Magnesium in PDB 7pvk: X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.

The structure of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg., PDB code: 7pvk 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)	51.90 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.63, 103.77, 132.21, 90, 98.5, 90
R / Rfree (%)	19.4 / 22.3

The structure of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Zinc	(Zn)	10 atoms

The binding sites of Magnesium atom in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. (pdb code 7pvk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg., PDB code: 7pvk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:73.8 occ:1.00 O A:ASN60 1.6 96.2 1.0 F1 A:BEF602 1.9 68.1 1.0 O A:HOH720 2.3 65.6 1.0 OD2 A:ASP58 2.3 115.9 1.0 OD1 A:ASP15 2.4 97.0 1.0 C A:ASN60 2.8 95.1 1.0 HB3 A:ASN60 2.9 111.2 1.0 OD2 A:ASP15 3.0 101.3 1.0 CG A:ASP15 3.0 102.8 1.0 BE A:BEF602 3.2 71.6 1.0 CG A:ASP58 3.4 110.6 1.0 HA A:MSE61 3.4 160.5 1.0 HG2 A:MSE61 3.5 143.7 1.0 HZ2 A:LYS87 3.5 133.7 1.0 CA A:ASN60 3.6 93.5 1.0 CB A:ASN60 3.6 93.1 1.0 HG3 A:MSE61 3.7 143.7 1.0 N A:MSE61 3.8 133.2 1.0 HD22 A:ASN60 3.8 153.2 1.0 H A:ASN60 3.8 111.7 1.0 OD1 A:ASP58 3.9 116.8 1.0 H A:ASP15 4.0 115.1 1.0 HZ1 A:LYS87 4.0 133.7 1.0 N A:ASN60 4.0 93.4 1.0 CG A:MSE61 4.0 119.7 1.0 CA A:MSE61 4.0 133.6 1.0 F3 A:BEF602 4.1 75.1 1.0 NZ A:LYS87 4.2 111.3 1.0 HG3 A:GLU16 4.2 132.2 1.0 ND2 A:ASN60 4.2 127.6 1.0 CG A:ASN60 4.3 112.0 1.0 F2 A:BEF602 4.4 80.1 1.0 CB A:ASP15 4.4 101.6 1.0 OD1 A:ASP14 4.4 98.4 1.0 HB2 A:ASN60 4.4 111.2 1.0 HA A:ASN60 4.5 111.7 1.0 HE3 A:LYS87 4.5 132.5 1.0 HB3 A:ASP58 4.6 119.2 1.0 HB3 A:ASP15 4.6 122.0 1.0 H A:MSE61 4.6 159.9 1.0 CB A:MSE61 4.6 129.4 1.0 CB A:ASP58 4.6 99.2 1.0 N A:ASP15 4.7 95.8 1.0 H A:GLU16 4.7 122.8 1.0 HZ3 A:LYS87 4.8 133.7 1.0 HD21 A:ASN60 4.9 153.2 1.0 CE A:LYS87 4.9 110.3 1.0 CG A:ASP14 5.0 93.0 1.0 C A:GLU59 5.0 98.2 1.0

Magnesium binding site 2 out of 4 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:114.1 occ:1.00 O B:ASN60 1.4 120.1 1.0 OD1 B:ASP15 1.9 153.7 1.0 F1 B:BEF602 1.9 113.2 1.0 OD2 B:ASP58 2.0 121.8 1.0 O B:HOH707 2.4 87.7 1.0 C B:ASN60 2.6 128.7 1.0 CG B:ASP15 2.7 149.3 1.0 BE B:BEF602 2.9 114.5 1.0 OD2 B:ASP15 3.0 170.9 1.0 HG3 B:MSE61 3.0 171.3 1.0 CG B:ASP58 3.0 120.2 1.0 HB3 B:ASN60 3.2 161.6 1.0 HA B:MSE61 3.2 168.4 1.0 H B:ASP15 3.3 133.3 1.0 OD1 B:ASP58 3.5 119.9 1.0 HG2 B:MSE61 3.6 171.3 1.0 N B:MSE61 3.6 133.3 1.0 CA B:ASN60 3.6 134.0 1.0 CG B:MSE61 3.7 142.7 1.0 OD1 B:ASP14 3.7 148.8 1.0 H B:ASN60 3.8 166.1 1.0 CA B:MSE61 3.8 140.2 1.0 CB B:ASN60 3.8 134.6 1.0 F2 B:BEF602 3.9 110.4 1.0 N B:ASN60 3.9 138.3 1.0 HG3 B:GLU16 4.0 184.6 1.0 CB B:ASP15 4.1 124.9 1.0 N B:ASP15 4.1 111.0 1.0 F3 B:BEF602 4.1 114.3 1.0 HB3 B:ASP58 4.2 141.6 1.0 HB3 B:ASP15 4.3 150.0 1.0 CB B:ASP58 4.3 117.9 1.0 H B:GLU16 4.3 242.1 1.0 CB B:MSE61 4.3 141.1 1.0 HB2 B:ASN60 4.4 161.6 1.0 H B:MSE61 4.4 160.0 1.0 HA B:ASP14 4.4 176.4 1.0 CG B:ASP14 4.4 147.8 1.0 HA B:ASN60 4.4 160.9 1.0 HE3 B:LYS87 4.6 130.3 1.0 CA B:ASP15 4.7 126.3 1.0 HZ3 B:LYS108 4.7 151.7 1.0 HZ1 B:LYS108 4.7 151.7 1.0 HZ2 B:LYS87 4.7 131.6 1.0 HB2 B:ASP15 4.7 150.0 1.0 C B:GLU59 4.8 138.4 1.0 HB2 B:ASP58 4.8 141.6 1.0 HZ2 B:LYS108 4.8 151.7 1.0 OD2 B:ASP14 4.8 142.9 1.0 HB2 B:MSE61 4.8 169.3 1.0 HD22 B:ASN60 4.8 163.4 1.0 CG B:GLU16 4.9 153.8 1.0 HZ1 B:LYS87 4.9 131.6 1.0 NZ B:LYS108 5.0 126.4 1.0 N B:GLU16 5.0 201.7 1.0 CG B:ASN60 5.0 135.6 1.0

Magnesium binding site 3 out of 4 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:61.9 occ:1.00 O C:ASN60 1.7 91.8 1.0 OD2 C:ASP58 2.0 84.0 1.0 OD1 C:ASP15 2.0 101.9 1.0 F1 C:BEF602 2.1 53.0 1.0 O C:HOH722 2.3 49.0 1.0 O C:HOH775 2.4 72.1 1.0 CG C:ASP15 2.6 99.8 1.0 OD2 C:ASP15 2.7 102.7 1.0 C C:ASN60 2.8 82.0 1.0 CG C:ASP58 3.1 80.3 1.0 HB3 C:ASN60 3.2 102.2 1.0 HG2 C:MSE61 3.2 107.3 1.0 BE C:BEF602 3.3 52.0 1.0 HA C:MSE61 3.4 110.1 1.0 H C:ASP15 3.7 104.2 1.0 OD1 C:ASP58 3.7 85.1 1.0 H C:ASN60 3.7 94.2 1.0 CA C:ASN60 3.7 81.9 1.0 HG3 C:MSE61 3.8 107.3 1.0 N C:MSE61 3.8 95.0 1.0 HG3 C:GLU16 3.9 103.2 1.0 CB C:ASN60 3.9 85.1 1.0 CG C:MSE61 3.9 89.3 1.0 N C:ASN60 4.0 78.4 1.0 CB C:ASP15 4.0 92.8 1.0 CA C:MSE61 4.0 91.7 1.0 F3 C:BEF602 4.2 57.3 1.0 HB3 C:ASP15 4.2 111.4 1.0 OD1 C:ASP14 4.2 73.7 1.0 HB3 C:ASP58 4.3 95.0 1.0 HZ2 C:LYS87 4.3 99.2 1.0 CB C:ASP58 4.3 79.1 1.0 H C:GLU16 4.4 95.5 1.0 N C:ASP15 4.4 86.8 1.0 OE2 C:GLU16 4.4 85.4 1.0 F2 C:BEF602 4.5 53.2 1.0 CB C:MSE61 4.6 91.1 1.0 HZ2 C:LYS108 4.6 79.7 1.0 H C:MSE61 4.6 114.1 1.0 HA C:ASN60 4.6 98.4 1.0 HB2 C:ASN60 4.6 102.2 1.0 HD3 C:PRO62 4.6 101.6 1.0 HB2 C:ASP15 4.6 111.4 1.0 CG C:ASN60 4.7 86.1 1.0 HZ1 C:LYS108 4.7 79.7 1.0 HB2 C:ASP58 4.7 95.0 1.0 CG C:GLU16 4.7 86.0 1.0 CA C:ASP15 4.8 84.8 1.0 HD3 C:LYS87 4.8 100.1 1.0 HZ3 C:LYS87 4.9 99.2 1.0 HA C:ASP14 4.9 87.6 1.0 CD C:GLU16 4.9 83.6 1.0 CG C:ASP14 4.9 71.9 1.0 HZ3 C:LYS108 4.9 79.7 1.0 NZ C:LYS108 4.9 66.4 1.0 N C:GLU16 5.0 79.5 1.0 H C:GLU59 5.0 90.5 1.0 NZ C:LYS87 5.0 82.6 1.0 HD2 C:LYS87 5.0 100.1 1.0

Magnesium binding site 4 out of 4 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:81.5 occ:1.00 F1 D:BEF602 1.8 77.7 1.0 O D:ASN60 1.9 113.4 1.0 OD2 D:ASP58 2.1 107.7 1.0 O D:HOH739 2.1 73.0 1.0 OD1 D:ASP15 2.1 110.8 1.0 O D:HOH719 2.2 80.2 1.0 BE D:BEF602 3.0 74.2 1.0 CG D:ASP15 3.0 110.9 1.0 C D:ASN60 3.1 104.6 1.0 CG D:ASP58 3.1 102.8 1.0 OD2 D:ASP15 3.2 116.8 1.0 HB3 D:ASN60 3.3 152.9 1.0 OD1 D:ASP58 3.6 104.3 1.0 HG2 D:MSE61 3.6 141.1 1.0 HG3 D:MSE61 3.7 141.1 1.0 H D:ASN60 3.7 125.9 1.0 HG3 D:GLU16 3.7 143.4 1.0 HZ2 D:LYS87 3.7 148.9 1.0 H D:ASP15 3.8 102.0 1.0 HA D:MSE61 3.8 151.8 1.0 CA D:ASN60 3.9 110.6 1.0 CB D:ASN60 4.0 127.4 1.0 F2 D:BEF602 4.0 79.3 1.0 OD1 D:ASP14 4.1 86.0 1.0 N D:ASN60 4.1 104.9 1.0 F3 D:BEF602 4.1 73.0 1.0 CG D:MSE61 4.1 117.5 1.0 N D:MSE61 4.1 127.8 1.0 HD22 D:ASN60 4.3 218.8 1.0 HB3 D:ASP58 4.3 119.8 1.0 CB D:ASP58 4.4 99.7 1.0 OE1 D:GLU16 4.4 114.2 1.0 CB D:ASP15 4.4 102.4 1.0 CA D:MSE61 4.4 126.5 1.0 H D:GLU16 4.4 149.4 1.0 HZ1 D:LYS87 4.5 148.9 1.0 NZ D:LYS87 4.5 124.0 1.0 N D:ASP15 4.5 85.0 1.0 HB3 D:ASP15 4.6 123.0 1.0 CG D:ASN60 4.6 154.9 1.0 CG D:GLU16 4.6 119.4 1.0 ND2 D:ASN60 4.7 182.3 1.0 HZ2 D:LYS108 4.7 113.9 1.0 CG D:ASP14 4.8 85.5 1.0 HB2 D:ASN60 4.8 152.9 1.0 HB2 D:ASP58 4.8 119.8 1.0 HZ3 D:LYS87 4.8 148.9 1.0 HA D:ASP14 4.8 112.5 1.0 HA D:ASN60 4.8 132.8 1.0 CB D:MSE61 4.9 124.4 1.0 HG2 D:GLU16 4.9 143.4 1.0 H D:MSE61 4.9 153.5 1.0 CD D:GLU16 5.0 116.2 1.0 OD2 D:ASP14 5.0 81.0 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