Magnesium in PDB 4i0n: Pore Forming Protein

The structure of Pore Forming Protein, PDB code: 4i0n was solved by X.Yan, C.J.Porter, S.P.Hardy, D.Steer, A.I.Smith, N.Quinset, V.Hughes, J.K.Cheung, A.L.Keyburn, M.Kaldhusdal, R.J.Moore, T.L.Bannam, J.C.Whisstock, J.I.Rood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.40 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.444, 29.698, 56.265, 90.00, 99.09, 90.00
R / Rfree (%)	16.8 / 20.5

The binding sites of Magnesium atom in the Pore Forming Protein (pdb code 4i0n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Pore Forming Protein, PDB code: 4i0n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Pore Forming Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pore Forming Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:35.4 occ:1.00 O A:HOH753 2.0 19.3 1.0 O A:HOH630 2.1 29.8 1.0 O A:HOH754 2.1 23.6 1.0 O A:HOH560 2.1 13.2 1.0 O A:HOH673 2.2 20.5 1.0 O A:HOH755 2.3 26.4 1.0 O A:GLY211 4.3 15.8 1.0 O A:HOH648 4.4 22.7 1.0 OE1 A:GLU207 4.4 22.1 1.0 CA A:GLY211 4.5 14.9 1.0 O A:HOH571 4.7 16.6 1.0 O A:HOH709 4.9 25.9 1.0 C A:GLY211 4.9 14.3 1.0

Magnesium binding site 2 out of 5 in the Pore Forming Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pore Forming Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:33.7 occ:1.00 O A:HOH751 2.0 27.9 1.0 O A:HOH697 2.0 25.8 1.0 O A:HOH752 2.1 12.9 1.0 O A:HOH682 2.2 23.1 1.0 OE1 A:GLU306 4.0 19.5 1.0 OE2 A:GLU275 4.1 15.0 1.0 O A:HOH681 4.7 25.8 1.0 NZ A:LYS123 4.8 20.8 1.0 OE2 A:GLU306 4.8 20.6 1.0 CD A:GLU306 4.8 19.5 1.0 OH A:TYR304 4.9 17.3 1.0

Magnesium binding site 3 out of 5 in the Pore Forming Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pore Forming Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:26.6 occ:1.00 O A:HOH597 2.0 15.2 1.0 O A:HOH746 2.0 23.1 1.0 O A:HOH611 2.1 21.6 1.0 O A:HOH535 2.1 11.5 1.0 O A:HOH745 2.2 20.8 1.0 OD2 A:ASP242 3.9 23.0 1.0 O A:HOH738 4.0 34.5 1.0 O A:HOH659 4.1 18.1 1.0 O A:SER250 4.1 14.2 1.0 OD1 A:ASP242 4.3 19.6 1.0 O A:LYS101 4.4 13.4 1.0 O A:HOH599 4.5 33.0 1.0 CG A:ASP242 4.5 20.0 1.0 CE A:LYS101 4.6 19.6 1.0 NZ A:LYS101 4.7 17.9 1.0

Magnesium binding site 4 out of 5 in the Pore Forming Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pore Forming Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:31.5 occ:1.00 O A:HOH559 2.1 16.2 1.0 O A:HOH699 2.1 21.9 1.0 O A:HOH704 2.1 24.6 1.0 OD1 A:ASP63 2.2 13.3 1.0 O A:HOH603 2.4 15.8 1.0 CG A:ASP63 3.2 12.5 1.0 OD2 A:ASP63 3.5 13.4 1.0 O A:THR64 4.1 11.8 1.0 O A:HOH657 4.2 22.4 1.0 N A:THR64 4.4 11.6 1.0 CB A:ASP63 4.5 10.3 1.0 O A:HOH654 4.7 31.4 1.0 CA A:ASP63 4.8 10.7 1.0 OG1 A:THR64 4.9 16.8 0.5 CG2 A:THR64 5.0 15.9 0.5

Magnesium binding site 5 out of 5 in the Pore Forming Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pore Forming Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:29.6 occ:1.00 O A:HOH757 2.1 18.4 1.0 O A:HOH706 2.1 19.2 1.0 O A:HOH649 2.1 12.9 1.0 O A:HOH748 2.1 19.0 1.0 O A:HOH749 2.2 30.6 1.0 O A:HOH583 2.2 19.7 1.0 OD1 A:ASP195 4.0 26.7 1.0 OD1 A:ASN197 4.1 16.8 1.0 CB A:ASN197 4.2 14.2 1.0 O A:HOH666 4.2 26.9 1.0 OD2 A:ASP195 4.3 27.8 1.0 CG A:ASP195 4.4 23.4 1.0 CG A:ASN197 4.6 15.9 1.0 N A:ASN197 4.8 13.8 1.0

X.X.Yan, C.J.Porter, S.P.Hardy, D.Steer, A.I.Smith, N.S.Quinsey, V.Hughes, J.K.Cheung, A.L.Keyburn, M.Kaldhusdal, R.J.Moore, T.L.Bannam, J.C.Whisstock, J.I.Rood. Structural and Functional Analysis of the Pore-Forming Toxin Netb From Clostridium Perfringens Mbio V. 4 00019 2013.
ISSN: ESSN 2150-7511
PubMed: 23386432
DOI: 10.1128/MBIO.00019-13