Magnesium in PDB 7vhr: Apostichopus Japonicus Ferritin

All present enzymatic activity of Apostichopus Japonicus Ferritin:
1.16.3.1;

The structure of Apostichopus Japonicus Ferritin, PDB code: 7vhr was solved by Y.Wu, X.R.Su, T.H.Ming, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.66 / 2.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	126.82, 178.78, 126.71, 90, 90.26, 90
R / Rfree (%)	19 / 26.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Magnesium atom in the Apostichopus Japonicus Ferritin (pdb code 7vhr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 40 binding sites of Magnesium where determined in the Apostichopus Japonicus Ferritin, PDB code: 7vhr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:2.7 occ:1.00 OE1 A:GLU60 2.1 30.0 1.0 CD2 A:HIS63 2.3 44.8 1.0 OE2 A:GLU25 2.3 40.7 1.0 CD A:GLU60 3.2 30.0 1.0 CG A:HIS63 3.3 44.4 1.0 NE2 A:HIS63 3.3 47.5 1.0 CD A:GLU25 3.5 39.9 1.0 NE2 A:GLN139 3.6 49.6 1.0 CB A:HIS63 3.7 40.8 1.0 OE2 A:GLU60 3.8 30.0 1.0 OE1 A:GLU25 4.0 45.1 1.0 CG1 A:VAL108 4.2 39.1 1.0 CG A:GLU60 4.4 30.0 1.0 ND1 A:HIS63 4.5 46.2 1.0 CE1 A:HIS63 4.5 48.0 1.0 CB A:GLU60 4.5 30.0 1.0 CA A:GLU60 4.6 42.9 1.0 CG A:GLU25 4.8 39.3 1.0 OE1 A:GLU105 4.8 47.3 1.0 CB A:GLU25 4.9 39.1 1.0 CD A:GLN139 4.9 44.3 1.0

Magnesium binding site 2 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:42.7 occ:1.00 OE1 G:GLU132 2.6 56.2 1.0 OE2 A:GLU132 2.6 62.2 1.0 O F:HOH365 2.7 42.2 1.0 OE2 G:GLU132 2.8 59.4 1.0 OE1 F:GLU132 2.8 55.7 1.0 OE1 A:GLU132 3.0 66.0 1.0 OE2 F:GLU132 3.0 55.1 1.0 CD G:GLU132 3.0 55.1 1.0 CD A:GLU132 3.2 58.0 1.0 CD F:GLU132 3.3 51.9 1.0 CG G:GLU132 4.5 48.9 1.0 CG A:GLU132 4.7 51.7 1.0 CG F:GLU132 4.8 47.8 1.0

Magnesium binding site 3 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:2.6 occ:1.00 OE2 B:GLU60 2.2 34.4 1.0 OE1 B:GLU25 2.2 43.1 1.0 ND1 B:HIS63 2.2 42.6 1.0 CE1 B:HIS63 3.0 38.6 1.0 CD B:GLU60 3.1 42.4 1.0 NE2 B:GLN139 3.1 48.6 1.0 CD B:GLU25 3.2 41.7 1.0 CG B:HIS63 3.3 39.3 1.0 O B:HOH314 3.3 49.1 1.0 OE1 B:GLU60 3.4 57.2 1.0 OE2 B:GLU25 3.5 47.1 1.0 CB B:HIS63 3.8 38.1 1.0 OE2 B:GLU105 4.0 58.2 1.0 NE2 B:HIS63 4.2 35.7 1.0 CD2 B:HIS63 4.3 35.4 1.0 CD B:GLN139 4.4 43.5 1.0 CG B:GLU60 4.5 38.3 1.0 CG B:GLU25 4.6 37.9 1.0 CA B:GLU60 4.8 37.7 1.0 CB B:GLU60 5.0 36.9 1.0 CB B:GLU25 5.0 37.4 1.0

Magnesium binding site 4 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:50.4 occ:1.00 OE2 B:GLU132 2.5 49.4 1.0 OE1 B:GLU132 2.5 53.8 1.0 OE1 I:GLU132 2.7 76.0 1.0 OE2 C:GLU132 2.9 52.3 1.0 CD B:GLU132 2.9 47.8 1.0 OE1 C:GLU132 3.1 60.7 1.0 O B:HOH323 3.1 30.6 1.0 OE2 I:GLU132 3.3 77.4 1.0 CD C:GLU132 3.4 53.6 1.0 CD I:GLU132 3.4 68.0 1.0 CG B:GLU132 4.4 43.4 1.0 O I:HOH330 4.8 27.8 1.0 CG C:GLU132 4.9 50.1 1.0 CG I:GLU132 4.9 59.4 1.0 O C:HOH308 4.9 25.9 1.0

Magnesium binding site 5 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:1.1 occ:1.00 OE2 C:GLU60 2.2 33.6 1.0 CD2 C:HIS63 2.3 31.5 1.0 OE1 C:GLU25 2.5 53.9 1.0 CG C:HIS63 3.2 30.6 1.0 CD C:GLU25 3.3 43.7 1.0 NE2 C:HIS63 3.3 30.3 1.0 OE2 C:GLU25 3.4 45.1 1.0 CD C:GLU60 3.4 39.8 1.0 NE2 C:GLN139 3.6 42.2 1.0 CB C:HIS63 3.7 28.9 1.0 OE1 C:GLU60 4.0 52.5 1.0 CG1 C:VAL108 4.1 29.2 1.0 ND1 C:HIS63 4.4 32.5 1.0 CE1 C:HIS63 4.5 31.6 1.0 CG C:GLU60 4.6 40.3 1.0 CA C:GLU60 4.7 37.0 1.0 CG C:GLU25 4.7 39.6 1.0 CB C:GLU60 4.8 37.4 1.0 CD C:GLN139 4.9 36.5 1.0 OE1 C:GLU105 4.9 58.2 1.0

Magnesium binding site 6 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:1.5 occ:1.00 OE1 D:GLU25 2.2 40.6 1.0 ND1 D:HIS63 2.3 38.1 1.0 OE2 D:GLU60 2.4 30.9 1.0 CE1 D:HIS63 3.0 36.8 1.0 CD D:GLU25 3.3 37.2 1.0 CG D:HIS63 3.4 34.7 1.0 NE2 D:GLN139 3.5 38.6 1.0 CD D:GLU60 3.6 38.6 1.0 OE2 D:GLU25 3.7 41.9 1.0 CB D:HIS63 3.8 34.5 1.0 CG1 D:VAL108 4.2 30.2 1.0 NE2 D:HIS63 4.2 31.4 1.0 OE1 D:GLU60 4.3 45.1 1.0 CD2 D:HIS63 4.4 33.6 1.0 OE1 D:GLU105 4.4 45.7 1.0 CA D:GLU60 4.5 33.3 1.0 CB D:GLU60 4.5 34.2 1.0 CG D:GLU60 4.6 36.1 1.0 CG D:GLU25 4.7 32.8 1.0 CD D:GLN139 4.7 37.3 1.0 O D:HOH346 5.0 47.9 1.0

Magnesium binding site 7 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:27.5 occ:1.00 O K:HOH372 2.9 21.1 1.0 O M:HOH323 3.0 31.6 1.0 O D:HOH345 3.0 35.4 1.0 O M:HOH301 3.0 32.0 1.0 MG K:MG202 3.1 37.7 1.0 OE2 D:GLU132 4.2 55.9 1.0 OE2 K:GLU132 4.2 53.1 1.0 OE2 M:GLU132 4.5 54.1 1.0 OE1 D:GLU132 4.6 63.9 1.0 OD2 M:ASP120 4.7 53.0 1.0 CD D:GLU132 4.8 55.4 1.0 OE1 M:GLU132 4.8 51.5 1.0 OE1 K:GLU132 4.9 53.8 1.0 O D:HOH340 4.9 38.9 1.0 CD K:GLU132 5.0 50.3 1.0

Magnesium binding site 8 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:60.2 occ:1.00 O E:HOH301 1.8 59.4 1.0 O L:HOH347 2.2 46.4 1.0 O E:HOH321 2.4 55.8 1.0 OG1 E:THR133 3.1 32.7 1.0 OD1 E:ASP129 3.2 48.8 1.0 OD1 L:ASP129 3.3 39.9 1.0 OD1 O:ASP129 3.9 45.4 1.0 OG1 L:THR133 3.9 42.2 1.0 CB E:THR133 4.3 32.4 1.0 CG E:ASP129 4.3 48.9 1.0 OG1 O:THR133 4.3 31.6 1.0 CG L:ASP129 4.5 40.3 1.0 CA E:THR133 4.7 33.7 1.0 CG2 E:THR133 4.8 30.0 1.0 OD2 E:ASP129 4.8 56.4 1.0

Magnesium binding site 9 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:1.5 occ:1.00 OE1 E:GLU60 2.0 55.1 1.0 ND1 E:HIS63 2.4 42.5 1.0 OE1 E:GLU25 2.4 34.1 1.0 O E:HOH317 2.6 61.4 1.0 CD E:GLU60 3.1 40.1 1.0 CE1 E:HIS63 3.3 40.4 1.0 CD E:GLU25 3.4 31.6 1.0 CG E:HIS63 3.5 40.8 1.0 NE2 E:GLN139 3.5 40.9 1.0 OE2 E:GLU25 3.7 31.2 1.0 OE2 E:GLU60 3.7 30.3 1.0 CB E:HIS63 3.8 40.1 1.0 CG2 E:VAL108 4.2 35.5 1.0 CG E:GLU60 4.3 38.7 1.0 NE2 E:HIS63 4.5 38.7 1.0 CA E:GLU60 4.5 37.7 1.0 CD2 E:HIS63 4.5 40.0 1.0 CB E:GLU60 4.6 38.4 1.0 CG E:GLU25 4.7 31.7 1.0 OE1 E:GLU105 4.8 43.1 1.0 CD E:GLN139 4.8 36.6 1.0

Magnesium binding site 10 out of 40 in the Apostichopus Japonicus Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Apostichopus Japonicus Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg203 b:49.5 occ:1.00 OE2 O:GLU132 2.7 44.6 1.0 MG O:MG202 2.8 33.3 1.0 OE1 E:GLU132 2.8 59.5 1.0 OE1 L:GLU132 2.8 62.0 1.0 OE1 O:GLU132 2.9 48.0 1.0 OE2 L:GLU132 2.9 55.5 1.0 CD O:GLU132 3.1 46.5 1.0 OE2 E:GLU132 3.2 55.9 1.0 CD L:GLU132 3.2 56.1 1.0 CD E:GLU132 3.4 54.2 1.0 O O:HOH336 4.0 33.1 1.0 O E:HOH358 4.3 41.0 1.0 O L:HOH344 4.5 32.8 1.0 CG O:GLU132 4.7 42.5 1.0 CG L:GLU132 4.8 50.2 1.0 CG E:GLU132 4.9 47.3 1.0

Y.Wu, T.Ming, C.Huo, X.Qiu, C.Su, C.Lu, J.Zhou, Y.Li, X.Su. Crystallographic Characterization of A Marine Invertebrate Ferritin From the Sea Cucumber Apostichopus Japonicus. Febs Open Bio V. 12 664 2022.
ISSN: ESSN 2211-5463
PubMed: 35090095
DOI: 10.1002/2211-5463.13375