Magnesium in PDB 4ykh: Thirty Minutes Iron Loaded Human H Ferritin

All present enzymatic activity of Thirty Minutes Iron Loaded Human H Ferritin:
1.16.3.1;

The structure of Thirty Minutes Iron Loaded Human H Ferritin, PDB code: 4ykh was solved by C.Pozzi, F.Di Pisa, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.07 / 1.52
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	184.050, 184.050, 184.050, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.7

The structure of Thirty Minutes Iron Loaded Human H Ferritin also contains other interesting chemical elements:

Iron	(Fe)	7 atoms
Chlorine	(Cl)	12 atoms

The binding sites of Magnesium atom in the Thirty Minutes Iron Loaded Human H Ferritin (pdb code 4ykh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Thirty Minutes Iron Loaded Human H Ferritin, PDB code: 4ykh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Thirty Minutes Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg209 b:8.0 occ:0.40 O A:HOH437 2.1 14.2 0.4 O A:HOH413 2.1 15.7 0.8 O A:HOH326 4.2 16.0 1.0 O A:HOH430 4.5 28.5 1.0 NZ A:LYS86 4.5 14.5 0.8 O A:HOH427 4.6 29.0 1.0 CD A:LYS86 4.7 13.1 1.0 CE A:LYS87 4.7 14.8 0.6

Magnesium binding site 2 out of 4 in the Thirty Minutes Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:12.1 occ:0.60 O A:HOH438 2.2 18.9 0.6 O A:HOH355 2.2 16.9 0.6 O A:HOH349 2.2 24.6 0.6 OD1 A:ASP131 4.1 11.5 0.6 O A:HOH315 4.2 25.7 1.0 OD2 A:ASP131 4.3 11.4 0.4 CG2 A:THR135 4.4 13.2 1.0 OD2 A:ASP131 4.5 11.7 0.6 OG1 A:THR135 4.7 13.3 1.0 CG A:ASP131 4.8 11.3 0.6 O A:HOH425 5.0 23.3 0.3

Magnesium binding site 3 out of 4 in the Thirty Minutes Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg211 b:14.0 occ:0.60 O A:HOH612 1.9 15.6 0.6 O A:HOH536 2.0 21.9 0.6 O A:HOH576 2.1 25.5 0.6 O A:HOH607 2.2 21.2 0.6 O A:HOH467 2.2 20.0 0.6 O A:HOH454 2.3 15.6 1.0 OD1 A:ASN25 4.2 9.1 1.0 O A:HOH520 4.4 26.5 1.0 CL A:CL220 4.4 22.0 0.6 O A:ARG22 4.4 9.8 1.0 O A:HOH493 4.6 21.3 1.0 O A:HOH527 4.9 32.8 1.0 O A:HOH471 4.9 21.5 1.0 CB A:LEU26 4.9 9.2 1.0 CG A:ASN25 5.0 8.8 1.0 CB A:ASN25 5.0 8.6 1.0

Magnesium binding site 4 out of 4 in the Thirty Minutes Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg212 b:17.9 occ:0.60 O A:HOH516 2.0 20.6 0.6 O A:HOH466 2.0 10.1 0.6 O A:HOH517 2.1 19.2 0.6 O A:HOH618 2.1 29.8 0.6 O A:HOH525 2.2 22.6 0.6 O A:HOH583 2.2 31.4 0.6 O A:HOH356 3.9 39.6 1.0 O A:HOH502 4.1 32.4 1.0 O A:LYS124 4.2 11.2 1.0 O A:HOH433 4.2 17.7 1.0 OD1 A:ASN11 4.3 10.9 1.0 O A:HOH398 4.5 24.5 1.0 O A:HOH480 4.6 22.0 1.0 O A:HOH350 4.7 15.7 1.0 CB A:ASN125 4.7 12.7 1.0 C A:LYS124 5.0 11.4 1.0

C.Pozzi, F.Di Pisa, C.Bernacchioni, S.Ciambellotti, P.Turano, S.Mangani. Iron Binding to Human Heavy-Chain Ferritin. Acta Crystallogr.,Sect.D V. 71 1909 2015.
ISSN: ESSN 1399-0047
PubMed: 26327381
DOI: 10.1107/S1399004715013073