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Iron in PDB 4mn9: Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q

Enzymatic activity of Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q

All present enzymatic activity of Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q:
1.16.3.1;

Protein crystallography data

The structure of Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q, PDB code: 4mn9 was solved by S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.47 / 1.15
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.930, 183.930, 183.930, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 15.3

Other elements in 4mn9:

The structure of Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Chlorine (Cl) 10 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q (pdb code 4mn9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q, PDB code: 4mn9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4mn9

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Iron binding site 1 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:7.5
occ:0.80
 OE1 A:GLU23 2.0 8.7 1.0
O A:HOH418 2.1 11.5 1.0
OE1 A:GLU58 2.1 10.4 1.0
O A:HOH373 2.1 9.8 1.0
ND1 A:HIS61 2.2 9.6 1.0
CD A:GLU23 3.0 8.3 1.0
CD A:GLU58 3.0 10.2 1.0
CE1 A:HIS61 3.1 9.7 1.0
CG A:HIS61 3.2 9.0 1.0
OE2 A:GLU23 3.3 9.8 1.0
OE2 A:GLU58 3.4 11.5 1.0
CB A:HIS61 3.6 8.2 1.0
FE A:FE202 3.8 16.0 0.3
CG1 A:VAL106 3.9 7.1 1.0
OE1 A:GLN137 4.1 9.6 1.0
NE2 A:HIS61 4.2 10.3 1.0
O A:HOH349 4.3 11.2 1.0
CD2 A:HIS61 4.3 9.5 1.0
CG A:GLU23 4.3 7.7 1.0
CG A:GLU58 4.3 8.8 1.0
CA A:GLU58 4.4 7.2 1.0
CB A:GLU58 4.6 7.7 1.0
CB A:GLU23 4.6 6.5 1.0
O A:HOH623 4.8 10.1 0.6
CD A:GLN137 4.9 8.7 1.0
CA A:GLU23 4.9 5.9 1.0
CG2 A:VAL106 4.9 7.0 1.0
CB A:VAL106 4.9 6.6 1.0
O A:GLU58 4.9 7.4 1.0

Iron binding site 2 out of 6 in 4mn9

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Iron binding site 2 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:16.0
occ:0.30
 OE2 A:GLU58 1.9 11.5 1.0
O A:HOH623 2.0 10.1 0.6
O A:HOH418 2.1 11.5 1.0
OE1 A:GLU103 2.3 11.2 1.0
OE2 A:GLU103 2.5 12.3 1.0
O A:HOH622 2.7 12.2 0.7
CD A:GLU103 2.7 10.6 1.0
FE A:FE203 2.8 8.6 0.4
CD A:GLU58 3.0 10.2 1.0
OE1 A:GLN137 3.5 9.6 1.0
OE1 A:GLU58 3.6 10.4 1.0
FE A:FE201 3.8 7.5 0.8
CE1 A:HIS61 4.0 9.7 1.0
OD2 A:ASP140 4.1 13.1 0.5
NE2 A:GLN137 4.1 8.7 1.0
OE1 A:GLN54 4.1 15.4 0.8
CG A:GLU103 4.1 9.2 1.0
CG A:GLU58 4.2 8.8 1.0
O A:HOH625 4.2 23.1 1.0
OD2 A:ASP140 4.2 10.5 0.5
CD A:GLN137 4.2 8.7 1.0
ND1 A:HIS61 4.4 9.6 1.0
CE2 A:TYR30 4.5 7.5 1.0
OH A:TYR30 4.8 9.9 1.0
OE2 A:GLU136 4.8 14.1 0.8
O A:HOH373 4.9 9.8 1.0
CB A:GLU103 4.9 7.9 1.0
CG A:ASP140 4.9 10.4 0.5

Iron binding site 3 out of 6 in 4mn9

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Iron binding site 3 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:8.6
occ:0.40
 OE1 A:GLN54 1.7 15.4 0.8
OD2 A:ASP140 1.8 13.1 0.5
OD2 A:ASP140 2.0 10.5 0.5
O A:HOH622 2.1 12.2 0.7
O A:HOH623 2.2 10.1 0.6
O A:HOH625 2.3 23.1 1.0
OE2 A:GLU103 2.3 12.3 1.0
CD A:GLN54 2.7 14.9 0.8
OE1 A:GLN54 2.8 13.8 0.2
FE A:FE202 2.8 16.0 0.3
CG A:ASP140 3.0 12.9 0.5
CG A:ASP140 3.2 10.4 0.5
NE2 A:GLN54 3.2 15.3 0.8
CD A:GLU103 3.3 10.6 1.0
OE1 A:GLU103 3.6 11.2 1.0
FE A:FE204 3.7 13.3 0.4
CD A:GLN54 3.7 13.7 0.2
CB A:ASP140 3.8 12.7 0.5
CB A:ASP140 3.9 10.3 0.5
OE2 A:GLU58 3.9 11.5 1.0
OD1 A:ASP140 3.9 13.5 0.5
OE2 A:GLU136 4.0 14.1 0.8
CG A:GLN54 4.0 14.5 0.8
OD1 A:ASP140 4.1 10.4 0.5
OH A:TYR30 4.1 9.9 1.0
CG A:GLN54 4.2 13.5 0.2
CE2 A:TYR30 4.4 7.5 1.0
OE1 A:GLU57 4.4 14.8 0.5
O A:HOH627 4.5 15.1 0.2
CG A:GLU103 4.5 9.2 1.0
CZ A:TYR30 4.5 8.1 1.0
CB A:GLN54 4.6 13.9 0.8
CB A:GLN54 4.6 13.3 0.2
NE2 A:GLN54 4.7 13.8 0.2
CA A:GLN54 4.8 13.1 0.2
CA A:GLN54 4.8 13.4 0.8
O A:HOH418 4.9 11.5 1.0
CD A:GLU58 4.9 10.2 1.0
NH1 A:ARG143 4.9 10.6 0.5
OE1 A:GLU57 5.0 21.6 0.2

Iron binding site 4 out of 6 in 4mn9

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Iron binding site 4 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:13.3
occ:0.40
 O A:HOH626 2.0 18.2 0.4
O A:HOH627 2.1 15.1 0.2
O A:HOH625 2.1 23.1 1.0
OE2 A:GLU136 2.2 14.1 0.8
OD1 A:ASP140 2.2 10.4 0.5
OD2 A:ASP140 2.5 10.5 0.5
CG A:ASP140 2.6 10.4 0.5
O A:HOH628 2.9 15.3 0.2
CD A:GLU136 3.1 13.2 0.8
OE1 A:GLU136 3.4 14.2 0.8
OE2 A:GLU57 3.5 22.4 0.2
OD2 A:ASP140 3.6 13.1 0.5
NH1 A:ARG143 3.6 10.6 0.5
OE1 A:GLU57 3.6 21.6 0.2
FE A:FE203 3.7 8.6 0.4
CD A:GLU57 3.7 11.2 0.2
CG A:ASP140 3.7 12.9 0.5
O A:HOH623 3.8 10.1 0.6
OE1 A:GLU57 3.8 14.8 0.5
NE2 A:GLN54 3.9 15.3 0.8
O A:HOH465 3.9 23.2 1.0
O A:HOH546 3.9 18.6 0.2
OE1 A:GLN54 3.9 13.8 0.2
CB A:ASP140 4.0 12.7 0.5
CB A:ASP140 4.1 10.3 0.5
O A:HOH433 4.2 21.0 1.0
OD1 A:ASP140 4.2 13.5 0.5
CD A:GLU57 4.2 13.4 0.5
OE1 A:GLN54 4.4 15.4 0.8
OE2 A:GLU57 4.5 14.0 0.5
CG A:GLU136 4.5 12.1 0.8
CD A:GLN54 4.6 14.9 0.8
CZ A:ARG143 4.7 10.3 0.5
FE A:FE205 4.7 15.8 0.2
CG A:GLU57 4.7 15.7 0.5
O A:HOH622 4.9 12.2 0.7
O A:GLU136 4.9 8.3 1.0
CA A:ASP140 4.9 10.2 0.5
CA A:ASP140 4.9 12.3 0.5
CD A:GLN54 5.0 13.7 0.2

Iron binding site 5 out of 6 in 4mn9

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Iron binding site 5 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:15.8
occ:0.25
 OE2 A:GLU57 2.0 14.0 0.5
O A:HOH653 2.1 16.1 0.2
O A:HOH629 2.1 17.2 0.2
OE2 A:GLU53 2.2 9.0 0.2
O A:HOH628 2.2 15.3 0.2
O A:HOH546 2.2 18.6 0.2
OE1 A:GLU57 3.0 21.6 0.2
CD A:GLU57 3.1 13.4 0.5
CD A:GLU53 3.2 8.9 0.2
O A:HOH627 3.3 15.1 0.2
OE1 A:GLU57 3.4 14.8 0.5
OE2 A:GLU57 3.5 22.4 0.2
CD A:GLU57 3.6 11.2 0.2
CG A:GLU53 3.6 14.1 0.5
CG A:GLU53 3.7 8.9 0.2
O A:HOH626 4.0 18.2 0.4
OE1 A:GLU53 4.1 15.2 0.5
O A:HOH431 4.1 18.0 1.0
NH1 A:ARG143 4.2 10.6 0.5
CD A:GLU53 4.2 14.5 0.5
OE1 A:GLU53 4.3 9.0 0.2
CG A:GLU57 4.4 11.6 0.5
NH2 A:ARG143 4.5 10.5 0.5
O A:HOH522 4.6 23.7 1.0
FE A:FE204 4.7 13.3 0.4
NE2 A:GLN54 4.7 15.3 0.8
NH1 A:ARG143 4.8 15.3 0.5
CZ A:ARG143 4.8 10.3 0.5
NE2 A:GLN54 4.9 13.8 0.2
CB A:GLU53 4.9 13.7 0.5
CB A:GLU53 4.9 8.8 0.5
OE1 A:GLN54 5.0 13.8 0.2

Iron binding site 6 out of 6 in 4mn9

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Iron binding site 6 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:5.5
occ:0.20
 O A:HOH412 2.2 7.8 0.2
NE2 A:HIS169 2.3 7.5 1.0
CL A:CL224 2.4 5.9 0.2
CE1 A:HIS169 3.1 7.4 1.0
CD2 A:HIS169 3.4 7.4 1.0
ND1 A:HIS169 4.3 7.2 1.0
O A:HOH573 4.3 27.9 1.0
CG A:HIS169 4.5 7.2 1.0

Reference:

S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli. Crystallographic Snapshots of Iron in Frog M Ferritin To Be Published.
Page generated: Mon Aug 5 06:58:30 2024

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