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Magnesium in PDB 4lpj: One Minute Iron Loaded Frog M Ferritin

Enzymatic activity of One Minute Iron Loaded Frog M Ferritin

All present enzymatic activity of One Minute Iron Loaded Frog M Ferritin:
1.16.3.1;

Protein crystallography data

The structure of One Minute Iron Loaded Frog M Ferritin, PDB code: 4lpj was solved by S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.28 / 1.27
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.300, 184.300, 184.300, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 17.5

Other elements in 4lpj:

The structure of One Minute Iron Loaded Frog M Ferritin also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 13 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the One Minute Iron Loaded Frog M Ferritin (pdb code 4lpj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the One Minute Iron Loaded Frog M Ferritin, PDB code: 4lpj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 4lpj

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Magnesium binding site 1 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:15.5
occ:0.60
 OE1 A:GLU136 2.1 16.4 0.6
OE2 A:GLU57 2.1 14.9 0.6
O A:HOH622 2.1 18.2 0.6
O A:HOH641 2.1 17.9 0.6
O A:HOH629 2.2 15.2 0.6
OD2 A:ASP140 2.2 23.0 1.0
CG A:ASP140 3.0 17.8 1.0
CD A:GLU57 3.1 15.1 0.6
OD1 A:ASP140 3.1 22.7 1.0
CD A:GLU136 3.3 16.6 0.6
OE1 A:GLU57 3.4 15.6 0.6
O A:GLU136 3.8 17.1 1.0
CB A:GLU136 3.8 16.2 0.6
O A:HOH642 3.9 16.0 0.5
CG A:GLU136 4.0 16.1 0.6
OE2 A:GLU136 4.2 17.1 0.6
C A:GLU136 4.3 15.9 1.0
CG A:GLU57 4.4 14.4 0.6
CB A:ASP140 4.4 13.9 1.0
CA A:GLU136 4.5 16.8 1.0
MG A:MG212 4.5 19.2 0.5
O A:HOH508 4.5 37.7 1.0
O A:HOH443 4.6 29.0 1.0
O A:HOH652 4.7 43.0 1.0
MG A:MG206 4.7 12.4 0.5
NE2 A:HIS61 4.9 18.3 0.5
CE1 A:HIS61 4.9 18.5 0.5

Magnesium binding site 2 out of 13 in 4lpj

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Magnesium binding site 2 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:16.4
occ:0.80
 O A:HOH381 2.0 15.2 0.8
O A:HOH644 2.0 20.0 0.8
O A:HOH635 2.1 21.3 0.8
O A:HOH333 2.1 12.6 0.8
O A:HOH495 2.1 18.6 0.8
OG A:SER10 2.1 14.0 1.0
CB A:SER10 3.2 12.8 1.0
O A:HOH588 3.9 40.7 1.0
CA A:SER10 3.9 11.0 1.0
O A:SER10 4.1 10.6 1.0
OE1 A:GLU13 4.2 11.4 1.0
O A:HOH336 4.3 18.4 1.0
O A:HOH620 4.3 48.3 1.0
C A:SER10 4.3 10.4 1.0
O A:HOH474 4.4 34.1 1.0
O A:HOH378 4.4 17.2 1.0
O A:HOH627 4.5 45.3 1.0
O A:HOH645 4.5 33.2 1.0
O A:HOH547 4.5 35.7 1.0
CD A:GLU13 4.6 9.9 1.0

Magnesium binding site 3 out of 13 in 4lpj

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Magnesium binding site 3 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:17.3
occ:0.70
 O A:HOH568 2.0 30.5 0.7
O A:HOH619 2.1 28.5 0.7
O A:HOH632 2.1 21.8 0.7
O A:HOH498 2.1 33.7 0.7
O A:HOH623 2.2 32.5 0.7
O A:HOH476 2.3 25.5 0.7
OD2 A:ASP127 4.0 18.1 1.0
O A:HOH575 4.4 52.4 1.0
O A:HOH596 4.6 42.8 1.0
OD1 A:ASP127 4.6 17.7 1.0
OG A:SER131 4.7 16.1 0.5
O A:HOH546 4.7 28.1 1.0
CG A:ASP127 4.7 15.7 1.0
OG A:SER131 4.8 16.1 0.5
CB A:SER131 5.0 15.9 0.5
CB A:SER131 5.0 15.7 0.5

Magnesium binding site 4 out of 13 in 4lpj

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Magnesium binding site 4 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:12.3
occ:0.30
 O A:HOH345 2.1 13.8 0.9
O A:HOH405 2.1 15.3 0.9
OE2 A:GLU130 3.9 14.5 0.4
OE2 A:GLU130 3.9 13.5 0.6
O A:HOH431 4.1 21.8 1.0
O A:HOH402 4.3 17.0 1.0
O A:HOH372 4.3 21.0 1.0
OE1 A:GLU130 4.3 14.1 0.6
OE1 A:GLU130 4.5 15.2 0.4
CD A:GLU130 4.6 13.6 0.6
CD A:GLU130 4.6 14.6 0.4

Magnesium binding site 5 out of 13 in 4lpj

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Magnesium binding site 5 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:12.4
occ:0.50
 O A:HOH642 1.7 16.0 0.5
OE1 A:GLN137 1.9 21.1 1.0
OE2 A:GLU136 2.0 17.1 0.6
O A:HOH380 2.2 13.1 0.5
O A:HOH631 2.2 23.1 0.8
MG A:MG212 2.5 19.2 0.5
CD A:GLU136 2.9 16.6 0.6
CE1 A:HIS61 3.0 18.5 0.5
CD A:GLN137 3.1 17.4 1.0
OE1 A:GLU136 3.2 16.4 0.6
FE A:FE2201 3.3 16.2 0.3
ND1 A:HIS61 3.6 18.1 0.5
NE2 A:GLN137 3.7 16.7 1.0
ND1 A:HIS61 3.9 15.2 0.5
OE1 A:GLU103 3.9 11.0 0.5
CE1 A:HIS61 4.0 15.2 0.5
OE2 A:GLU58 4.0 21.8 1.0
NE2 A:HIS61 4.1 18.3 0.5
OD2 A:ASP140 4.1 23.0 1.0
OE1 A:GLU58 4.1 19.7 1.0
OE1 A:GLU103 4.2 12.8 0.5
CA A:GLN137 4.3 12.0 1.0
CG A:GLN137 4.3 18.2 1.0
CG A:GLU136 4.3 16.1 0.6
CB A:GLN137 4.4 14.9 1.0
OE2 A:GLU57 4.4 14.9 0.6
N A:GLN137 4.5 14.4 1.0
CD A:GLU58 4.5 17.6 1.0
O A:HOH443 4.5 29.0 1.0
OE2 A:GLU23 4.6 10.9 0.5
MG A:MG202 4.7 15.5 0.6
CG A:HIS61 4.8 17.6 0.5
O A:TYR133 4.8 15.3 1.0
CG1 A:VAL106 4.9 11.1 1.0
C A:GLU136 4.9 15.9 1.0

Magnesium binding site 6 out of 13 in 4lpj

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Magnesium binding site 6 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:17.8
occ:0.60
 O A:HOH592 2.0 20.3 0.6
O A:HOH653 2.0 21.0 0.6
O A:HOH494 2.1 14.5 0.6
O A:HOH634 2.1 21.6 0.6
O A:HOH530 2.1 23.3 0.6
O A:HOH559 2.1 23.4 0.6
O A:HOH359 4.2 19.8 1.0
O A:HOH613 4.4 51.3 1.0
O A:HOH338 4.4 17.0 1.0
O A:HOH525 4.6 32.9 1.0

Magnesium binding site 7 out of 13 in 4lpj

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Magnesium binding site 7 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:14.6
occ:0.25
 O A:HOH450 2.1 18.4 0.8
O A:HOH408 2.1 18.3 0.8
O A:HOH372 4.4 21.0 1.0
O A:HOH526 4.4 42.0 1.0
CG2 A:THR118 4.4 12.3 1.0
O A:HOH330 4.5 16.4 1.0
O A:HOH399 4.7 16.9 1.0

Magnesium binding site 8 out of 13 in 4lpj

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Magnesium binding site 8 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:7.6
occ:0.40
 O A:HOH383 1.9 12.8 0.8
O A:HOH357 1.9 10.7 0.8
O A:HOH341 2.0 8.6 0.4
O A:HOH403 2.1 9.3 0.4
O A:HOH319 4.1 13.4 1.0
CD A:LYS82 4.2 12.1 0.5
O A:HOH400 4.2 17.2 1.0
CE A:LYS82 4.3 12.5 0.5
NZ A:LYS82 4.4 10.7 0.5
CE A:LYS83 4.6 9.5 0.5
CD A:LYS82 4.7 10.3 0.5
CE A:LYS82 4.8 10.6 0.5
O A:HOH377 4.9 23.4 1.0
CE A:LYS83 5.0 12.6 0.5

Magnesium binding site 9 out of 13 in 4lpj

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Magnesium binding site 9 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:14.8
occ:0.80
 O A:HOH517 2.0 18.1 0.8
O A:HOH448 2.0 16.0 0.8
O A:HOH630 2.1 21.1 0.8
O A:HOH497 2.1 20.4 0.8
O A:HOH647 2.1 19.6 0.8
O A:HOH591 2.1 13.0 0.8
O A:HOH461 4.1 29.4 1.0
OD1 A:ASN21 4.2 9.0 1.0
O A:HOH412 4.3 20.1 1.0
O A:ARG18 4.4 9.8 1.0
CL A:CL225 4.5 17.9 0.7
O A:HOH608 4.5 45.9 1.0
O A:HOH401 4.5 17.8 1.0
O A:HOH541 4.6 39.7 1.0
O A:HOH406 4.7 21.6 1.0
O A:HOH418 4.7 22.7 1.0
CB A:LEU22 4.8 9.7 1.0
O A:HOH582 5.0 46.0 1.0

Magnesium binding site 10 out of 13 in 4lpj

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Magnesium binding site 10 out of 13 in the One Minute Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of One Minute Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:18.2
occ:0.50
 O A:HOH649 1.9 23.5 0.5
O A:HOH633 2.0 12.8 0.5
O A:HOH658 2.0 33.6 1.0
O A:HOH580 2.2 25.1 0.5
O A:HOH595 2.2 26.6 0.5
NE2 A:HIS45 3.6 14.2 0.5
CD2 A:HIS45 3.7 14.3 0.5
CE1 A:HIS45 4.1 14.4 0.5
CG A:HIS45 4.3 13.9 0.5
O A:HOH444 4.3 33.1 1.0
ND1 A:HIS45 4.5 14.4 0.5
ND1 A:HIS45 4.8 16.0 0.5

Reference:

S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli. Crystallographic Snapshots of Iron in Frog M Ferritin To Be Published.
Page generated: Mon Aug 11 20:02:52 2025

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