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Iron in PDB 4ykh: Thirty Minutes Iron Loaded Human H Ferritin

Enzymatic activity of Thirty Minutes Iron Loaded Human H Ferritin

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

Protein crystallography data

The structure of Thirty Minutes Iron Loaded Human H Ferritin, PDB code: 4ykh 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) 28.07 / 1.52
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.050, 184.050, 184.050, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.7

Other elements in 4ykh:

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

Magnesium (Mg) 4 atoms
Chlorine (Cl) 12 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 7 in 4ykh

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Iron binding site 1 out of 7 in the Thirty 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:11.8
occ:1.00
OE2 A:GLU62 2.0 13.2 1.0
OE2 A:GLU27 2.1 11.0 1.0
O A:HOH616 2.1 12.4 1.0
O A:HOH610 2.2 18.6 1.0
ND1 A:HIS65 2.2 12.0 1.0
O A:HOH474 2.9 20.5 1.0
CE1 A:HIS65 3.1 12.6 1.0
CD A:GLU62 3.1 12.7 1.0
CD A:GLU27 3.1 10.8 1.0
CG A:HIS65 3.2 11.8 1.0
OE1 A:GLU62 3.5 13.4 1.0
OE1 A:GLU27 3.5 11.2 1.0
FE A:FE2205 3.5 14.9 0.4
CB A:HIS65 3.6 10.9 1.0
O A:HOH487 4.0 21.9 1.0
OE1 A:GLN141 4.1 10.2 0.5
OE1 A:GLN141 4.2 12.1 0.5
NE2 A:HIS65 4.2 12.8 1.0
CG1 A:VAL110 4.3 13.9 1.0
CD2 A:HIS65 4.3 12.3 1.0
CG A:GLU62 4.4 11.7 1.0
CG A:GLU27 4.4 10.4 1.0
CA A:GLU62 4.5 10.5 1.0
CB A:GLU62 4.7 10.7 1.0
CB A:GLU27 4.8 9.6 1.0
CD A:GLN141 4.8 10.3 0.5
OE1 A:GLU107 4.9 15.5 1.0
O A:GLU62 5.0 10.1 1.0
NE2 A:GLN141 5.0 11.8 0.5

Iron binding site 2 out of 7 in 4ykh

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Iron binding site 2 out of 7 in the Thirty 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:11.3
occ:0.20
O A:HOH332 2.1 11.3 1.0
O A:HOH403 2.1 12.9 1.0
OE2 A:GLU134 3.9 11.2 1.0
O A:HOH426 4.2 12.7 1.0
OE1 A:GLU134 4.2 11.7 1.0
O A:HOH450 4.4 14.9 1.0
CD A:GLU134 4.5 11.4 1.0

Iron binding site 3 out of 7 in 4ykh

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Iron binding site 3 out of 7 in the Thirty 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:14.6
occ:0.50
O A:HOH617 2.1 10.2 0.5
OE1 A:GLU61 2.1 12.2 0.5
O A:HOH613 2.1 16.8 0.5
OE1 A:GLN58 2.1 15.0 1.0
O A:HOH589 2.2 14.5 0.5
O A:HOH606 2.2 13.8 0.5
CD A:GLU61 3.1 11.9 0.5
CD A:GLN58 3.1 14.2 1.0
OE2 A:GLU61 3.4 12.2 0.5
NE2 A:GLN58 3.5 15.4 1.0
O A:HOH483 4.0 21.5 1.0
O A:HOH506 4.2 27.2 1.0
O A:HOH462 4.2 18.2 1.0
O A:HOH455 4.3 18.0 1.0
O A:HOH488 4.4 21.2 1.0
O A:HOH496 4.4 20.5 1.0
CG A:GLU61 4.4 11.9 1.0
O A:HOH507 4.5 28.7 1.0
CG A:GLN58 4.5 13.1 1.0
O A:HOH500 4.7 26.1 1.0
CB A:GLU61 4.8 11.1 1.0
O A:HOH544 4.8 13.4 0.3
CA A:GLN58 4.9 11.1 1.0
CB A:GLN58 5.0 11.8 1.0
CD2 A:HIS57 5.0 15.2 0.8

Iron binding site 4 out of 7 in 4ykh

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Iron binding site 4 out of 7 in the Thirty 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:14.9
occ:0.40
OE1 A:GLU107 1.8 15.5 1.0
O A:HOH610 1.9 18.6 1.0
OE1 A:GLU62 1.9 13.4 1.0
OE2 A:GLU107 2.2 15.4 1.0
CD A:GLU107 2.3 14.3 1.0
O A:HOH474 2.4 20.5 1.0
CD A:GLU62 3.0 12.7 1.0
OE2 A:GLU62 3.3 13.2 1.0
OE1 A:GLN141 3.5 10.2 0.5
FE A:FE2202 3.5 11.8 1.0
O A:HOH483 3.7 21.5 1.0
CG A:GLU107 3.8 12.9 1.0
NE2 A:GLN141 3.8 11.8 0.5
NE2 A:GLN141 3.9 10.3 0.5
O A:HOH455 4.0 18.0 1.0
O A:HOH507 4.1 28.7 1.0
OE1 A:GLN141 4.1 12.1 0.5
CD A:GLN141 4.1 10.3 0.5
CG A:GLU62 4.3 11.7 1.0
CD A:GLN141 4.3 11.6 0.5
O A:HOH606 4.4 13.8 0.5
CE1 A:HIS65 4.4 12.6 1.0
CE2 A:TYR34 4.6 11.9 1.0
ND1 A:HIS65 4.6 12.0 1.0
O A:HOH616 4.6 12.4 1.0
CB A:GLU107 4.6 11.9 1.0
OH A:TYR34 4.9 14.0 1.0
CA A:GLU107 4.9 11.2 1.0

Iron binding site 5 out of 7 in 4ykh

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Iron binding site 5 out of 7 in the Thirty 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:8.8
occ:0.25
O A:HOH386 2.2 13.0 0.2
NE2 A:HIS173 2.2 9.4 1.0
CL A:CL214 2.4 10.3 0.2
CE1 A:HIS173 3.1 9.4 1.0
CD2 A:HIS173 3.3 9.4 1.0
ND1 A:HIS173 4.2 9.6 1.0
CG A:HIS173 4.4 9.7 1.0
O A:HOH416 4.5 32.9 1.0

Iron binding site 6 out of 7 in 4ykh

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Iron binding site 6 out of 7 in the Thirty 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:15.7
occ:0.20
O A:HOH301 1.9 29.3 0.6
O A:HOH309 2.0 16.4 0.6
OD1 A:ASP131 2.6 11.2 0.4
OD2 A:ASP131 3.6 11.7 0.6
CG A:ASP131 3.7 11.2 0.4
O A:HOH425 4.0 23.3 0.3
OD2 A:ASP131 4.1 11.4 0.4
OG1 A:THR135 4.2 13.3 1.0
OE1 A:GLU134 4.3 11.7 1.0
O A:HOH355 4.6 16.9 0.6
CG A:ASP131 4.7 11.3 0.6
CB A:ASP131 5.0 11.0 0.4

Iron binding site 7 out of 7 in 4ykh

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

b:21.7
occ:0.30
O A:HOH595 1.9 13.2 0.3
OE2 A:GLU61 2.0 12.2 0.5
O A:HOH544 2.1 13.4 0.3
NE2 A:HIS57 2.1 15.4 0.8
O A:HOH592 2.2 18.5 0.3
O A:HOH619 2.5 31.3 0.3
CE1 A:HIS57 2.9 15.7 0.8
CD A:GLU61 3.1 11.9 0.5
CD2 A:HIS57 3.3 15.2 0.8
CG A:GLU61 3.7 11.9 1.0
O A:HOH589 3.9 14.5 0.5
ND1 A:HIS57 4.1 15.5 0.8
OE1 A:GLU61 4.1 12.2 0.5
CG A:HIS57 4.3 14.0 0.8
O A:HOH613 4.7 16.8 0.5

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: Sun Dec 13 15:53:09 2020

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