Zinc in PDB 4mjt: Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin

The structure of Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin, PDB code: 4mjt was solved by P.Leone, A.Roussel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.34 / 2.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.400, 146.200, 144.320, 90.00, 122.80, 90.00
R / Rfree (%)	18.2 / 21.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin (pdb code 4mjt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 27 binding sites of Zinc where determined in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin, PDB code: 4mjt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


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 the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:56.2 occ:1.00 OD1 A:ASP266 2.0 51.3 1.0 ND1 A:HIS268 2.2 50.9 1.0 CG A:ASP266 2.8 51.8 1.0 CE1 A:HIS268 3.0 50.3 1.0 OD2 A:ASP266 3.0 57.8 1.0 CG A:HIS268 3.2 49.5 1.0 CB A:HIS268 3.7 46.5 1.0 CD A:PRO267 4.1 51.6 1.0 NE2 A:HIS268 4.2 50.7 1.0 CB A:ASP266 4.2 47.3 1.0 CD2 A:HIS268 4.3 51.0 1.0 N A:HIS268 4.3 46.7 1.0 CA A:ASP266 4.6 47.2 1.0 CA A:HIS268 4.6 46.1 1.0 N A:PRO267 4.7 50.0 1.0 CA B:ALA198 4.7 36.9 1.0 CB B:ALA198 4.8 37.5 1.0 C A:ASP266 4.9 53.2 1.0

Zinc binding site 2 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


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 the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:83.8 occ:0.89 OD2 A:ASP237 2.0 81.6 1.0 OD2 A:ASP235 2.1 68.1 1.0 CG A:ASP237 3.0 70.7 1.0 CG A:ASP235 3.0 59.0 1.0 OD1 A:ASP237 3.3 73.1 1.0 OD1 A:ASP235 3.4 58.7 1.0 OE2 I:GLU144 4.1 82.2 1.0 CE I:LYS46 4.3 88.2 1.0 CB A:ASP235 4.3 44.4 1.0 NH2 A:ARG241 4.3 77.0 1.0 O A:HOH459 4.3 44.8 1.0 CB A:ASP237 4.3 46.5 1.0 NZ I:LYS46 4.4 94.3 1.0 OG1 A:THR238 4.4 48.9 1.0 CD I:GLU144 4.7 88.6 1.0 CG I:GLU144 4.8 58.3 1.0 N A:THR238 5.0 40.8 1.0

Zinc binding site 3 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


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 the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:97.5 occ:1.00 OD1 A:ASP75 2.2 70.0 1.0 NE2 J:HIS13 2.5 92.5 1.0 OD2 A:ASP75 2.6 78.9 1.0 CG A:ASP75 2.7 68.4 1.0 CE1 J:HIS13 3.3 92.2 1.0 CD2 J:HIS13 3.4 92.8 1.0 O A:HOH450 3.5 62.9 1.0 CB A:ASP75 4.2 48.1 1.0 ND1 J:HIS13 4.4 92.8 1.0 CG J:HIS13 4.5 90.9 1.0 CB A:ASN82 4.9 48.9 1.0

Zinc binding site 4 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


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 the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:55.0 occ:1.00 OD1 B:ASP266 2.0 56.0 1.0 ND1 B:HIS268 2.1 52.8 1.0 CG B:ASP266 2.8 56.3 1.0 CE1 B:HIS268 2.9 52.0 1.0 OD2 B:ASP266 3.1 65.9 1.0 CG B:HIS268 3.2 50.9 1.0 CB B:HIS268 3.6 47.4 1.0 CD B:PRO267 4.0 46.5 1.0 NE2 B:HIS268 4.1 52.2 1.0 CB B:ASP266 4.2 44.6 1.0 N B:HIS268 4.2 47.2 1.0 CD2 B:HIS268 4.2 52.4 1.0 CA B:HIS268 4.6 46.6 1.0 CA B:ASP266 4.6 43.1 1.0 N B:PRO267 4.6 44.9 1.0 CA C:ALA198 4.6 46.9 1.0 CB C:ALA198 4.7 47.4 1.0 C B:ASP266 4.9 47.6 1.0

Zinc binding site 5 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


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 the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.6 occ:1.00 OD2 B:ASP235 2.4 68.0 1.0 OD2 B:ASP237 2.5 83.2 1.0 CG B:ASP235 3.3 54.1 1.0 CG B:ASP237 3.4 68.1 1.0 CB B:ASP237 3.4 40.0 1.0 OD1 B:ASP235 3.6 53.8 1.0 OE2 A:GLU144 3.6 88.9 1.0 NZ A:LYS46 3.8 92.7 1.0 CE A:LYS46 3.9 78.7 1.0 O B:HOH463 4.1 38.8 1.0 NH2 B:ARG241 4.3 75.2 1.0 CD A:GLU144 4.4 88.7 1.0 CG A:GLU144 4.5 55.8 1.0 CB B:ASP235 4.5 34.8 1.0 OD1 B:ASP237 4.6 70.7 1.0 OG1 B:THR238 4.6 44.9 1.0 CA B:ASP237 4.8 36.5 1.0 N B:THR238 5.0 36.3 1.0

Zinc binding site 6 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


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 the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:73.2 occ:1.00 OD1 B:ASP75 2.1 53.4 1.0 NE2 K:HIS13 2.4 71.9 1.0 O B:HOH485 2.5 36.7 1.0 O B:HOH490 2.8 55.4 1.0 CG B:ASP75 2.8 51.7 1.0 OD2 B:ASP75 2.9 61.9 1.0 O B:HOH466 2.9 51.9 1.0 CD2 K:HIS13 3.4 72.1 1.0 CE1 K:HIS13 3.4 71.6 1.0 CB B:ASP75 4.3 31.7 1.0 CG K:HIS13 4.5 70.1 1.0 ND1 K:HIS13 4.5 72.0 1.0 CB B:ASN82 4.7 32.9 1.0

Zinc binding site 7 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:75.2 occ:1.00 OD1 C:ASP266 2.0 68.3 1.0 ND1 C:HIS268 2.1 72.9 1.0 CG C:ASP266 2.9 68.9 1.0 CE1 C:HIS268 2.9 72.6 1.0 OD2 C:ASP266 3.1 75.0 1.0 CG C:HIS268 3.2 70.6 1.0 CB C:HIS268 3.6 66.4 1.0 NE2 C:HIS268 4.1 72.8 1.0 CD C:PRO267 4.2 64.7 1.0 CD2 C:HIS268 4.2 72.9 1.0 CB C:ASP266 4.3 61.2 1.0 N C:HIS268 4.3 64.8 1.0 CA C:HIS268 4.6 64.9 1.0 CA C:ASP266 4.7 59.8 1.0 N C:PRO267 4.7 62.9 1.0 CA D:ALA198 4.9 70.9 1.0 CB D:ALA198 5.0 71.5 1.0

Zinc binding site 8 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:78.6 occ:0.57 OD1 C:ASP237 2.3 78.0 1.0 OD2 C:ASP237 2.4 84.1 1.0 OD2 C:ASP235 2.5 63.0 1.0 CG C:ASP237 2.6 74.4 1.0 O C:HOH412 3.2 70.8 1.0 CG C:ASP235 3.3 52.8 1.0 OD1 C:ASP235 3.6 51.5 1.0 NZ B:LYS46 3.7 85.5 1.0 CE B:LYS46 3.9 76.2 1.0 NH2 C:ARG241 4.0 90.2 1.0 CB C:ASP237 4.1 47.2 1.0 OE2 B:GLU144 4.2 73.5 1.0 OG1 C:THR238 4.3 45.5 1.0 CB C:ASP235 4.7 39.4 1.0 CD B:LYS46 4.8 64.2 1.0 CD B:GLU144 4.9 76.2 1.0 CG B:GLU144 4.9 45.7 1.0

Zinc binding site 9 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:85.8 occ:1.00 OD1 C:ASP75 2.1 64.3 1.0 NE2 L:HIS13 2.5 0.7 1.0 CG C:ASP75 2.8 62.9 1.0 OD2 C:ASP75 2.9 69.2 1.0 O C:HOH439 3.0 34.6 1.0 CD2 L:HIS13 3.4 0.8 1.0 CE1 L:HIS13 3.5 0.4 1.0 CB C:ASP75 4.3 48.0 1.0 O C:HOH440 4.5 41.2 1.0 CG L:HIS13 4.6 100.0 1.0 ND1 L:HIS13 4.6 0.9 1.0 CB C:ASN82 4.7 47.0 1.0

Zinc binding site 10 out of 27 in the Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Oligomeric Pore-Forming Toxin Pro-Monalysin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:82.3 occ:1.00 OD1 D:ASP266 2.1 81.0 1.0 ND1 D:HIS268 2.2 75.5 1.0 CG D:ASP266 2.9 80.3 1.0 CE1 D:HIS268 3.0 74.8 1.0 OD2 D:ASP266 3.2 85.5 1.0 CG D:HIS268 3.4 73.3 1.0 CB D:HIS268 3.9 69.5 1.0 CD D:PRO267 4.0 71.2 1.0 NE2 D:HIS268 4.2 75.0 1.0 CB D:ASP266 4.3 71.0 1.0 CD2 D:HIS268 4.4 75.1 1.0 N D:HIS268 4.4 68.5 1.0 CA D:ASP266 4.6 69.6 1.0 N D:PRO267 4.7 69.9 1.0 CA D:HIS268 4.8 68.3 1.0 C D:ASP266 5.0 73.7 1.0

P.Leone, A.Roussel. A Monalysin Toxin Hypothetical Pore Formation Mechanism Deduced From X-Ray and Cryoem Studies To Be Published.