET337 4.6 50.9 1.0 C3 A:GOL817 4.6 90.5 1.0 ND2 A:ASN490 4.8 79.8 1.0 CB A:GLU336 4.8 54.8 1.0 C A:MET337 4.8 55.6 1.0 CA A:GLU336 4.9 53.4 1.0 CD A:ARG338 4.9 77.1 1.0 CG A:ASN490 5.0 88.3 1.0

Zinc binding site 5 out of 8 in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:0.5 occ:1.00 OD2 A:ASP481 2.1 97.1 1.0 NE2 A:HIS532 2.1 77.9 1.0 CG A:ASP481 2.4 94.9 1.0 OD1 A:ASP481 2.5 96.5 1.0 O A:HOH908 2.6 73.8 1.0 O A:HOH939 2.6 59.8 1.0 CD2 A:HIS532 2.9 75.6 1.0 CE1 A:HIS532 3.3 78.0 1.0 CB A:ASP481 3.8 86.5 1.0 CG A:HIS532 4.1 72.7 1.0 CB A:TYR534 4.1 73.3 1.0 ND1 A:HIS532 4.3 76.1 1.0 N A:TYR534 4.4 69.7 1.0 CB A:TYR479 4.8 73.0 1.0 CA A:TYR534 4.9 70.5 1.0

Zinc binding site 6 out of 8 in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:0.9 occ:1.00 OD2 A:ASP333 2.1 99.7 1.0 NE2 A:HIS358 2.1 89.1 1.0 O3 A:GOL819 2.1 100.0 1.0 O2 A:GOL819 2.2 0.3 1.0 C3 A:GOL819 3.0 0.1 1.0 CE1 A:HIS358 3.1 87.1 1.0 C2 A:GOL819 3.1 99.5 1.0 CG A:ASP333 3.1 87.9 1.0 CD2 A:HIS358 3.2 91.4 1.0 OD1 A:ASP333 3.5 91.0 1.0 ND1 A:HIS358 4.2 88.3 1.0 C1 A:GOL819 4.3 98.4 1.0 CG A:HIS358 4.3 88.9 1.0 CB A:ASP333 4.5 66.9 1.0 OD1 A:ASP331 5.0 75.7 1.0

Zinc binding site 7 out of 8 in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn808 b:50.0 occ:1.00 OE2 A:GLU155 2.1 52.9 1.0 OD2 A:ASP152 2.1 64.4 1.0 CL A:CL814 2.4 53.4 1.0 CG A:ASP152 2.9 54.8 1.0 CD A:GLU155 3.0 57.1 1.0 OD1 A:ASP152 3.0 57.0 1.0 CG A:GLU155 3.3 46.2 1.0 NH2 A:ARG157 3.8 86.4 1.0 CB A:GLU155 3.9 43.2 1.0 NH2 A:ARG139 4.0 70.5 1.0 OE1 A:GLU155 4.1 67.0 1.0 NH1 A:ARG139 4.3 81.7 1.0 CB A:ASP152 4.4 39.7 1.0 CZ A:ARG157 4.5 91.7 1.0 CZ A:ARG139 4.6 85.9 1.0 N A:GLU155 4.8 42.6 1.0 NE A:ARG157 4.9 78.7 1.0 CB A:ALA154 5.0 44.8 1.0

Zinc binding site 8 out of 8 in the Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral- Microbiomic Porphyromonas Gingivalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn809 b:80.7 occ:1.00 ND1 A:HIS341 2.0 70.8 1.0 O2 A:CAC813 2.1 1.0 1.0 CG A:HIS341 2.8 67.6 1.0 O A:HOH941 2.8 44.7 0.5 CE1 A:HIS341 3.0 70.1 1.0 AS A:CAC813 3.1 0.4 1.0 CB A:HIS341 3.1 63.4 1.0 O A:HOH902 3.3 50.2 1.0 O1 A:CAC813 3.6 0.7 1.0 CA A:HIS341 3.7 60.6 1.0 C1 A:CAC813 3.8 0.0 1.0 CD2 A:HIS341 3.9 69.1 1.0 NE2 A:HIS341 3.9 69.5 1.0 N A:HIS341 4.6 58.3 1.0 CD A:PRO401 4.6 71.2 1.0 C A:HIS341 4.7 61.4 1.0 C2 A:CAC813 4.9 0.4 1.0 O A:HIS341 4.9 60.2 1.0 O A:GLY399 4.9 80.5 1.0

A.M.Lasica, T.Goulas, D.Mizgalska, X.Zhou, I.De Diego, M.Ksiazek, M.Madej, Y.Guo, T.Guevara, M.Nowak, B.Potempa, A.Goel, M.Sztukowska, A.T.Prabhakar, M.Bzowska, M.Widziolek, I.B.Thgersen, J.J.Enghild, M.Simonian, A.W.Kulczyk, K.A.Nguyen, J.Potempa, F.X.Gomis-Ruth. Structural and Functional Probing of Porz, An Essential Bacterial Surface Component of the Type-IX Secretion System of Human Oral-Microbiomic Porphyromonas Gingivalis. Sci Rep V. 6 37708 2016.
ISSN: ESSN 2045-2322
PubMed: 27883039
DOI: 10.1038/SREP37708