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Iron in PDB 5j9v: Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

Enzymatic activity of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

All present enzymatic activity of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A:
1.16.3.1;

Protein crystallography data

The structure of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j9v was solved by C.Pozzi, F.Di Pisa, S.Mangani, C.Bernacchioni, P.Turano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.15 / 1.16
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.744, 183.744, 183.744, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 13.8

Other elements in 5j9v:

The structure of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 17 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A (pdb code 5j9v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j9v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 5j9v

Go back to Iron Binding Sites List in 5j9v
Iron binding site 1 out of 7 in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:10.2
occ:0.80
 OE1 A:GLU23 2.0 10.7 1.0
O A:HOH314 2.0 17.1 0.8
OE1 A:GLU58 2.0 15.0 1.0
O A:HOH322 2.2 12.8 1.0
ND1 A:HIS61 2.2 12.7 1.0
O A:HOH426 2.7 3.6 0.2
CD A:GLU23 3.0 9.8 1.0
CE1 A:HIS61 3.0 14.4 1.0
CD A:GLU58 3.1 12.4 1.0
CG A:HIS61 3.3 11.5 1.0
OE2 A:GLU23 3.3 12.6 1.0
OE2 A:GLU58 3.5 15.8 1.0
FE A:FE2202 3.6 13.4 0.6
CB A:HIS61 3.7 8.9 1.0
OE1 A:GLN137 3.9 12.0 0.4
CG1 A:VAL106 4.1 12.2 1.0
OE1 A:GLN137 4.1 14.3 0.6
NE2 A:HIS61 4.2 15.4 1.0
O A:HOH436 4.2 15.9 1.0
CD2 A:HIS61 4.3 12.9 1.0
CG A:GLU23 4.3 8.9 1.0
CG A:GLU58 4.4 10.8 1.0
CA A:GLU58 4.5 9.4 1.0
CB A:GLU58 4.6 9.9 1.0
O A:HOH316 4.7 10.4 0.6
CB A:GLU23 4.7 8.1 1.0
NE2 A:GLN137 4.8 13.1 0.6
CD A:GLN137 4.8 12.4 0.4
CD A:GLN137 4.9 12.4 0.6
O A:HOH321 5.0 20.8 0.6
OE1 A:GLU103 5.0 13.1 0.4

Iron binding site 2 out of 7 in 5j9v

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Iron binding site 2 out of 7 in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:13.4
occ:0.60
 OE2 A:GLU58 1.9 15.8 1.0
O A:HOH314 2.0 17.1 0.8
O A:HOH321 2.1 20.8 0.6
OE1 A:GLU103 2.2 13.1 0.4
OE1 A:GLU103 2.2 11.7 0.6
OE2 A:GLU103 2.3 11.7 0.6
OE2 A:GLU103 2.3 13.6 0.4
O A:HOH426 2.5 3.6 0.2
CD A:GLU103 2.6 12.6 0.4
CD A:GLU103 2.6 11.4 0.6
CD A:GLU58 2.9 12.4 1.0
OE1 A:GLU58 3.3 15.0 1.0
OE1 A:GLN137 3.6 12.0 0.4
FE A:FE2201 3.6 10.2 0.8
NE2 A:GLN137 3.8 13.1 0.6
O A:HOH458 3.8 19.4 0.6
O A:HOH316 4.1 10.4 0.6
O A:HOH307 4.1 16.1 0.5
CG A:GLU103 4.1 11.7 0.4
CG A:GLU103 4.1 10.6 0.6
NE2 A:GLN137 4.1 12.6 0.4
CG A:GLU58 4.2 10.8 1.0
CD A:GLN137 4.3 12.4 0.4
OE1 A:GLN137 4.3 14.3 0.6
CE1 A:HIS61 4.4 14.4 1.0
CE2 A:TYR30 4.4 12.5 0.9
CD A:GLN137 4.4 12.4 0.6
O A:HOH571 4.6 18.5 0.6
ND1 A:HIS61 4.6 12.7 1.0
OH A:TYR30 4.6 14.4 0.9
O A:HOH322 4.7 12.8 1.0
ND1 A:HIS54 4.8 18.2 0.5
CB A:GLU103 4.9 11.0 0.4
CB A:GLU103 4.9 9.9 0.6

Iron binding site 3 out of 7 in 5j9v

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Iron binding site 3 out of 7 in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:8.1
occ:0.25
 O A:HOH492 2.2 10.7 0.2
NE2 A:HIS169 2.3 8.4 1.0
CL A:CL214 2.4 8.5 0.2
CE1 A:HIS169 3.1 8.4 1.0
CD2 A:HIS169 3.3 8.1 1.0
ND1 A:HIS169 4.3 8.2 1.0
O A:HOH526 4.4 34.6 1.0
CG A:HIS169 4.4 8.4 1.0

Iron binding site 4 out of 7 in 5j9v

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Iron binding site 4 out of 7 in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:11.5
occ:0.20
 O A:HOH629 2.1 9.7 0.8
O A:HOH621 2.1 8.6 0.8
OE2 A:GLU130 3.9 11.9 1.0
O A:HOH565 4.2 14.2 1.0
OE1 A:GLU130 4.3 14.5 1.0
O A:HOH404 4.3 18.0 1.0
CD A:GLU130 4.5 11.9 1.0

Iron binding site 5 out of 7 in 5j9v

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Iron binding site 5 out of 7 in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:15.6
occ:0.20
 O A:HOH590 1.7 21.6 0.6
O A:HOH467 2.1 20.1 0.6
OD1 A:ASP127 3.8 14.8 1.0
OG A:SER131 4.2 11.2 0.6
OE1 A:GLU130 4.2 14.5 1.0
O A:HOH402 4.3 30.9 1.0
O A:HOH540 4.8 14.5 0.8
CG A:ASP127 4.9 12.2 1.0
CB A:GLU130 4.9 10.0 1.0

Iron binding site 6 out of 7 in 5j9v

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Iron binding site 6 out of 7 in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:13.2
occ:0.30
 O A:HOH338 2.0 10.3 0.8
O A:HOH324 2.0 10.4 0.4
O A:HOH634 2.1 11.5 0.4
O A:HOH627 2.1 12.4 0.8
OD2 A:ASP80 4.1 8.6 1.0
OD1 A:ASP80 4.1 7.5 1.0
CG A:ASP80 4.5 7.2 1.0
O A:HOH438 4.8 13.4 1.0

Iron binding site 7 out of 7 in 5j9v

Go back to Iron Binding Sites List in 5j9v
Iron binding site 7 out of 7 in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:13.2
occ:0.30
 O A:HOH552 2.0 13.9 0.4
O A:HOH385 2.0 11.2 0.4
O A:HOH563 2.0 12.2 0.4
O A:HOH633 2.1 16.8 0.4
O A:HOH630 2.1 15.7 0.4
O A:HOH401 2.2 11.7 0.8
O A:HOH615 4.1 23.9 1.0
OD1 A:ASN21 4.3 8.4 1.0
O A:HOH548 4.3 22.4 1.0
O A:ARG18 4.4 8.1 1.0
CL A:CL219 4.5 18.3 0.6
O A:HOH530 4.5 22.6 1.0
O A:HOH593 4.7 20.3 1.0
O A:HOH484 4.8 56.2 1.0
CB A:LEU22 4.8 8.4 1.0
O A:HOH637 4.9 38.7 1.0
O A:HOH619 5.0 24.8 1.0

Reference:

C.Bernacchioni, C.Pozzi, F.Di Pisa, S.Mangani, P.Turano. Ferroxidase Activity in Eukaryotic Ferritin Is Controlled By Accessory-Iron-Binding Sites in the Catalytic Cavity. Chemistry V. 22 16213 2016.
ISSN: ISSN 0947-6539
PubMed: 27650996
DOI: 10.1002/CHEM.201602842
Page generated: Tue Aug 6 02:25:34 2024

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