Atomistry » Iron » PDB 4xry-4yoq » 4ykh
Atomistry »
  Iron »
    PDB 4xry-4yoq »
      4ykh »

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

Go back to Iron Binding Sites List in 4ykh
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

Go back to Iron Binding Sites List in 4ykh
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

Go back to Iron Binding Sites List in 4ykh
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

Go back to Iron Binding Sites List in 4ykh
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

Go back to Iron Binding Sites List in 4ykh
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

Go back to Iron Binding Sites List in 4ykh
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

Go back to Iron Binding Sites List in 4ykh
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: Mon Aug 5 16:12:42 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy