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Iron in PDB 4lyu: Fifteen Minutes Iron Loaded Frog M Ferritin

Enzymatic activity of Fifteen Minutes Iron Loaded Frog M Ferritin

All present enzymatic activity of Fifteen Minutes Iron Loaded Frog M Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Fifteen Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyu 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) 31.08 / 1.75
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.843, 183.843, 183.843, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 20.4

Other elements in 4lyu:

The structure of Fifteen Minutes Iron Loaded Frog M Ferritin also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Chlorine (Cl) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Fifteen Minutes Iron Loaded Frog M Ferritin (pdb code 4lyu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Fifteen Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4lyu

Go back to Iron Binding Sites List in 4lyu
Iron binding site 1 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:17.5
occ:0.70
 OE1 A:GLU23 2.0 15.9 1.0
OE1 A:GLU58 2.0 19.7 1.0
O A:HOH301 2.1 22.7 1.0
O A:HOH302 2.1 18.4 1.0
ND1 A:HIS61 2.4 18.0 1.0
CD A:GLU23 2.9 14.9 1.0
CD A:GLU58 3.1 19.3 1.0
OE2 A:GLU23 3.1 16.7 1.0
CE1 A:HIS61 3.2 18.6 1.0
CG A:HIS61 3.4 16.5 1.0
OE2 A:GLU58 3.6 21.6 1.0
O A:HOH464 3.6 30.6 0.7
CB A:HIS61 3.7 15.0 1.0
FE A:FE2203 3.8 28.4 0.7
CG1 A:VAL106 4.0 11.1 1.0
OE1 A:GLN137 4.1 18.1 1.0
O A:HOH424 4.3 20.5 1.0
CG A:GLU23 4.3 13.3 1.0
CG A:GLU58 4.4 16.8 1.0
NE2 A:HIS61 4.4 18.5 1.0
O A:HOH413 4.4 25.4 1.0
CA A:GLU58 4.5 13.8 1.0
CD2 A:HIS61 4.5 17.8 1.0
CB A:GLU58 4.6 15.1 1.0
CB A:GLU23 4.8 11.4 1.0
CD A:GLN137 5.0 16.6 1.0

Iron binding site 2 out of 6 in 4lyu

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Iron binding site 2 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:42.4
occ:0.40
 ND1 A:HIS54 2.5 21.9 1.0
FE A:FE2203 2.5 28.4 0.7
O A:HOH413 2.8 25.4 1.0
OE2 A:GLU58 2.9 21.6 1.0
OE2 A:GLU103 3.0 19.9 1.0
CE1 A:HIS54 3.1 22.7 1.0
OD2 A:ASP140 3.4 21.9 1.0
OE2 A:GLU57 3.4 28.9 1.0
CG A:HIS54 3.6 19.6 1.0
CD A:GLU103 3.6 17.8 1.0
OE1 A:GLU103 3.8 19.1 1.0
CD A:GLU57 3.9 26.7 1.0
CD A:GLU58 3.9 19.3 1.0
CE2 A:TYR30 4.0 14.7 1.0
OE1 A:GLU57 4.0 30.6 1.0
CG A:ASP140 4.1 18.4 1.0
OH A:TYR30 4.1 18.2 1.0
CB A:HIS54 4.1 16.2 1.0
CZ A:TYR30 4.3 15.8 1.0
O A:HOH301 4.3 22.7 1.0
NE2 A:HIS54 4.4 23.6 1.0
FE A:FE2205 4.4 36.4 0.5
CG A:GLU58 4.5 16.8 1.0
CB A:ASP140 4.5 15.4 1.0
O A:HIS54 4.6 12.6 1.0
CD2 A:HIS54 4.6 21.3 1.0
CA A:HIS54 4.6 14.3 1.0
OE1 A:GLU58 4.8 19.7 1.0
CG A:GLU57 4.8 22.8 1.0
CD2 A:TYR30 4.8 13.3 1.0
O A:HOH464 4.9 30.6 0.7
OD1 A:ASP140 4.9 19.7 1.0
CG A:GLU103 4.9 15.2 1.0

Iron binding site 3 out of 6 in 4lyu

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Iron binding site 3 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:28.4
occ:0.70
 OE2 A:GLU58 1.8 21.6 1.0
O A:HOH413 1.9 25.4 1.0
O A:HOH301 2.1 22.7 1.0
OE2 A:GLU103 2.1 19.9 1.0
OE1 A:GLU103 2.4 19.1 1.0
FE A:FE2202 2.5 42.4 0.4
O A:HOH464 2.5 30.6 0.7
CD A:GLU103 2.6 17.8 1.0
CD A:GLU58 2.8 19.3 1.0
OE1 A:GLU58 3.3 19.7 1.0
FE A:FE2201 3.8 17.5 0.7
NE2 A:GLN137 4.0 17.9 1.0
OE1 A:GLN137 4.1 18.1 1.0
CG A:GLU58 4.1 16.8 1.0
CG A:GLU103 4.1 15.2 1.0
OD2 A:ASP140 4.2 21.9 1.0
CE2 A:TYR30 4.3 14.7 1.0
CD A:GLN137 4.4 16.6 1.0
OE2 A:GLU57 4.5 28.9 1.0
OH A:TYR30 4.5 18.2 1.0
CE1 A:HIS61 4.7 18.6 1.0
ND1 A:HIS54 4.8 21.9 1.0
ND1 A:HIS61 4.8 18.0 1.0
O A:HOH302 4.8 18.4 1.0
CZ A:TYR30 4.9 15.8 1.0
CB A:GLU103 4.9 13.4 1.0

Iron binding site 4 out of 6 in 4lyu

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Iron binding site 4 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:37.1
occ:0.50
 OE2 A:GLU136 2.2 26.9 1.0
OE1 A:GLU136 2.2 27.9 1.0
CD A:GLU136 2.5 25.5 1.0
NE2 A:HIS61 2.9 18.5 1.0
CD2 A:HIS61 3.6 17.8 1.0
O A:HOH434 3.7 29.7 1.0
CG A:GLU57 3.8 22.8 1.0
CG A:GLU136 4.0 23.3 1.0
CE1 A:HIS61 4.1 18.6 1.0
CD A:GLU57 4.2 26.7 1.0
OE2 A:GLU57 4.2 28.9 1.0
CB A:GLU136 4.9 19.6 1.0
CG A:HIS61 4.9 16.5 1.0

Iron binding site 5 out of 6 in 4lyu

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Iron binding site 5 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:36.4
occ:0.50
 O A:HOH303 2.2 50.3 1.0
OD1 A:ASP140 2.4 19.7 1.0
OD2 A:ASP140 2.4 21.9 1.0
OE1 A:GLU57 2.5 30.6 1.0
OE2 A:GLU57 2.6 28.9 1.0
CG A:ASP140 2.7 18.4 1.0
CD A:GLU57 2.8 26.7 1.0
OE1 A:GLU136 3.3 27.9 1.0
CG A:GLU136 3.7 23.3 1.0
CD A:GLU136 4.0 25.5 1.0
CB A:ASP140 4.2 15.4 1.0
CG A:GLU57 4.3 22.8 1.0
CE1 A:HIS54 4.4 22.7 1.0
FE A:FE2202 4.4 42.4 0.4
O A:GLU136 4.6 14.9 1.0
O A:HOH413 4.7 25.4 1.0
O A:HOH438 4.7 31.5 1.0
ND1 A:HIS54 4.9 21.9 1.0
NE2 A:HIS54 4.9 23.6 1.0

Iron binding site 6 out of 6 in 4lyu

Go back to Iron Binding Sites List in 4lyu
Iron binding site 6 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:10.7
occ:0.25
 CL A:CL215 2.2 14.2 0.2
NE2 A:HIS169 2.3 9.9 1.0
O A:HOH304 2.4 16.5 0.2
CE1 A:HIS169 3.1 10.1 1.0
CD2 A:HIS169 3.3 10.5 1.0
ND1 A:HIS169 4.3 10.3 1.0
CG A:HIS169 4.4 10.1 1.0

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: Tue Aug 5 12:35:32 2025

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