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Iron in PDB 4zl6: Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)

Enzymatic activity of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)

All present enzymatic activity of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H):
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H), PDB code: 4zl6 was solved by S.Pfaffen, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.28 / 1.90
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 126.720, 126.720, 170.310, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.4

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) (pdb code 4zl6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H), PDB code: 4zl6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 4zl6

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Iron binding site 1 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:38.2
occ:0.40
 NE2 B:HIS51 2.0 34.2 1.0
OE2 B:GLU130 2.0 42.2 1.0
OE1 B:GLN126 2.2 72.4 1.0
O B:HOH351 2.2 35.1 1.0
CD B:GLN126 2.8 53.6 1.0
CD2 B:HIS51 3.0 31.2 1.0
CD B:GLU130 3.0 31.2 1.0
CE1 B:HIS51 3.0 32.2 1.0
CG B:GLN126 3.3 38.5 1.0
OE1 B:GLU130 3.4 27.0 1.0
FE B:FE202 3.5 30.6 1.0
O B:HOH311 3.6 26.6 1.0
CD B:GLU47 3.6 55.2 1.0
OE1 B:GLU47 3.8 62.5 1.0
OE2 B:GLU47 3.8 65.7 1.0
NE2 B:GLN126 3.8 58.1 1.0
CG B:GLU47 3.9 39.8 1.0
ND1 B:HIS51 4.1 34.4 1.0
CG B:HIS51 4.1 28.6 1.0
OE1 B:GLN127 4.2 37.6 1.0
CG B:GLU130 4.3 26.5 1.0
FE B:FE203 4.3 31.6 0.7
CB B:GLN126 4.6 27.9 1.0
NE2 B:HIS44 4.7 31.9 1.0
O B:HOH344 4.8 42.7 1.0
OE2 B:GLU48 4.9 26.8 1.0

Iron binding site 2 out of 24 in 4zl6

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Iron binding site 2 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:30.6
occ:1.00
 O B:HOH351 2.1 35.1 1.0
OE2 B:GLU48 2.1 26.8 1.0
OE1 B:GLU130 2.1 27.0 1.0
OE2 B:GLU94 2.2 30.2 1.0
O B:HOH311 2.2 26.6 1.0
NE2 B:HIS44 2.3 31.9 1.0
CD B:GLU48 3.0 25.5 1.0
CD B:GLU94 3.1 29.2 1.0
CD B:GLU130 3.1 31.2 1.0
CD2 B:HIS44 3.2 31.4 1.0
OE1 B:GLU94 3.3 29.1 1.0
CE1 B:HIS44 3.4 30.9 1.0
OE1 B:GLU48 3.4 25.9 1.0
OE2 B:GLU130 3.4 42.2 1.0
FE B:FE201 3.5 38.2 0.4
FE B:FE203 3.7 31.6 0.7
OH B:TYR22 4.1 22.3 1.0
CG B:GLU48 4.2 24.4 1.0
OE1 B:GLN127 4.3 37.6 1.0
ND2 B:ASN97 4.3 35.1 1.0
CG B:GLU130 4.4 26.5 1.0
CG B:GLU94 4.4 24.8 1.0
CG B:HIS44 4.4 29.6 1.0
CE2 B:TYR22 4.5 21.0 1.0
ND1 B:HIS44 4.5 33.1 1.0
OE1 B:GLU47 4.6 62.5 1.0
NE2 B:HIS51 4.6 34.2 1.0
CD2 B:HIS51 4.6 31.2 1.0
CZ B:TYR22 4.6 20.0 1.0
CB B:GLU130 4.7 22.8 1.0

Iron binding site 3 out of 24 in 4zl6

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Iron binding site 3 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe203

b:31.6
occ:0.65
 OE1 B:GLU48 2.0 25.9 1.0
OE1 B:GLU15 2.1 32.1 1.0
O B:HOH311 2.3 26.6 1.0
O B:HOH344 2.3 42.7 1.0
CD2 B:HIS51 3.0 31.2 1.0
CD B:GLU48 3.1 25.5 1.0
CD B:GLU15 3.1 29.7 1.0
OE2 B:GLU15 3.4 38.5 1.0
ND2 B:ASN97 3.5 35.1 1.0
OE2 B:GLU48 3.5 26.8 1.0
FE B:FE202 3.7 30.6 1.0
CG B:HIS51 3.9 28.6 1.0
O B:HOH351 4.0 35.1 1.0
NE2 B:HIS51 4.0 34.2 1.0
OE1 B:GLN127 4.1 37.6 1.0
CB B:HIS51 4.2 24.6 1.0
CG B:ASN97 4.2 39.2 1.0
FE B:FE201 4.3 38.2 0.4
CG B:GLU48 4.4 24.4 1.0
CG B:GLU15 4.5 23.1 1.0
CA B:GLU48 4.5 20.4 1.0
OE1 B:GLU94 4.6 29.1 1.0
CB B:GLU48 4.7 20.7 1.0
CB B:ASN97 4.7 31.3 1.0
OD1 B:ASN97 4.9 32.3 1.0
CD B:GLN127 4.9 29.8 1.0
OE2 B:GLU94 4.9 30.2 1.0
CB B:GLU15 5.0 19.8 1.0

Iron binding site 4 out of 24 in 4zl6

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Iron binding site 4 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe204

b:58.5
occ:1.00
 OE1 B:GLU3 2.1 59.7 1.0
OD2 B:ASP6 2.6 37.9 1.0
CD B:GLU3 2.8 50.5 1.0
OE2 B:GLU3 2.9 43.8 1.0
O B:HOH359 3.1 45.2 1.0
FE B:FE206 3.2 34.7 0.5
FE B:FE205 3.2 40.8 0.5
NH2 B:ARG10 3.7 76.4 1.0
CG B:ASP6 3.8 34.5 1.0
OE1 B:GLU2 4.1 53.9 1.0
CG B:GLU3 4.3 48.1 1.0
CB B:ASP6 4.4 30.1 1.0
O B:HOH372 4.5 52.4 1.0
OD1 B:ASP6 4.7 38.0 1.0
CA B:GLU3 4.8 35.7 1.0
OE2 B:GLU2 4.8 61.8 1.0
CD B:GLU2 4.9 53.5 1.0
CZ B:ARG10 4.9 61.0 1.0
CB B:GLU3 4.9 38.9 1.0

Iron binding site 5 out of 24 in 4zl6

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Iron binding site 5 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe205

b:40.8
occ:0.50
 OE2 B:GLU3 2.2 43.8 1.0
OE1 B:GLU2 2.2 53.9 1.0
O B:HOH372 2.5 52.4 1.0
O B:HOH359 2.6 45.2 1.0
CD B:GLU2 3.1 53.5 1.0
FE B:FE206 3.1 34.7 0.5
FE B:FE204 3.2 58.5 1.0
CD B:GLU3 3.3 50.5 1.0
OE2 B:GLU2 3.5 61.8 1.0
OE1 B:GLU3 3.8 59.7 1.0
OD2 B:ASP6 4.2 37.9 1.0
CG B:GLU2 4.3 54.4 1.0
CB B:GLU2 4.5 47.4 1.0
CG B:GLU3 4.5 48.1 1.0
N B:GLU3 4.9 32.5 1.0
C B:GLU2 4.9 35.3 1.0

Iron binding site 6 out of 24 in 4zl6

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Iron binding site 6 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe206

b:34.7
occ:0.50
 OE2 B:GLU2 2.2 61.8 1.0
OD2 B:ASP6 2.2 37.9 1.0
O B:HOH305 2.3 41.5 1.0
O B:HOH372 2.6 52.4 1.0
CG B:ASP6 2.9 34.5 1.0
OD1 B:ASP6 2.9 38.0 1.0
CD B:GLU2 2.9 53.5 1.0
OE1 B:GLU2 3.0 53.9 1.0
FE B:FE205 3.1 40.8 0.5
FE B:FE204 3.2 58.5 1.0
CB B:ASP6 4.3 30.1 1.0
OE2 B:GLU3 4.4 43.8 1.0
CG B:GLU2 4.4 54.4 1.0
OE1 B:GLU3 4.5 59.7 1.0
O B:HOH359 4.7 45.2 1.0
O B:GLU2 4.7 31.2 1.0
CD B:GLU3 4.8 50.5 1.0

Iron binding site 7 out of 24 in 4zl6

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Iron binding site 7 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:28.6
occ:0.60
 OE1 A:GLU48 2.1 26.4 1.0
O A:HOH328 2.2 44.1 1.0
OE1 A:GLU15 2.2 27.1 1.0
O A:HOH321 2.4 27.4 1.0
CD2 A:HIS51 3.0 26.5 1.0
CD A:GLU48 3.1 26.1 1.0
CD A:GLU15 3.1 29.5 1.0
OE2 A:GLU15 3.3 32.9 1.0
OE2 A:GLU48 3.4 27.1 1.0
ND2 A:ASN97 3.4 34.5 1.0
FE A:FE202 3.8 28.1 1.0
O A:HOH359 3.9 28.8 1.0
O A:HOH335 3.9 47.7 1.0
CG A:HIS51 3.9 27.5 1.0
NE2 A:HIS51 4.0 30.5 1.0
OE1 A:GLN127 4.1 33.5 1.0
CG A:ASN97 4.2 41.5 1.0
CB A:HIS51 4.2 24.5 1.0
CG A:GLU48 4.4 21.6 1.0
CG A:GLU15 4.5 23.9 1.0
FE A:FE203 4.5 36.1 0.5
CA A:GLU48 4.5 18.1 1.0
OE1 A:GLU94 4.6 26.9 1.0
CB A:GLU48 4.7 19.5 1.0
CB A:ASN97 4.7 32.7 1.0
OD1 A:ASN97 4.9 36.8 1.0
OE2 A:GLU94 4.9 27.2 1.0
CB A:GLU15 5.0 20.4 1.0

Iron binding site 8 out of 24 in 4zl6

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Iron binding site 8 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:28.1
occ:1.00
 O A:HOH359 2.0 28.8 1.0
OE2 A:GLU48 2.1 27.1 1.0
OE1 A:GLU130 2.1 24.8 1.0
OE2 A:GLU94 2.2 27.2 1.0
O A:HOH321 2.2 27.4 1.0
NE2 A:HIS44 2.3 27.8 1.0
CD A:GLU130 3.0 34.9 1.0
CD A:GLU48 3.1 26.1 1.0
CD A:GLU94 3.1 25.6 1.0
CE1 A:HIS44 3.2 31.7 1.0
CD2 A:HIS44 3.3 29.0 1.0
OE1 A:GLU94 3.4 26.9 1.0
OE2 A:GLU130 3.4 39.2 1.0
OE1 A:GLU48 3.5 26.4 1.0
FE A:FE203 3.6 36.1 0.5
FE A:FE201 3.8 28.6 0.6
OH A:TYR22 4.1 21.4 1.0
CG A:GLU48 4.3 21.6 1.0
ND2 A:ASN97 4.3 34.5 1.0
ND1 A:HIS44 4.3 31.3 1.0
CG A:GLU130 4.4 26.7 1.0
CG A:HIS44 4.4 28.1 1.0
CE2 A:TYR22 4.4 18.8 1.0
OE1 A:GLN127 4.4 33.5 1.0
CG A:GLU94 4.5 22.3 1.0
OE2 A:GLU47 4.5 52.6 1.0
NE2 A:HIS51 4.6 30.5 1.0
CZ A:TYR22 4.6 18.6 1.0
CD2 A:HIS51 4.6 26.5 1.0
CB A:GLU130 4.7 23.2 1.0
O A:HOH335 5.0 47.7 1.0

Iron binding site 9 out of 24 in 4zl6

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Iron binding site 9 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:36.1
occ:0.45
 OE2 A:GLU130 2.0 39.2 1.0
NE2 A:HIS51 2.0 30.5 1.0
O A:HOH359 2.2 28.8 1.0
OE1 A:GLN126 2.4 56.3 1.0
OE2 A:GLU47 2.4 52.6 1.0
CD A:GLN126 2.7 53.0 1.0
CE1 A:HIS51 3.0 34.0 1.0
CD A:GLU130 3.0 34.9 1.0
CD2 A:HIS51 3.1 26.5 1.0
O A:HOH335 3.2 47.7 1.0
NE2 A:GLN126 3.3 58.2 1.0
CG A:GLN126 3.4 41.7 1.0
OE1 A:GLU130 3.4 24.8 1.0
CD A:GLU47 3.5 48.5 1.0
FE A:FE202 3.6 28.1 1.0
O A:HOH321 3.7 27.4 1.0
CG A:GLU47 3.8 35.1 1.0
ND1 A:HIS51 4.1 33.4 1.0
CG A:HIS51 4.2 27.5 1.0
CG A:GLU130 4.2 26.7 1.0
FE A:FE201 4.5 28.6 0.6
NE2 A:HIS44 4.6 27.8 1.0
OE1 A:GLN127 4.6 33.5 1.0
OE1 A:GLU47 4.6 51.6 1.0
CB A:GLN126 4.7 29.0 1.0
OE2 A:GLU48 4.9 27.1 1.0
O A:HOH328 4.9 44.1 1.0

Iron binding site 10 out of 24 in 4zl6

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Iron binding site 10 out of 24 in the Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Pmftn Variant E44H Soaked in Iron (3 H) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:37.3
occ:0.40
 OE2 C:GLU130 1.9 40.6 1.0
O C:HOH304 2.0 32.6 1.0
NE2 C:HIS51 2.1 35.0 1.0
OE1 C:GLN126 2.1 67.9 1.0
CD C:GLN126 2.7 49.5 1.0
OE2 C:GLU47 2.7 54.1 1.0
CD C:GLU130 2.9 35.3 1.0
CE1 C:HIS51 3.0 34.9 1.0
CD2 C:HIS51 3.1 29.3 1.0
OE1 C:GLU130 3.4 26.5 1.0
NE2 C:GLN126 3.4 64.0 1.0
CD C:GLU47 3.5 49.8 1.0
CG C:GLN126 3.5 39.2 1.0
O C:HOH311 3.5 25.9 1.0
FE C:FE203 3.6 27.8 0.9
CG C:GLU47 3.8 38.5 1.0
O C:HOH365 4.0 35.0 1.0
ND1 C:HIS51 4.1 33.3 1.0
CG C:HIS51 4.2 27.3 1.0
CG C:GLU130 4.2 31.6 1.0
OE1 C:GLN127 4.4 35.5 1.0
OE1 C:GLU47 4.5 56.7 1.0
FE C:FE202 4.5 30.8 0.7
NE2 C:HIS44 4.7 32.0 1.0
O C:HOH339 4.7 43.5 1.0
CB C:GLN126 4.8 29.2 1.0
OE2 C:GLU48 4.9 27.5 1.0

Reference:

S.Pfaffen, J.M.Bradley, R.Abdulqadir, M.R.Firme, G.R.Moore, N.E.Le Brun, M.E.Murphy. A Diatom Ferritin Optimized For Iron Oxidation But Not Iron Storage. J.Biol.Chem. V. 290 28416 2015.
ISSN: ESSN 1083-351X
PubMed: 26396187
DOI: 10.1074/JBC.M115.669713
Page generated: Mon Aug 5 18:19:05 2024

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