Zinc in PDB 7pva: 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc

The structure of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc, PDB code: 7pva 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)	68.59 / 1.91
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.48, 77.29, 138.83, 82.42, 81.61, 76.51
R / Rfree (%)	15.9 / 19.2

The structure of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc also contains other interesting chemical elements:

Fluorine	(F)	24 atoms
Magnesium	(Mg)	11 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc (pdb code 7pva). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc, PDB code: 7pva:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:47.6 occ:0.75 OD1 A:ASP239 2.1 44.5 1.0 OD2 A:ASP415 2.1 42.2 1.0 OG1 A:THR272 2.1 54.5 1.0 NE2 A:HIS416 2.2 37.9 1.0 OD2 A:ASP239 2.5 41.8 1.0 CG A:ASP239 2.6 36.5 1.0 HG23 A:THR272 2.8 53.9 1.0 F2 A:BEF611 2.9 56.6 1.0 CD2 A:HIS416 2.9 39.4 1.0 CG A:ASP415 3.0 40.6 1.0 HD2 A:HIS416 3.0 47.2 1.0 CB A:THR272 3.1 47.9 1.0 OD1 A:ASP415 3.1 35.6 1.0 HA A:THR272 3.1 49.9 1.0 BE A:BEF611 3.1 53.9 1.0 CE1 A:HIS416 3.2 41.2 1.0 CG2 A:THR272 3.4 44.9 1.0 CA A:THR272 3.4 41.5 1.0 HE1 A:HIS416 3.5 49.4 1.0 H A:THR272 3.6 44.1 1.0 N A:THR272 3.7 36.8 1.0 HG21 A:THR272 3.9 53.9 1.0 HB A:THR272 3.9 57.5 1.0 H A:ASN240 4.0 47.1 1.0 CB A:ASP239 4.0 31.5 1.0 HD3 A:ARG276 4.1 43.8 1.0 CG A:HIS416 4.1 38.7 1.0 F3 A:BEF611 4.1 53.0 1.0 HG22 A:THR272 4.2 53.9 1.0 ND1 A:HIS416 4.2 38.1 1.0 F1 A:BEF611 4.2 58.2 1.0 HB2 A:ASN240 4.3 48.0 1.0 HA A:ASP239 4.3 41.9 1.0 CB A:ASP415 4.4 40.3 1.0 O A:HOH1051 4.4 80.8 1.0 HB2 A:ARG276 4.4 49.7 1.0 N A:ASN240 4.4 39.3 1.0 HB3 A:ASP239 4.5 37.8 1.0 HB2 A:ASP415 4.5 48.4 1.0 HH11 A:ARG276 4.5 47.5 1.0 HA A:ALA271 4.5 50.2 1.0 HB2 A:ASP239 4.5 37.8 1.0 C A:ALA271 4.6 40.6 1.0 HE1 A:HIS500 4.6 58.7 1.0 CA A:ASP239 4.6 34.9 1.0 OD1 A:ASP361 4.6 59.9 1.0 HB2 A:ASP361 4.7 58.4 1.0 HB3 A:ASP415 4.8 48.4 1.0 CG A:ASP361 4.8 58.9 1.0 CE1 A:HIS500 4.8 48.9 1.0 C A:THR272 4.9 41.9 1.0 C A:ASP239 4.9 36.3 1.0 ZN A:ZN604 4.9 46.4 0.2 HD1 A:HIS416 5.0 45.7 1.0 HA A:ASN240 5.0 45.9 1.0

Zinc binding site 2 out of 6 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:46.4 occ:0.22 NE2 A:HIS365 2.0 74.1 1.0 F2 A:BEF611 2.1 56.6 1.0 NE2 A:HIS500 2.2 52.2 1.0 OD1 A:ASP361 2.2 59.9 1.0 O C:HOH796 2.6 63.4 1.0 OD2 A:ASP361 2.9 68.2 1.0 CG A:ASP361 2.9 58.9 1.0 CE1 A:HIS365 3.0 73.7 1.0 CD2 A:HIS365 3.0 70.0 1.0 CE1 A:HIS500 3.1 48.9 1.0 HE1 A:HIS365 3.1 88.5 1.0 CD2 A:HIS500 3.2 47.6 1.0 HE1 A:HIS500 3.2 58.7 1.0 HD2 A:HIS365 3.3 84.1 1.0 BE A:BEF611 3.3 53.9 1.0 HD2 A:HIS500 3.4 57.1 1.0 F3 A:BEF611 3.5 53.0 1.0 HD22 A:ASN240 3.5 54.2 1.0 F1 A:BEF611 3.7 58.2 1.0 HE1 A:HIS416 3.8 49.4 1.0 ND1 A:HIS365 4.1 72.7 1.0 CG A:HIS365 4.2 68.9 1.0 O A:HOH1114 4.2 62.0 1.0 ND2 A:ASN240 4.2 45.2 1.0 ND1 A:HIS500 4.2 48.6 1.0 CG A:HIS500 4.3 46.2 1.0 HD21 A:ASN240 4.4 54.2 1.0 CB A:ASP361 4.4 48.7 1.0 OG1 A:THR272 4.4 54.5 1.0 CE1 A:HIS416 4.5 41.2 1.0 HB2 A:ASN240 4.6 48.0 1.0 HB2 A:ASP361 4.7 58.4 1.0 OD1 A:ASP239 4.8 44.5 1.0 NE2 A:HIS416 4.8 37.9 1.0 O A:ASP361 4.8 39.3 1.0 OE1 C:GLU302 4.8 119.3 1.0 HA A:ASP361 4.9 54.4 1.0 HD1 A:HIS365 4.9 87.3 1.0 O A:HOH974 4.9 44.6 1.0 ZN A:ZN603 4.9 47.6 0.8 HB3 A:ASP361 4.9 58.4 1.0 HD1 A:HIS500 5.0 58.3 1.0

Zinc binding site 3 out of 6 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:36.7 occ:0.16 OG1 B:THR272 1.6 45.5 1.0 HG1 B:THR272 1.7 54.6 1.0 NE2 B:HIS416 2.1 40.8 1.0 OD2 B:ASP239 2.2 60.2 1.0 BE B:BEF615 2.2 88.5 1.0 OD2 B:ASP415 2.5 45.2 1.0 CD2 B:HIS416 2.8 35.9 1.0 HD2 B:HIS416 2.8 43.1 1.0 F3 B:BEF615 3.0 84.6 1.0 F1 B:BEF615 3.0 92.2 1.0 CB B:THR272 3.0 37.7 1.0 CG B:ASP239 3.2 59.9 1.0 CG B:ASP415 3.2 43.2 1.0 CE1 B:HIS416 3.2 36.9 1.0 OD1 B:ASP415 3.2 36.3 1.0 F2 B:BEF615 3.3 89.4 1.0 H B:THR272 3.4 44.3 1.0 HA B:THR272 3.4 38.5 1.0 HH11 B:ARG276 3.5 69.0 1.0 OD1 B:ASP239 3.5 64.2 1.0 HE1 B:HIS416 3.5 44.3 1.0 HB B:THR272 3.6 45.3 1.0 CA B:THR272 3.6 32.0 1.0 N B:THR272 3.7 36.9 1.0 H B:ASN240 3.8 49.2 1.0 HB2 B:ASN240 3.9 49.8 1.0 HG21 B:THR272 3.9 51.3 1.0 CG2 B:THR272 3.9 42.7 1.0 HG23 B:THR272 4.0 51.3 1.0 CG B:HIS416 4.0 31.4 1.0 NH1 B:ARG276 4.1 57.5 1.0 HA B:ASP239 4.1 43.1 1.0 ND1 B:HIS416 4.2 38.7 1.0 N B:ASN240 4.2 41.0 1.0 HH12 B:ARG276 4.3 69.0 1.0 CB B:ASP239 4.4 46.1 1.0 HA B:ALA271 4.5 36.6 1.0 CB B:ASP415 4.5 30.6 1.0 HB2 B:ASP415 4.6 36.8 1.0 HE B:ARG276 4.6 61.4 1.0 HA B:ASN240 4.6 48.0 1.0 CA B:ASP239 4.6 35.9 1.0 C B:ALA271 4.7 34.6 1.0 HE2 B:HIS500 4.7 51.5 1.0 CB B:ASN240 4.7 41.5 1.0 HB2 B:ASP239 4.7 55.3 1.0 H B:HIS416 4.8 36.1 1.0 CA B:ASN240 4.8 40.0 1.0 C B:ASP239 4.8 33.6 1.0 HG22 B:THR272 4.8 51.3 1.0 HB2 B:ARG276 4.8 40.6 1.0 HO1 B:GOL608 4.9 126.3 1.0 CZ B:ARG276 4.9 56.9 1.0 NE2 B:HIS500 5.0 42.9 1.0 HD1 B:HIS416 5.0 46.4 1.0

Zinc binding site 4 out of 6 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:45.3 occ:0.59 OD2 C:ASP415 2.0 47.7 1.0 NE2 C:HIS416 2.0 51.2 1.0 OG1 C:THR272 2.1 56.2 1.0 OD1 C:ASP239 2.1 49.7 1.0 OD2 C:ASP239 2.3 47.5 1.0 CG C:ASP239 2.5 43.9 1.0 CD2 C:HIS416 2.8 50.5 1.0 F1 C:BEF610 2.8 56.7 1.0 HG23 C:THR272 2.8 64.8 1.0 CG C:ASP415 2.9 42.6 1.0 HD2 C:HIS416 2.9 60.6 1.0 BE C:BEF610 3.0 53.2 1.0 CB C:THR272 3.0 50.4 1.0 CE1 C:HIS416 3.1 53.0 1.0 OD1 C:ASP415 3.1 39.1 1.0 HA C:THR272 3.1 49.4 1.0 CG2 C:THR272 3.4 54.0 1.0 HE1 C:HIS416 3.4 63.6 1.0 CA C:THR272 3.4 41.1 1.0 H C:THR272 3.6 46.5 1.0 N C:THR272 3.7 38.7 1.0 HG21 C:THR272 3.8 64.8 1.0 HB C:THR272 3.9 60.5 1.0 H C:ASN240 3.9 49.1 1.0 CB C:ASP239 3.9 39.8 1.0 CG C:HIS416 4.0 49.7 1.0 HD3 C:ARG276 4.0 49.2 1.0 ND1 C:HIS416 4.1 50.0 1.0 F3 C:BEF610 4.1 56.5 1.0 F2 C:BEF610 4.2 59.3 1.0 HG22 C:THR272 4.2 64.8 1.0 HA C:ASP239 4.2 43.9 1.0 CB C:ASP415 4.3 43.7 1.0 HB2 C:ARG276 4.3 48.8 1.0 HB2 C:ASN240 4.4 59.0 1.0 N C:ASN240 4.4 40.9 1.0 HB2 C:ASP239 4.4 47.8 1.0 HB2 C:ASP415 4.4 52.5 1.0 HB3 C:ASP239 4.4 47.8 1.0 HH11 C:ARG276 4.5 50.3 1.0 CA C:ASP239 4.6 36.5 1.0 C C:ALA271 4.6 42.8 1.0 HE1 C:HIS500 4.6 59.6 1.0 HA C:ALA271 4.7 53.0 1.0 OD1 C:ASP361 4.7 49.1 1.0 CG C:ASP361 4.7 48.5 1.0 HB3 C:ASP415 4.7 52.5 1.0 O C:HOH800 4.7 69.7 1.0 HB2 C:ASP361 4.8 51.3 1.0 OD2 C:ASP361 4.8 54.1 1.0 ZN C:ZN604 4.8 55.5 0.2 C C:ASP239 4.9 38.8 1.0 HD1 C:HIS416 4.9 60.1 1.0 C C:THR272 4.9 39.4 1.0 CE1 C:HIS500 4.9 49.7 1.0 CD C:ARG276 5.0 41.0 1.0

Zinc binding site 5 out of 6 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn604 b:55.5 occ:0.21 F1 C:BEF610 2.0 56.7 1.0 NE2 C:HIS365 2.2 89.3 1.0 OD1 C:ASP361 2.3 49.1 1.0 NE2 C:HIS500 2.4 48.2 1.0 O C:HOH1001 2.6 79.3 1.0 OD2 C:ASP361 2.8 54.1 1.0 CG C:ASP361 2.9 48.5 1.0 BE C:BEF610 3.1 53.2 1.0 CE1 C:HIS365 3.1 91.2 1.0 CD2 C:HIS365 3.1 87.8 1.0 CE1 C:HIS500 3.2 49.7 1.0 HE1 C:HIS365 3.2 109.5 1.0 HE1 C:HIS500 3.3 59.6 1.0 HD2 C:HIS365 3.3 105.4 1.0 F3 C:BEF610 3.4 56.5 1.0 CD2 C:HIS500 3.4 45.2 1.0 F2 C:BEF610 3.5 59.3 1.0 HE1 C:HIS416 3.6 63.6 1.0 HD2 C:HIS500 3.7 54.3 1.0 HD22 C:ASN240 3.8 60.9 1.0 ND1 C:HIS365 4.2 89.7 1.0 CG C:HIS365 4.2 82.5 1.0 O A:HOH1077 4.3 77.0 1.0 OG1 C:THR272 4.3 56.2 1.0 ND1 C:HIS500 4.3 47.8 1.0 O C:HOH1017 4.4 94.3 1.0 CE1 C:HIS416 4.4 53.0 1.0 CB C:ASP361 4.4 42.7 1.0 CG C:HIS500 4.5 44.7 1.0 ND2 C:ASN240 4.5 50.7 1.0 HB2 C:ASN240 4.7 59.0 1.0 OD1 C:ASP239 4.7 49.7 1.0 NE2 C:HIS416 4.7 51.2 1.0 HD21 C:ASN240 4.7 60.9 1.0 HB2 C:ASP361 4.7 51.3 1.0 ZN C:ZN603 4.8 45.3 0.6 HA C:ASP361 4.9 51.9 1.0 HB3 C:ASP361 4.9 51.3 1.0 O C:ASP361 4.9 39.5 1.0 HD1 C:HIS365 4.9 107.7 1.0

Zinc binding site 6 out of 6 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:41.1 occ:0.15 OG1 D:THR272 1.4 56.9 1.0 HG1 D:THR272 1.6 68.3 1.0 HE2 D:HIS416 1.7 65.9 1.0 OD2 D:ASP239 2.0 61.4 0.5 OD2 D:ASP415 2.0 55.8 1.0 OD1 D:ASP239 2.1 61.1 0.5 NE2 D:HIS416 2.3 54.9 1.0 HD2 D:HIS416 2.6 61.5 1.0 CD2 D:HIS416 2.7 51.2 1.0 CB D:THR272 2.7 49.1 1.0 CG D:ASP415 2.7 46.2 1.0 CG D:ASP239 2.8 56.3 0.5 BE D:BEF610 2.8 97.7 1.0 OD1 D:ASP415 2.9 44.6 1.0 OD1 D:ASP239 2.9 54.9 0.5 HA D:THR272 2.9 57.0 1.0 F3 D:BEF610 3.2 102.0 1.0 CA D:THR272 3.2 47.5 1.0 CG D:ASP239 3.4 56.9 0.5 H D:THR272 3.4 54.4 1.0 HG21 D:THR272 3.4 55.2 1.0 HB D:THR272 3.4 58.9 1.0 CG2 D:THR272 3.4 46.0 1.0 CE1 D:HIS416 3.4 52.1 1.0 HG23 D:THR272 3.5 55.2 1.0 N D:THR272 3.6 45.3 1.0 F1 D:BEF610 3.6 94.5 1.0 H D:ASN240 3.8 46.9 0.5 H D:ASN240 3.8 46.9 0.5 HE1 D:HIS416 3.9 62.5 1.0 F2 D:BEF610 3.9 96.0 1.0 CG D:HIS416 3.9 49.1 1.0 HD3 D:ARG276 4.0 61.9 1.0 HA D:ASP239 4.0 52.9 0.5 HA D:ASP239 4.1 52.8 0.5 CB D:ASP415 4.1 40.1 1.0 OD2 D:ASP239 4.1 62.4 0.5 CB D:ASP239 4.1 51.3 0.5 HB2 D:ASP415 4.1 48.2 1.0 HH11 D:ARG276 4.2 69.1 1.0 HB2 D:ARG276 4.2 54.5 1.0 ND1 D:HIS416 4.2 52.1 1.0 HB2 D:ASN240 4.3 54.5 1.0 CB D:ASP239 4.3 51.1 0.5 HB2 D:ASP239 4.3 61.3 0.5 N D:ASN240 4.3 39.1 1.0 HG22 D:THR272 4.4 55.2 1.0 HB3 D:ASP239 4.5 61.6 0.5 CA D:ASP239 4.6 44.0 0.5 C D:ALA271 4.6 48.9 1.0 CA D:ASP239 4.6 44.0 0.5 HB3 D:ASP415 4.6 48.2 1.0 C D:THR272 4.7 47.4 1.0 H D:HIS416 4.7 45.3 1.0 HA D:ALA271 4.8 60.3 1.0 HB2 D:ASP239 4.8 61.6 0.5 NH1 D:ARG276 4.8 57.5 1.0 H D:ASP415 4.8 45.4 1.0 C D:ASP239 4.9 42.5 0.5 C D:ASP239 4.9 42.6 0.5 CD D:ARG276 4.9 51.6 1.0 O D:HOH928 4.9 76.3 1.0 HE1 D:HIS500 5.0 60.8 1.0 N D:HIS416 5.0 37.8 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