Calcium 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:

Zinc	(Zn)	8 atoms
Arsenic	(As)	1 atom
Chlorine	(Cl)	1 atom

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

Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca801 b:81.4 occ:1.00 OD1 A:ASP530 2.4 78.8 1.0 O A:ASP520 2.4 69.3 1.0 OD1 A:ASP529 2.4 86.2 1.0 O A:THR523 2.4 82.8 1.0 OG1 A:THR523 2.4 84.2 1.0 O A:THR526 2.4 88.1 1.0 CG A:ASP529 3.2 87.0 1.0 C A:THR526 3.4 89.7 1.0 C A:THR523 3.4 82.0 1.0 OD2 A:ASP529 3.4 92.0 1.0 CB A:THR523 3.5 85.0 1.0 C A:ASP520 3.5 68.8 1.0 CG A:ASP530 3.6 79.2 1.0 CA A:THR523 3.8 78.6 1.0 N A:THR523 4.0 77.2 1.0 CA A:THR526 4.1 86.8 1.0 OD2 A:ASP530 4.2 84.5 1.0 N A:ASP530 4.2 75.2 1.0 N A:THR527 4.3 86.4 1.0 N A:THR526 4.3 85.2 1.0 CA A:ASP520 4.3 63.6 1.0 CB A:THR526 4.3 96.2 1.0 CB A:ASP529 4.5 80.7 1.0 N A:ARG521 4.6 65.6 1.0 OG1 A:THR526 4.6 96.8 1.0 CA A:THR527 4.6 84.8 1.0 N A:PRO524 4.6 76.6 1.0 C A:ASP529 4.6 80.9 1.0 N A:ASP529 4.7 82.0 1.0 CB A:ASP530 4.7 72.4 1.0 CB A:ARG521 4.7 64.4 1.0 CA A:ASP530 4.7 71.9 1.0 O A:ARG521 4.8 78.7 1.0 CG2 A:THR523 4.8 82.7 1.0 CB A:ASP520 4.8 63.9 1.0 CA A:ASP529 4.8 79.7 1.0 C A:ARG521 4.8 74.3 1.0 C A:THR527 4.9 89.8 1.0 CA A:ARG521 4.9 66.8 1.0 CA A:PRO524 5.0 75.6 1.0

Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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:Ca810 b:87.3 occ:1.00 OE1 A:GLU688 2.4 71.4 1.0 OE2 A:GLU688 2.4 0.5 1.0 OD2 A:ASP761 2.7 1.0 1.0 CD A:GLU688 2.7 0.6 1.0 CG2 A:VAL763 3.6 0.1 1.0 CG A:ASP761 3.8 0.7 1.0 CG A:GLU688 4.2 0.9 1.0 CB A:SER764 4.4 1.0 1.0 CB A:VAL763 4.5 0.7 1.0 CB A:ASP761 4.5 0.4 1.0 CG A:GLN713 4.6 0.6 1.0 O A:GLY684 4.6 0.3 1.0 N A:SER764 4.7 1.0 1.0 OD1 A:ASP761 4.8 0.3 1.0 OE1 A:GLN713 4.8 0.9 1.0 CB A:GLU688 4.9 0.3 1.0 O A:GLY682 4.9 0.8 1.0

Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca 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:Ca811 b:99.0 occ:1.00 OD2 A:ASP672 2.4 0.4 1.0 CG A:ASP672 3.1 93.7 1.0 OD1 A:ASP672 3.2 97.5 1.0 CB A:ASP672 4.4 74.0 1.0 OG A:SER651 4.7 79.7 1.0 CB A:SER651 4.7 69.7 1.0 O A:LEU650 4.8 71.4 1.0

Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca 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:Ca812 b:0.1 occ:1.00 OD2 A:ASP468 2.4 92.8 1.0 OD1 A:ASP468 2.9 87.9 1.0 CG A:ASP468 3.0 88.1 1.0 OE1 A:GLN470 3.4 0.6 1.0 CB A:GLN470 4.0 86.3 1.0 CD A:GLN470 4.0 1.0 1.0 OG A:SER471 4.1 95.5 1.0 CB A:SER471 4.2 90.2 1.0 N A:SER471 4.3 84.9 1.0 CB A:ASP468 4.4 79.9 1.0 CG A:GLN470 4.6 0.4 1.0 NE2 A:GLN470 4.7 0.8 1.0 CA A:SER471 4.9 86.8 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