Zinc in PDB 7pv7: Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.

The structure of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator., PDB code: 7pv7 was solved by C.A.Schmitz, M.Madej, J.Potempa, M.Sola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.40 / 2.41
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.83, 77.08, 138.73, 82.26, 81.36, 76.41
R / Rfree (%)	18.6 / 21.6

The structure of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. also contains other interesting chemical elements:

Fluorine	(F)	24 atoms
Magnesium	(Mg)	9 atoms

The binding sites of Zinc atom in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. (pdb code 7pv7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator., PDB code: 7pv7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:125.0 occ:0.79 OD2 D:ASP415 2.0 95.2 1.0 OG1 D:THR272 2.1 104.9 1.0 HE2 D:HIS416 2.2 65.0 1.0 HG1 D:THR272 2.3 125.8 1.0 NE2 D:HIS416 2.5 54.2 1.0 CG D:ASP415 2.6 66.1 1.0 HD2 D:HIS416 2.7 64.6 1.0 CD2 D:HIS416 2.7 53.9 1.0 OD1 D:ASP239 2.7 77.9 1.0 OD1 D:ASP415 2.8 69.9 1.0 HA D:THR272 2.8 58.3 1.0 CB D:THR272 3.0 63.9 1.0 HG23 D:THR272 3.0 64.3 1.0 HG21 D:THR272 3.2 64.3 1.0 CG2 D:THR272 3.2 53.6 1.0 CA D:THR272 3.2 48.6 1.0 H D:THR272 3.4 49.4 1.0 CE1 D:HIS416 3.5 54.2 1.0 H D:ASN240 3.5 47.5 1.0 N D:THR272 3.6 41.1 1.0 CG D:HIS416 3.8 51.4 1.0 HB D:THR272 3.8 76.7 1.0 CG D:ASP239 3.9 74.7 1.0 CB D:ASP415 3.9 49.3 1.0 HB2 D:ASP415 4.0 59.1 1.0 HE1 D:HIS416 4.0 65.0 1.0 HA D:ASP239 4.0 63.7 1.0 F1 D:BEF607 4.0 94.6 1.0 ND1 D:HIS416 4.2 53.1 1.0 HB2 D:ARG276 4.2 60.2 1.0 HG22 D:THR272 4.2 64.3 1.0 HD3 D:ARG276 4.2 72.0 1.0 N D:ASN240 4.2 39.6 1.0 HB3 D:ASP239 4.3 77.5 1.0 BE D:BEF607 4.3 93.1 1.0 O D:HOH901 4.3 72.8 1.0 HB3 D:ASP415 4.4 59.1 1.0 HH11 D:ARG276 4.5 81.2 1.0 HB2 D:ASN240 4.5 53.6 1.0 CB D:ASP239 4.5 64.6 1.0 C D:ALA271 4.5 38.4 1.0 H D:HIS416 4.6 48.6 1.0 CA D:ASP239 4.7 53.1 1.0 H D:ASP415 4.7 50.2 1.0 C D:THR272 4.7 50.0 1.0 N D:HIS416 4.8 40.5 1.0 HA D:ALA271 4.8 47.5 1.0 HA D:ASN240 4.8 47.6 1.0 OD2 D:ASP239 4.9 79.0 1.0 CA D:ASP415 4.9 41.1 1.0 C D:ASP239 5.0 46.5 1.0 CB D:HIS416 5.0 46.8 1.0 C D:ASP415 5.0 38.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:39.6 occ:0.62 F1 C:BEF612 1.9 49.0 1.0 OD2 C:ASP415 2.0 54.2 1.0 NE2 C:HIS416 2.0 54.5 1.0 OG1 C:THR272 2.1 76.2 1.0 OD1 C:ASP239 2.2 42.5 1.0 OD2 C:ASP239 2.4 41.8 1.0 CG C:ASP239 2.6 42.4 1.0 CD2 C:HIS416 2.6 51.9 1.0 HD2 C:HIS416 2.7 62.2 1.0 CG C:ASP415 2.8 47.6 1.0 BE C:BEF612 2.9 58.7 1.0 OD1 C:ASP415 2.9 47.7 1.0 CE1 C:HIS416 3.1 51.7 1.0 CB C:THR272 3.3 58.3 1.0 HA C:THR272 3.3 59.7 1.0 HE1 C:HIS416 3.5 62.0 1.0 HG23 C:THR272 3.6 63.1 1.0 CA C:THR272 3.7 49.7 1.0 CG C:HIS416 3.8 50.1 1.0 CG2 C:THR272 3.8 52.6 1.0 H C:ASN240 3.8 58.1 1.0 HG21 C:THR272 3.8 63.1 1.0 ND1 C:HIS416 3.9 50.9 1.0 N C:THR272 4.0 44.5 1.0 H C:THR272 4.0 53.4 1.0 F3 C:BEF612 4.0 65.9 1.0 CB C:ASP239 4.0 41.1 1.0 HB C:THR272 4.0 69.9 1.0 F2 C:BEF612 4.0 68.5 1.0 HD3 C:ARG276 4.1 54.8 1.0 HB2 C:ASN240 4.2 59.6 1.0 HA C:ASP239 4.2 49.3 1.0 CB C:ASP415 4.2 43.6 1.0 N C:ASN240 4.3 48.4 1.0 HH11 C:ARG276 4.3 58.3 1.0 HB2 C:ARG276 4.3 53.6 1.0 HB2 C:ASP415 4.3 52.3 1.0 HB2 C:ASP239 4.4 49.3 1.0 CA C:ASP239 4.5 41.1 1.0 HB3 C:ASP239 4.6 49.3 1.0 HB3 C:ASP415 4.6 52.3 1.0 C C:ALA271 4.7 40.3 1.0 H C:HIS416 4.7 47.1 1.0 HD1 C:HIS416 4.7 61.1 1.0 ZN C:ZN604 4.7 82.5 0.7 HG22 C:THR272 4.7 63.1 1.0 C C:ASP239 4.7 43.5 1.0 HA C:ALA271 4.7 48.3 1.0 OD1 C:ASP361 4.7 92.0 1.0 HB2 C:ASP361 4.8 72.6 1.0 HA C:ASN240 4.9 59.5 1.0 H C:ASP415 4.9 47.9 1.0 O C:HOH774 4.9 66.1 1.0 N C:HIS416 4.9 39.2 1.0 CA C:ASN240 5.0 49.6 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn604 b:82.5 occ:0.67 OD1 C:ASP361 2.1 92.0 1.0 NE2 C:HIS365 2.2 86.4 1.0 NE2 C:HIS500 2.3 57.6 1.0 O1 C:GOL607 2.6 88.4 1.0 HE1 C:HIS365 2.7 93.2 1.0 CE1 C:HIS365 2.8 77.7 1.0 F1 C:BEF612 2.9 49.0 1.0 CG C:ASP361 3.0 72.7 1.0 CE1 C:HIS500 3.1 58.7 1.0 CD2 C:HIS500 3.2 56.8 1.0 HE1 C:HIS500 3.2 70.4 1.0 F2 C:BEF612 3.2 68.5 1.0 HD22 C:ASN240 3.3 61.6 1.0 BE C:BEF612 3.3 58.7 1.0 OD2 C:ASP361 3.3 75.8 1.0 F3 C:BEF612 3.3 65.9 1.0 HE1 C:HIS416 3.3 62.0 1.0 CD2 C:HIS365 3.4 77.2 1.0 HD2 C:HIS500 3.5 68.2 1.0 H31 C:GOL607 3.8 99.3 1.0 HD2 C:HIS365 3.8 92.7 1.0 C1 C:GOL607 4.0 88.3 1.0 ND2 C:ASN240 4.0 51.4 1.0 CE1 C:HIS416 4.0 51.7 1.0 ND1 C:HIS365 4.0 77.2 1.0 ND1 C:HIS500 4.1 57.9 1.0 H2 C:GOL607 4.1 103.3 1.0 CG C:HIS500 4.2 56.0 1.0 NE2 C:HIS416 4.3 54.5 1.0 HB2 C:ASN240 4.3 59.6 1.0 HD21 C:ASN240 4.3 61.6 1.0 C3 C:GOL607 4.3 82.7 1.0 O3 C:GOL607 4.4 80.2 1.0 CG C:HIS365 4.4 73.9 1.0 C2 C:GOL607 4.4 86.1 1.0 CB C:ASP361 4.4 60.5 1.0 OG1 C:THR272 4.4 76.2 1.0 H11 C:GOL607 4.5 105.9 1.0 H12 C:GOL607 4.5 105.9 1.0 OD1 C:ASP239 4.6 42.5 1.0 HB2 C:ASP361 4.6 72.6 1.0 O C:HOH836 4.6 60.1 1.0 HA C:ASP361 4.6 66.3 1.0 ZN C:ZN603 4.7 39.6 0.6 HD1 C:HIS365 4.7 92.6 1.0 HD1 C:HIS500 4.9 69.5 1.0 O2 C:FMT610 4.9 76.1 1.0 O C:ASP361 5.0 51.5 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:90.9 occ:0.59 HG1 B:THR272 1.8 106.4 1.0 OG1 B:THR272 1.9 88.7 1.0 NE2 B:HIS416 2.3 42.1 1.0 OD2 B:ASP415 2.6 47.7 1.0 OD2 B:ASP239 2.8 66.2 1.0 BE B:BEF611 3.0 92.1 1.0 CD2 B:HIS416 3.0 41.1 1.0 HD2 B:HIS416 3.1 49.3 1.0 OD1 B:ASP239 3.2 64.0 1.0 CB B:THR272 3.2 60.9 1.0 F3 B:BEF611 3.2 90.9 1.0 CG B:ASP239 3.2 62.5 1.0 CE1 B:HIS416 3.2 42.8 1.0 CG B:ASP415 3.3 45.2 1.0 OD1 B:ASP415 3.3 46.1 1.0 HA B:THR272 3.3 51.7 1.0 HE1 B:HIS416 3.5 51.3 1.0 H B:THR272 3.6 45.7 1.0 CA B:THR272 3.6 43.1 1.0 HG23 B:THR272 3.7 67.3 1.0 N B:THR272 3.8 38.1 1.0 HG21 B:THR272 3.8 67.3 1.0 CG2 B:THR272 3.8 56.0 1.0 HB2 B:ASN240 3.8 60.2 1.0 H B:ASN240 3.8 53.4 1.0 HB B:THR272 3.9 73.0 1.0 F1 B:BEF611 4.0 90.0 1.0 F2 B:BEF611 4.0 94.6 1.0 CG B:HIS416 4.0 39.1 1.0 ND1 B:HIS416 4.1 41.3 1.0 N B:ASN240 4.2 44.5 1.0 HA B:ASP239 4.2 57.2 1.0 HD3 B:ARG276 4.4 51.9 1.0 CB B:ASP239 4.5 54.1 1.0 HA B:ASN240 4.6 54.1 1.0 HA B:ALA271 4.6 42.3 1.0 C B:ALA271 4.6 36.0 1.0 CB B:ASN240 4.7 50.2 1.0 CB B:ASP415 4.7 40.6 1.0 HH11 B:ARG276 4.7 57.2 1.0 CA B:ASP239 4.7 47.7 1.0 HB2 B:ASP415 4.7 48.7 1.0 HG22 B:THR272 4.7 67.3 1.0 HB2 B:ARG276 4.7 48.3 1.0 CA B:ASN240 4.8 45.1 1.0 HB3 B:ASP239 4.8 65.0 1.0 C B:ASP239 4.8 45.6 1.0 HE1 B:HIS500 4.8 53.9 1.0 HD1 B:HIS416 4.9 49.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:41.6 occ:0.66 OD2 A:ASP415 1.9 56.5 1.0 HE2 A:HIS416 2.0 56.6 1.0 OG1 A:THR272 2.2 87.1 1.0 OD1 A:ASP239 2.2 38.4 1.0 F1 A:BEF612 2.3 66.6 1.0 OD2 A:ASP239 2.4 37.9 1.0 NE2 A:HIS416 2.4 47.2 1.0 CG A:ASP239 2.6 36.9 1.0 CG A:ASP415 2.8 49.1 1.0 CE1 A:HIS416 3.1 47.0 1.0 CD2 A:HIS416 3.1 47.7 1.0 BE A:BEF612 3.1 68.6 1.0 OD1 A:ASP415 3.1 51.6 1.0 HA A:THR272 3.2 59.8 1.0 HG23 A:THR272 3.2 62.3 1.0 CB A:THR272 3.2 60.7 1.0 HD2 A:HIS416 3.3 57.3 1.0 HE1 A:HIS416 3.3 56.4 1.0 CA A:THR272 3.5 49.8 1.0 H A:THR272 3.6 54.0 1.0 CG2 A:THR272 3.6 51.9 1.0 N A:THR272 3.7 45.0 1.0 F3 A:BEF612 3.9 68.5 1.0 H A:ASN240 3.9 50.7 1.0 HG21 A:THR272 3.9 62.3 1.0 ND1 A:HIS416 4.0 45.7 1.0 CG A:HIS416 4.0 46.1 1.0 CB A:ASP239 4.0 35.4 1.0 HB A:THR272 4.1 72.8 1.0 CB A:ASP415 4.1 46.1 1.0 HB2 A:ASP415 4.2 55.4 1.0 HB2 A:ASN240 4.2 54.0 1.0 HA A:ASP239 4.2 45.6 1.0 HD3 A:ARG276 4.3 48.6 1.0 OD1 A:ASP361 4.3 91.0 1.0 N A:ASN240 4.3 42.3 1.0 F2 A:BEF612 4.5 76.5 1.0 HB2 A:ARG276 4.5 49.1 1.0 HB2 A:ASP239 4.5 42.4 1.0 HH11 A:ARG276 4.5 49.3 1.0 HA A:ALA271 4.5 56.0 1.0 C A:ALA271 4.5 46.3 1.0 HG22 A:THR272 4.5 62.3 1.0 HB3 A:ASP415 4.5 55.4 1.0 HB3 A:ASP239 4.5 42.4 1.0 CA A:ASP239 4.6 38.0 1.0 H A:HIS416 4.7 50.5 1.0 ZN A:ZN604 4.8 94.0 0.7 CG A:ASP361 4.8 70.6 1.0 C A:ASP239 4.8 40.4 1.0 HB2 A:ASP361 4.8 68.0 1.0 H A:ASP415 4.9 48.5 1.0 HE1 A:HIS500 5.0 57.6 1.0 HA A:ASN240 5.0 53.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:94.0 occ:0.70 OD1 A:ASP361 2.0 91.0 1.0 NE2 A:HIS365 2.1 94.5 1.0 NE2 A:HIS500 2.4 47.5 1.0 CG A:ASP361 2.7 70.6 1.0 OD2 A:ASP361 2.7 76.1 1.0 F1 A:BEF612 2.8 66.6 1.0 H31 A:GOL608 2.9 96.1 1.0 O C:HOH895 3.0 82.6 1.0 CE1 A:HIS365 3.0 87.0 1.0 CD2 A:HIS365 3.1 86.8 1.0 HD22 A:ASN240 3.2 56.5 1.0 HE1 A:HIS365 3.2 104.5 1.0 H32 A:GOL608 3.2 96.1 1.0 CD2 A:HIS500 3.3 47.8 1.0 HD2 A:HIS365 3.3 104.2 1.0 HD2 A:HIS500 3.4 57.4 1.0 CE1 A:HIS500 3.4 48.0 1.0 C3 A:GOL608 3.5 80.0 1.0 HE1 A:HIS416 3.5 56.4 1.0 BE A:BEF612 3.6 68.6 1.0 HE1 A:HIS500 3.6 57.6 1.0 F3 A:BEF612 3.6 68.5 1.0 F2 A:BEF612 3.9 76.5 1.0 ND2 A:ASN240 3.9 47.1 1.0 HO3 A:GOL608 4.0 89.3 1.0 CB A:ASP361 4.2 56.6 1.0 HE2 A:HIS416 4.2 56.6 1.0 ND1 A:HIS365 4.2 87.6 1.0 HD21 A:ASN240 4.2 56.5 1.0 O3 A:GOL608 4.2 74.5 1.0 CG A:HIS365 4.2 84.5 1.0 CE1 A:HIS416 4.3 47.0 1.0 HB2 A:ASN240 4.3 54.0 1.0 CG A:HIS500 4.4 47.8 1.0 ND1 A:HIS500 4.4 48.8 1.0 HB2 A:ASP361 4.5 68.0 1.0 OD1 A:ASP239 4.5 38.4 1.0 HA A:ASP361 4.5 60.3 1.0 OG1 A:THR272 4.5 87.1 1.0 NE2 A:HIS416 4.6 47.2 1.0 O A:ASP361 4.6 47.8 1.0 O A:HOH810 4.7 50.4 1.0 HB3 A:ASP361 4.7 68.0 1.0 ZN A:ZN603 4.8 41.6 0.7 CA A:ASP361 4.8 50.2 1.0 C2 A:GOL608 4.8 88.9 1.0 H2 A:GOL608 4.9 106.6 1.0 HD1 A:HIS365 4.9 105.1 1.0 H12 A:GOL608 5.0 111.6 1.0 CG A:ASN240 5.0 46.8 1.0 C A:ASP361 5.0 49.0 1.0

C.Schmitz, M.Madej, Z.Nowakowska, A.Cuppari, A.Jacula, M.Ksiazek, K.Mikruta, J.Wisniewski, N.Pudelko-Malik, A.Saran, N.Zeytuni, P.Mlynarz, R.J.Lamont, I.Uson, V.Siksnys, J.Potempa, M.Sola. Response Regulator Porx Coordinates Oligonucleotide Signalling and Gene Expression to Control the Secretion of Virulence Factors. Nucleic Acids Res. V. 50 12558 2022.
ISSN: ESSN 1362-4962
PubMed: 36464236
DOI: 10.1093/NAR/GKAC1103