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Iron in PDB 4oyn: Fifteen Minutes Iron Loaded Human H Ferritin

Enzymatic activity of Fifteen Minutes Iron Loaded Human H Ferritin

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

Protein crystallography data

The structure of Fifteen Minutes Iron Loaded Human H Ferritin, PDB code: 4oyn 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) 31.09 / 1.43
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.910, 183.910, 183.910, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 17.9

Other elements in 4oyn:

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

Magnesium (Mg) 3 atoms
Chlorine (Cl) 13 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Fifteen Minutes Iron Loaded Human H Ferritin (pdb code 4oyn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Fifteen Minutes Iron Loaded Human H Ferritin, PDB code: 4oyn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 4oyn

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Iron binding site 1 out of 7 in the Fifteen Minutes Iron Loaded Human H 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 Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:9.5
occ:1.00
 OE2 A:GLU62 2.1 12.2 1.0
OE2 A:GLU27 2.1 9.3 1.0
O A:HOH601 2.1 12.3 1.0
O A:HOH611 2.1 20.4 1.0
ND1 A:HIS65 2.2 11.0 1.0
O A:HOH445 2.7 12.7 1.0
CE1 A:HIS65 3.0 11.4 1.0
CD A:GLU62 3.1 11.5 1.0
CD A:GLU27 3.1 9.0 1.0
CG A:HIS65 3.2 10.6 1.0
OE1 A:GLU27 3.4 9.3 1.0
OE1 A:GLU62 3.4 12.2 1.0
FE A:FE204 3.5 11.5 0.5
CB A:HIS65 3.6 9.9 1.0
NE2 A:GLN141 4.0 9.7 0.5
O A:HOH485 4.0 19.9 1.0
NE2 A:HIS65 4.2 11.6 1.0
NE2 A:GLN141 4.2 10.6 0.5
CG1 A:VAL110 4.3 12.9 1.0
CD2 A:HIS65 4.3 11.1 1.0
CG A:GLU62 4.4 10.8 1.0
CG A:GLU27 4.4 8.8 1.0
CA A:GLU62 4.5 9.9 1.0
CB A:GLU62 4.7 10.2 1.0
CB A:GLU27 4.8 8.4 1.0
CD A:GLN141 4.8 9.8 0.5
O A:HOH489 4.9 17.1 0.5
OE1 A:GLU107 5.0 14.2 1.0
OE1 A:GLN141 5.0 11.0 0.5

Iron binding site 2 out of 7 in 4oyn

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Iron binding site 2 out of 7 in the Fifteen Minutes Iron Loaded Human H 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 Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:11.5
occ:0.50
 O A:HOH611 1.9 20.4 1.0
OE1 A:GLU107 1.9 14.2 1.0
OE1 A:GLU62 1.9 12.2 1.0
O A:HOH489 2.2 17.1 0.5
OE2 A:GLU107 2.3 14.3 1.0
CD A:GLU107 2.4 13.5 1.0
O A:HOH445 2.5 12.7 1.0
CD A:GLU62 3.0 11.5 1.0
OE2 A:GLU62 3.4 12.2 1.0
NE2 A:GLN141 3.5 9.7 0.5
FE A:FE203 3.5 9.5 1.0
O A:HOH463 3.7 16.7 1.0
OE1 A:GLN141 3.8 9.9 0.5
CG A:GLU107 3.9 12.6 1.0
OE1 A:GLN141 4.0 11.0 0.5
CD A:GLN141 4.1 9.8 0.5
NE2 A:GLN141 4.1 10.6 0.5
O A:HOH467 4.2 16.4 1.0
O A:HOH617 4.3 23.5 1.0
CG A:GLU62 4.3 10.8 1.0
CD A:GLN141 4.3 10.6 0.5
CE1 A:HIS65 4.3 11.4 1.0
O A:HOH494 4.3 13.4 0.5
ND1 A:HIS65 4.5 11.0 1.0
O A:HOH601 4.6 12.3 1.0
CE2 A:TYR34 4.6 10.6 1.0
CB A:GLU107 4.7 11.7 1.0
OH A:TYR34 4.8 12.0 1.0
CA A:GLU107 4.9 11.2 1.0

Iron binding site 3 out of 7 in 4oyn

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Iron binding site 3 out of 7 in the Fifteen Minutes Iron Loaded Human H 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 Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:14.0
occ:0.50
 O A:HOH599 2.0 14.4 0.5
O A:HOH613 2.0 10.7 0.5
OE1 A:GLU61 2.1 12.8 0.7
O A:HOH605 2.1 11.6 0.5
OE1 A:GLN58 2.2 13.7 1.0
O A:HOH494 2.2 13.4 0.5
CD A:GLU61 3.0 12.0 0.7
CD A:GLN58 3.1 12.8 1.0
OE2 A:GLU61 3.3 12.5 0.7
NE2 A:GLN58 3.5 13.8 1.0
O A:HOH463 4.1 16.7 1.0
O A:HOH486 4.2 23.8 1.0
O A:HOH467 4.3 16.4 1.0
O A:HOH454 4.4 16.9 1.0
CG A:GLU61 4.4 11.5 1.0
O A:HOH491 4.4 19.4 1.0
O A:HOH482 4.4 18.5 1.0
O A:HOH617 4.5 23.5 1.0
O A:HOH489 4.5 17.1 0.5
CG A:GLN58 4.5 12.0 1.0
O A:HOH501 4.7 28.7 1.0
O A:HOH597 4.7 15.0 0.5
CB A:GLU61 4.8 10.6 1.0
CA A:GLN58 4.9 10.3 1.0

Iron binding site 4 out of 7 in 4oyn

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Iron binding site 4 out of 7 in the Fifteen Minutes Iron Loaded Human H 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 Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:14.0
occ:0.50
 O A:HOH612 2.1 17.9 0.5
OE2 A:GLU61 2.1 12.5 0.7
NE2 A:HIS57 2.1 13.4 0.8
O A:HOH606 2.1 16.7 0.5
O A:HOH603 2.1 16.0 0.5
O A:HOH597 2.2 15.0 0.5
CE1 A:HIS57 3.0 13.7 0.8
CD2 A:HIS57 3.1 13.2 0.8
CD A:GLU61 3.2 12.0 0.7
CG A:GLU61 3.7 11.5 1.0
O A:HOH613 4.1 10.7 0.5
ND1 A:HIS57 4.1 13.5 0.8
OE1 A:GLU61 4.2 12.8 0.7
CG A:HIS57 4.2 12.6 0.8

Iron binding site 5 out of 7 in 4oyn

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Iron binding site 5 out of 7 in the Fifteen Minutes Iron Loaded Human H 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 Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:7.5
occ:0.25
 O A:HOH386 2.1 11.7 0.2
NE2 A:HIS173 2.2 8.3 1.0
CL A:CL210 2.4 8.6 0.2
CE1 A:HIS173 3.1 8.4 1.0
CD2 A:HIS173 3.3 8.5 1.0
ND1 A:HIS173 4.2 8.6 1.0
CG A:HIS173 4.4 8.6 1.0
O A:HOH416 4.4 31.7 1.0

Iron binding site 6 out of 7 in 4oyn

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Iron binding site 6 out of 7 in the Fifteen Minutes Iron Loaded Human H 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 Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:11.4
occ:0.20
 O A:HOH405 2.1 11.6 1.0
O A:HOH319 2.1 11.5 1.0
OE2 A:GLU134 3.9 12.1 1.0
OE1 A:GLU134 4.2 12.7 1.0
O A:HOH425 4.3 12.6 1.0
O A:HOH451 4.3 13.7 1.0
CD A:GLU134 4.5 12.1 1.0

Iron binding site 7 out of 7 in 4oyn

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Iron binding site 7 out of 7 in the Fifteen Minutes Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Fifteen Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe209

b:20.6
occ:0.20
 O A:HOH324 1.7 11.4 0.5
O A:HOH315 2.0 16.1 0.5
OD2 A:ASP131 3.7 14.1 1.0
O A:HOH422 3.8 28.2 0.3
OG1 A:THR135 4.2 14.3 1.0
OE1 A:GLU134 4.3 12.7 1.0
O A:HOH335 4.6 18.6 0.7
CG A:ASP131 4.7 13.4 1.0

Reference:

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
Page generated: Mon Aug 5 08:21:46 2024

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