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Iron in PDB 6iaf: Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N

Enzymatic activity of Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N

All present enzymatic activity of Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N:
1.16.3.1;

Protein crystallography data

The structure of Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N, PDB code: 6iaf 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) 22.44 / 1.35
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.720, 183.720, 183.720, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 14.1

Other elements in 6iaf:

The structure of Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Chlorine (Cl) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N (pdb code 6iaf). 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 Rana Catesbeiana H' Ferritin Variant H54N, PDB code: 6iaf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 6iaf

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Iron binding site 1 out of 7 in the Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


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 Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:7.4
occ:0.25
 O A:HOH497 2.2 9.4 0.2
NE2 A:HIS169 2.2 7.1 1.0
CL A:CL216 2.4 8.3 0.2
CE1 A:HIS169 3.1 7.8 1.0
CD2 A:HIS169 3.3 6.9 1.0
ND1 A:HIS169 4.3 7.4 1.0
CG A:HIS169 4.4 7.3 1.0
O A:HOH508 4.4 19.1 0.5

Iron binding site 2 out of 7 in 6iaf

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Iron binding site 2 out of 7 in the Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


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 Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:25.4
occ:0.40
 FE A:FE2202 0.0 25.4 0.4
FE A:FE2202 1.6 10.8 0.6
O A:HOH323 1.7 9.2 0.6
O A:HOH347 1.8 13.6 0.6
OE2 A:GLU58 1.9 12.2 0.4
O A:HOH323 1.9 14.3 0.4
OE1 A:GLU103 2.3 12.1 0.4
O A:HOH309 2.4 9.6 0.6
OE2 A:GLU103 2.4 12.1 0.6
OE2 A:GLU58 2.6 17.9 0.6
OE1 A:GLU103 2.7 8.7 0.6
OE2 A:GLU103 2.7 10.8 0.4
OE1 A:GLU58 2.7 19.6 0.6
CD A:GLU58 2.8 16.9 0.6
CD A:GLU103 2.8 11.4 0.4
CD A:GLU58 2.8 11.3 0.4
CD A:GLU103 2.9 10.4 0.6
OE1 A:GLU58 3.2 12.2 0.4
OD2 A:ASP140 3.4 17.8 1.0
OE1 A:GLN137 3.4 15.7 1.0
FE A:FE2203 3.6 17.3 0.4
CG A:GLU58 3.9 14.8 0.6
NE2 A:GLN137 4.1 12.8 1.0
CG A:GLU58 4.2 11.0 0.4
CD A:GLN137 4.2 14.5 1.0
OE2 A:GLU57 4.3 15.4 0.7
CG A:GLU103 4.3 10.4 0.4
CG A:GLU103 4.4 9.5 0.6
CE2 A:TYR30 4.5 9.4 1.0
CG A:ASP140 4.5 16.9 1.0
O A:HOH324 4.6 14.6 1.0
O A:HOH308 4.6 14.5 0.7
ND2 A:ASN54 4.8 9.0 0.2
OH A:TYR30 4.9 15.9 1.0
CE1 A:HIS61 4.9 24.7 1.0
ND1 A:HIS61 4.9 20.0 1.0
CB A:ASP140 5.0 12.2 1.0

Iron binding site 3 out of 7 in 6iaf

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Iron binding site 3 out of 7 in the Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


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 Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:10.8
occ:0.60
 FE A:FE2202 0.0 10.8 0.6
FE A:FE2202 1.6 25.4 0.4
O A:HOH323 2.1 14.3 0.4
O A:HOH309 2.1 9.6 0.6
OE1 A:GLU103 2.1 8.7 0.6
OD2 A:ASP140 2.2 17.8 1.0
OE1 A:GLU103 2.2 12.1 0.4
OE1 A:GLN137 2.3 15.7 1.0
O A:HOH347 2.3 13.6 0.6
O A:HOH323 2.4 9.2 0.6
CD A:GLU103 2.9 11.4 0.4
CD A:GLU103 3.0 10.4 0.6
OE2 A:GLU103 3.1 10.8 0.4
OE2 A:GLU103 3.1 12.1 0.6
CD A:GLN137 3.2 14.5 1.0
CG A:ASP140 3.3 16.9 1.0
OE2 A:GLU58 3.3 12.2 0.4
NE2 A:GLN137 3.4 12.8 1.0
OE2 A:GLU58 3.6 17.9 0.6
CB A:ASP140 3.8 12.2 1.0
OE2 A:GLU57 3.9 15.4 0.7
OE1 A:GLU58 4.1 19.6 0.6
CD A:GLU58 4.1 16.9 0.6
FE A:FE2203 4.1 17.3 0.4
CD A:GLU58 4.2 11.3 0.4
CG A:GLU103 4.3 10.4 0.4
O A:HOH308 4.3 14.5 0.7
OD1 A:ASP140 4.4 15.1 1.0
OE1 A:GLU58 4.4 12.2 0.4
CG A:GLU103 4.4 9.5 0.6
O A:HOH469 4.4 17.2 1.0
O A:HOH324 4.5 14.6 1.0
FE A:FE2204 4.5 13.7 0.7
CG A:GLN137 4.6 16.3 1.0
CA A:GLN137 4.7 10.6 1.0
CE1 A:HIS61 4.7 24.7 1.0
CB A:GLU103 4.9 9.9 0.4
O A:GLU136 4.9 10.8 1.0
CG A:GLU136 5.0 16.2 0.7
CD A:GLU57 5.0 15.2 0.7
CB A:GLU103 5.0 8.9 0.6

Iron binding site 4 out of 7 in 6iaf

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Iron binding site 4 out of 7 in the Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


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 Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:17.3
occ:0.40
 O A:HOH324 2.0 14.6 1.0
OE1 A:GLU58 2.0 12.2 0.4
O A:HOH323 2.1 14.3 0.4
OE1 A:GLU23 2.1 14.4 1.0
ND1 A:HIS61 2.4 20.0 1.0
OE1 A:GLU58 2.5 19.6 0.6
OE2 A:GLU58 2.5 17.9 0.6
CD A:GLU58 2.7 16.9 0.6
O A:HOH323 2.8 9.2 0.6
CD A:GLU23 2.9 10.5 1.0
OE2 A:GLU23 3.0 13.5 1.0
O A:HOH309 3.1 9.6 0.6
CD A:GLU58 3.1 11.3 0.4
CE1 A:HIS61 3.3 24.7 1.0
CG A:HIS61 3.5 14.2 1.0
FE A:FE2202 3.6 25.4 0.4
OE2 A:GLU58 3.6 12.2 0.4
CB A:HIS61 3.8 10.5 1.0
O A:HOH469 4.1 17.2 1.0
CG1 A:VAL106 4.1 9.8 1.0
FE A:FE2202 4.1 10.8 0.6
CG A:GLU58 4.1 14.8 0.6
OE1 A:GLN137 4.2 15.7 1.0
CG A:GLU23 4.3 9.2 1.0
CA A:GLU58 4.4 11.8 0.6
CA A:GLU58 4.4 9.7 0.4
CG A:GLU58 4.4 11.0 0.4
NE2 A:HIS61 4.4 21.5 1.0
CB A:GLU58 4.5 12.9 0.6
CD2 A:HIS61 4.6 16.5 1.0
CB A:GLU58 4.6 10.1 0.4
CD A:GLN137 4.8 14.5 1.0
CB A:GLU23 4.9 7.9 1.0
O A:HOH347 5.0 13.6 0.6

Iron binding site 5 out of 7 in 6iaf

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Iron binding site 5 out of 7 in the Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


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 Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:13.7
occ:0.70
 OE2 A:GLU136 2.0 17.5 0.7
O A:HOH308 2.1 14.5 0.7
O A:HOH476 2.1 16.3 0.7
OE2 A:GLU57 2.1 15.4 0.7
OD1 A:ASP140 2.2 15.1 1.0
OE1 A:GLU57 2.5 15.4 0.7
CD A:GLU57 2.7 15.2 0.7
CG A:ASP140 2.8 16.9 1.0
OD2 A:ASP140 2.9 17.8 1.0
OE2 A:GLU136 3.0 16.9 0.3
CD A:GLU136 3.1 17.4 0.7
CG A:GLU136 3.6 16.2 0.7
CG A:GLU136 3.6 15.4 0.3
CD A:GLU136 3.7 15.7 0.3
O A:HOH423 4.0 39.3 1.0
O A:HOH347 4.0 13.6 0.6
CG A:GLU57 4.2 14.0 1.0
NH2 A:ARG143 4.2 15.5 0.7
O A:HOH557 4.2 46.0 1.0
O A:HOH309 4.2 9.6 0.6
CB A:ASP140 4.2 12.2 1.0
OE1 A:GLU136 4.2 19.0 0.7
O A:HOH493 4.3 20.9 1.0
OD1 A:ASN54 4.3 10.1 0.4
ND2 A:ASN54 4.4 9.0 0.2
O A:HOH517 4.5 7.6 1.0
FE A:FE2202 4.5 10.8 0.6
O A:HOH322 4.6 26.0 0.5
O A:HOH467 4.6 26.5 1.0
O A:GLU136 4.7 10.8 1.0
CA A:ASP140 4.9 9.0 1.0
OE1 A:GLU136 4.9 16.5 0.3
OD1 A:ASN54 5.0 12.4 0.4

Iron binding site 6 out of 7 in 6iaf

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Iron binding site 6 out of 7 in the Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


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 Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:15.5
occ:0.25
 O A:HOH526 2.0 13.4 1.0
O A:HOH440 2.1 12.3 1.0
OE2 A:GLU130 3.8 12.7 1.0
O A:HOH593 4.2 15.7 1.0
OE1 A:GLU130 4.2 18.6 1.0
O A:HOH389 4.4 19.9 1.0
CD A:GLU130 4.4 14.6 1.0

Iron binding site 7 out of 7 in 6iaf

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Iron binding site 7 out of 7 in the Fifteen Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


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 Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:21.1
occ:0.20
 O A:HOH317 1.8 23.3 0.6
O A:HOH326 2.3 27.4 0.6
OD1 A:ASP127 3.7 18.3 1.0
OE1 A:GLU130 4.4 18.6 1.0
OG A:SER131 4.4 19.2 0.9
O A:HOH483 4.4 49.4 1.0
CG A:ASP127 4.8 15.3 1.0
O A:HOH480 4.9 18.4 0.5

Reference:

C.Pozzi, F.Di Pisa, D.Lalli, C.Rosa, P.Turano, S.Mangani. Effect of the Point Mutation H54N on the Ferroxidase Process of Rana Catesbeiana H' Ferritin. J.Inorg.Biochem. V. 197 10697 2019.
ISSN: ISSN 0162-0134
PubMed: 31075719
DOI: 10.1016/J.JINORGBIO.2019.110697
Page generated: Tue Aug 6 22:51:53 2024

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