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Iron in PDB 6i36: Sixty Minutes Iron Loaded Frog M Ferritin

Enzymatic activity of Sixty Minutes Iron Loaded Frog M Ferritin

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

Protein crystallography data

The structure of Sixty Minutes Iron Loaded Frog M Ferritin, PDB code: 6i36 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) 19.64 / 1.59
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.200, 184.200, 184.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 20.5

Other elements in 6i36:

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

Magnesium (Mg) 4 atoms
Chlorine (Cl) 15 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Sixty Minutes Iron Loaded Frog M Ferritin (pdb code 6i36). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Sixty Minutes Iron Loaded Frog M Ferritin, PDB code: 6i36:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6i36

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Iron binding site 1 out of 6 in the Sixty 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 Sixty Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:18.7
occ:0.50
 O A:HOH305 1.8 27.6 1.0
OE2 A:GLU58 1.9 10.7 0.5
O A:HOH311 1.9 8.9 0.5
OE2 A:GLU103 2.3 12.4 1.0
OE1 A:GLU103 2.4 12.8 1.0
OE1 A:GLU58 2.5 10.6 0.5
O A:HOH335 2.5 26.9 1.0
OE2 A:GLU58 2.6 10.9 0.5
CD A:GLU58 2.6 10.6 0.5
CD A:GLU103 2.7 11.6 1.0
CD A:GLU58 2.8 10.6 0.5
OE1 A:GLU58 3.2 10.4 0.5
FE A:FE2202 3.5 12.4 0.5
CG A:GLU58 3.8 10.3 0.5
O A:HOH349 3.9 30.3 1.0
NE2 A:GLN137 4.0 16.1 1.0
CG A:GLU58 4.0 10.3 0.5
OE1 A:GLN137 4.1 16.4 1.0
CG A:GLU103 4.2 10.3 1.0
OD2 A:ASP140 4.2 9.6 0.7
OE2 A:GLU57 4.3 14.3 0.7
CE2 A:TYR30 4.4 9.1 1.0
CD A:GLN137 4.5 14.7 1.0
CE1 A:HIS61 4.5 12.3 1.0
ND1 A:HIS61 4.7 11.8 1.0
O A:HOH310 4.7 12.2 1.0
OH A:TYR30 4.7 10.4 1.0
CD A:GLU57 4.8 13.8 0.7
ND1 A:HIS54 4.9 15.3 1.0

Iron binding site 2 out of 6 in 6i36

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Iron binding site 2 out of 6 in the Sixty 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 Sixty Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:12.4
occ:0.50
 OE1 A:GLU23 2.0 9.2 1.0
OE1 A:GLU58 2.0 10.4 0.5
O A:HOH311 2.1 8.9 0.5
O A:HOH310 2.2 12.2 1.0
ND1 A:HIS61 2.2 11.8 1.0
OE2 A:GLU58 2.5 10.9 0.5
OE1 A:GLU58 2.6 10.6 0.5
CD A:GLU58 2.8 10.6 0.5
CD A:GLU23 2.8 8.9 1.0
OE2 A:GLU23 3.0 9.6 1.0
CE1 A:HIS61 3.0 12.3 1.0
CD A:GLU58 3.1 10.6 0.5
CG A:HIS61 3.3 11.3 1.0
OE2 A:GLU58 3.5 10.7 0.5
FE A:FE2201 3.5 18.7 0.5
CB A:HIS61 3.8 10.6 1.0
CG1 A:VAL106 3.9 8.0 1.0
OE1 A:GLN137 4.1 16.4 1.0
CG A:GLU58 4.1 10.3 0.5
NE2 A:HIS61 4.2 12.5 1.0
CG A:GLU23 4.2 8.4 1.0
O A:HOH472 4.3 12.6 1.0
O A:HOH305 4.4 27.6 1.0
CD2 A:HIS61 4.4 11.9 1.0
CG A:GLU58 4.4 10.3 0.5
CA A:GLU58 4.4 10.1 0.5
CA A:GLU58 4.4 10.1 0.5
CB A:GLU58 4.5 10.2 0.5
O A:HOH349 4.5 30.3 1.0
CB A:GLU58 4.6 10.1 0.5
CB A:GLU23 4.7 7.7 1.0
CD A:GLN137 5.0 14.7 1.0
NE2 A:GLN137 5.0 16.1 1.0
CB A:VAL106 5.0 7.7 1.0

Iron binding site 3 out of 6 in 6i36

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Iron binding site 3 out of 6 in the Sixty 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 Sixty Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:7.6
occ:0.20
 NE2 A:HIS169 2.3 8.6 1.0
CL A:CL215 2.4 11.2 0.2
O A:HOH504 2.4 23.3 0.2
CE1 A:HIS169 3.1 8.8 1.0
CD2 A:HIS169 3.3 9.0 1.0
ND1 A:HIS169 4.3 9.0 1.0
CG A:HIS169 4.4 8.9 1.0
O A:HOH509 4.5 33.1 1.0

Iron binding site 4 out of 6 in 6i36

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Iron binding site 4 out of 6 in the Sixty 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 Sixty Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:51.7
occ:0.50
 OE1 A:GLU60 2.1 17.1 0.7
O A:HOH479 2.5 47.3 1.0
CD A:GLU60 3.3 16.2 0.7
OE2 A:GLU60 3.8 17.8 0.7
O A:HOH451 4.0 31.5 1.0
CA A:GLU57 4.3 10.9 1.0
CG A:GLU60 4.5 14.8 1.0
CG A:GLU57 4.6 13.2 1.0
CB A:GLU57 4.6 11.8 1.0
CB A:GLU60 4.6 12.9 1.0

Iron binding site 5 out of 6 in 6i36

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Iron binding site 5 out of 6 in the Sixty 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 Sixty Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:11.7
occ:0.20
 O A:HOH517 2.0 10.4 1.0
O A:HOH324 2.1 7.7 1.0
OE2 A:GLU130 3.8 9.6 1.0
O A:HOH565 4.2 10.4 1.0
OE1 A:GLU130 4.3 9.9 1.0
O A:HOH398 4.3 13.5 1.0
CD A:GLU130 4.5 9.7 1.0

Iron binding site 6 out of 6 in 6i36

Go back to Iron Binding Sites List in 6i36
Iron binding site 6 out of 6 in the Sixty 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 Sixty Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:15.4
occ:0.20
 O A:HOH414 1.9 26.9 1.0
O A:HOH313 2.1 28.5 1.0
OD1 A:ASP127 3.8 10.9 1.0
OG A:SER131 4.2 13.4 1.0
OE1 A:GLU130 4.3 9.9 1.0
O A:HOH444 4.8 17.3 0.8
CG A:ASP127 4.9 10.6 1.0
CB A:GLU130 5.0 9.6 1.0

Reference:

C.Pozzi, F.Di Pisa, D.Lalli, C.Rosa, E.Theil, P.Turano, S.Mangani. Time-Lapse Anomalous X-Ray Diffraction Shows How Fe(2+) Substrate Ions Move Through Ferritin Protein Nanocages to Oxidoreductase Sites. Acta Crystallogr.,Sect.D V. 71 941 2015.
ISSN: ISSN 0907-4449
PubMed: 25849404
DOI: 10.1107/S1399004715002333
Page generated: Tue Aug 6 22:03:58 2024

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