Iron in PDB 4zlw: Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)

All present enzymatic activity of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight):
1.16.3.1;

The structure of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight), PDB code: 4zlw 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)	48.55 / 2.00
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	175.051, 175.051, 175.051, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight) (pdb code 4zlw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 37 binding sites of Iron where determined in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight), PDB code: 4zlw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:49.5 occ:0.55 OE1 A:GLU48 2.1 45.3 1.0 OE1 A:GLU15 2.3 46.7 1.0 ND1 A:HIS51 2.7 46.8 1.0 O A:HOH302 2.7 52.6 1.0 CD A:GLU48 3.1 41.8 1.0 CD A:GLU15 3.1 47.0 1.0 OE2 A:GLU15 3.3 55.0 1.0 OE2 A:GLU48 3.4 52.6 1.0 CE1 A:HIS51 3.5 44.3 1.0 CG A:HIS51 3.7 42.0 1.0 ND2 A:ASN97 3.8 59.5 1.0 OE1 A:GLN127 3.9 42.6 1.0 CB A:HIS51 4.1 34.9 1.0 CG A:ASN97 4.4 64.8 1.0 CG A:GLU48 4.5 37.6 1.0 CG A:GLU15 4.6 39.2 1.0 NE2 A:HIS51 4.6 47.7 1.0 O A:HOH307 4.7 52.0 1.0 CA A:GLU48 4.8 32.2 1.0 CD2 A:HIS51 4.8 40.8 1.0 CB A:ASN97 4.8 53.7 1.0 CD A:GLN127 4.8 40.8 1.0 CB A:GLU48 4.9 33.0 1.0 CB A:GLU15 5.0 36.0 1.0

Iron binding site 2 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:58.5 occ:0.45 OE1 A:GLU44 2.1 65.2 1.0 OE1 A:GLU47 2.2 78.4 1.0 O A:HOH307 2.5 52.0 1.0 CD A:GLU44 3.0 55.2 1.0 CD A:GLU47 3.0 72.5 1.0 OE2 A:GLU47 3.2 73.7 1.0 FE A:FE204 3.2 65.2 0.5 OE2 A:GLU44 3.3 63.3 1.0 FE A:FE203 3.4 60.2 0.5 CB A:ALA130 4.2 36.8 1.0 O A:HOH350 4.3 62.6 1.0 CG A:GLU44 4.3 44.1 1.0 OE2 A:GLU94 4.5 44.9 1.0 CG A:GLU47 4.5 57.2 1.0 OH A:TYR22 4.7 35.7 1.0 OE2 A:GLU48 4.9 52.6 1.0 CB A:GLU44 4.9 38.0 1.0 O A:HOH312 4.9 56.8 1.0 CA A:ALA130 4.9 36.7 1.0

Iron binding site 3 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:60.2 occ:0.50 OE2 A:GLU44 2.2 63.3 1.0 O A:HOH350 2.2 62.6 1.0 OH A:TYR40 2.6 66.8 1.0 O A:HOH312 2.7 56.8 1.0 FE A:FE204 2.9 65.2 0.5 CD A:GLU44 3.0 55.2 1.0 FE A:FE202 3.4 58.5 0.5 CZ A:TYR40 3.5 61.1 1.0 OE1 A:GLU44 3.5 65.2 1.0 CG A:GLU44 4.0 44.1 1.0 OE2 A:GLU47 4.1 73.7 1.0 CD A:LYS133 4.1 61.8 1.0 CE2 A:TYR40 4.2 55.6 1.0 CE1 A:TYR40 4.2 59.6 1.0 NZ A:LYS133 4.2 64.7 1.0 CE A:LYS133 4.6 61.9 1.0 OE1 A:GLU47 4.9 78.4 1.0 CD A:GLU47 4.9 72.5 1.0

Iron binding site 4 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:65.2 occ:0.50 OE2 A:GLU47 2.0 73.7 1.0 O A:HOH350 2.0 62.6 1.0 O A:HOH312 2.6 56.8 1.0 FE A:FE203 2.9 60.2 0.5 CD A:GLU47 3.1 72.5 1.0 OE2 A:GLU44 3.1 63.3 1.0 FE A:FE202 3.2 58.5 0.5 OE1 A:GLU47 3.5 78.4 1.0 CD A:GLU44 3.9 55.2 1.0 OE1 A:GLU44 3.9 65.2 1.0 CG A:GLU47 4.4 57.2 1.0

Iron binding site 5 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:53.1 occ:0.60 O D:HOH318 1.8 58.8 1.0 OE1 D:GLU48 2.1 52.3 1.0 OE1 D:GLU15 2.2 41.5 1.0 ND1 D:HIS51 2.8 44.2 1.0 CD D:GLU48 3.1 39.8 1.0 CD D:GLU15 3.2 43.6 1.0 FE D:FE203 3.4 54.9 0.2 OE2 D:GLU48 3.4 49.6 1.0 OE2 D:GLU15 3.5 46.5 1.0 O D:HOH307 3.5 54.2 1.0 CE1 D:HIS51 3.6 44.5 1.0 CG D:HIS51 3.8 41.6 1.0 OD1 D:ASN97 3.9 48.7 1.0 CB D:HIS51 4.0 34.0 1.0 OE1 D:GLN127 4.1 36.9 1.0 CG D:ASN97 4.4 59.5 1.0 CG D:GLU48 4.4 35.7 1.0 CG D:GLU15 4.5 35.9 1.0 CA D:GLU48 4.6 31.4 1.0 CB D:GLU48 4.7 33.1 1.0 NE2 D:HIS51 4.8 46.9 1.0 CB D:ASN97 4.8 50.8 1.0 CB D:GLU15 4.9 31.7 1.0 CD2 D:HIS51 4.9 45.7 1.0 CA D:GLU15 5.0 31.2 1.0

Iron binding site 6 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:63.1 occ:0.55 OE1 D:GLU44 2.1 58.1 1.0 OE2 D:GLU47 2.1 66.5 1.0 O D:HOH320 2.4 46.0 1.0 FE D:FE205 2.5 55.8 0.5 CD D:GLU44 3.0 49.6 1.0 FE D:FE204 3.0 62.1 0.5 CD D:GLU47 3.1 62.0 1.0 OE2 D:GLU44 3.3 67.6 1.0 OE1 D:GLU47 3.4 67.7 1.0 O D:HOH307 4.2 54.2 1.0 O D:HOH359 4.2 61.9 1.0 CG D:GLU44 4.2 46.7 1.0 O D:HOH301 4.2 54.5 1.0 O D:HOH302 4.4 48.3 1.0 CB D:ALA130 4.4 34.6 1.0 CG D:GLU47 4.5 53.2 1.0 OE2 D:GLU94 4.6 43.6 1.0 CB D:GLU44 4.8 37.6 1.0 OH D:TYR22 4.8 34.3 1.0

Iron binding site 7 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe203 b:54.9 occ:0.20 O D:HOH318 1.8 58.8 1.0 OE2 D:GLU48 1.9 49.6 1.0 OD1 D:ASN97 2.0 48.7 1.0 O D:HOH307 2.0 54.2 1.0 OE1 D:GLU94 2.3 38.7 1.0 OE2 D:GLU94 2.3 43.6 1.0 CD D:GLU94 2.5 39.7 1.0 CD D:GLU48 2.9 39.8 1.0 CG D:ASN97 3.1 59.5 1.0 OE1 D:GLU48 3.1 52.3 1.0 FE D:FE201 3.4 53.1 0.6 O D:HOH320 3.4 46.0 1.0 CB D:ASN97 3.7 50.8 1.0 OE1 D:GLN127 3.8 36.9 1.0 CG D:GLU94 3.9 37.0 1.0 CG D:GLU48 4.2 35.7 1.0 ND2 D:ASN97 4.2 46.8 1.0 NE2 D:GLN127 4.2 41.4 1.0 CD D:GLN127 4.4 43.1 1.0 CE2 D:TYR22 4.6 27.1 1.0 OH D:TYR22 4.6 34.3 1.0 CA D:GLU94 4.7 34.5 1.0 CB D:GLU94 4.7 33.5 1.0 CB D:ALA18 4.8 30.6 1.0

Iron binding site 8 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe204 b:62.1 occ:0.45 OE2 D:GLU44 2.1 67.6 1.0 O D:HOH302 2.3 48.3 1.0 O D:HOH359 2.5 61.9 1.0 FE D:FE205 2.6 55.8 0.5 OH D:TYR40 2.8 61.8 1.0 CD D:GLU44 2.9 49.6 1.0 FE D:FE202 3.0 63.1 0.6 OE1 D:GLU44 3.3 58.1 1.0 CZ D:TYR40 3.7 47.5 1.0 O D:HOH301 3.7 54.5 1.0 CG D:GLU44 4.0 46.7 1.0 OE1 D:GLU47 4.3 67.7 1.0 CE2 D:TYR40 4.4 43.1 1.0 CE1 D:TYR40 4.4 51.2 1.0 OE2 D:GLU47 4.5 66.5 1.0 CG D:LYS133 4.7 54.3 1.0 NZ D:LYS133 4.7 71.3 1.0 CD D:GLU47 4.8 62.0 1.0

Iron binding site 9 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe205 b:55.8 occ:0.45 O D:HOH301 1.7 54.5 1.0 OE1 D:GLU47 2.1 67.7 1.0 O D:HOH359 2.3 61.9 1.0 FE D:FE202 2.5 63.1 0.6 FE D:FE204 2.6 62.1 0.5 O D:HOH302 2.7 48.3 1.0 CD D:GLU47 2.8 62.0 1.0 OE2 D:GLU47 2.8 66.5 1.0 OE2 D:GLU44 3.2 67.6 1.0 OE1 D:GLU44 3.3 58.1 1.0 CD D:GLU44 3.7 49.6 1.0 CG D:GLU47 4.2 53.2 1.0 O D:HOH320 4.8 46.0 1.0

Iron binding site 10 out of 37 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (Overnight)


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 E130A Soaked in Iron (Overnight) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:54.7 occ:0.60 O B:HOH345 1.6 82.9 1.0 OE1 B:GLU48 2.1 49.2 1.0 OE1 B:GLU15 2.2 50.3 1.0 ND1 B:HIS51 2.7 52.5 1.0 CD B:GLU48 3.1 40.0 1.0 CD B:GLU15 3.2 43.3 1.0 O B:HOH314 3.2 55.0 1.0 FE B:FE204 3.3 48.7 0.2 OE2 B:GLU48 3.3 55.6 1.0 OE2 B:GLU15 3.4 51.9 1.0 CE1 B:HIS51 3.5 61.5 1.0 OD1 B:ASN97 3.6 55.4 1.0 CG B:HIS51 3.8 47.7 1.0 CB B:HIS51 4.1 37.2 1.0 OE1 B:GLN127 4.1 41.5 1.0 CG B:ASN97 4.2 57.5 1.0 CG B:GLU48 4.5 38.1 1.0 CG B:GLU15 4.5 35.9 1.0 CB B:ASN97 4.7 54.5 1.0 CA B:GLU48 4.7 33.1 1.0 NE2 B:HIS51 4.7 57.8 1.0 O B:HOH302 4.8 45.4 1.0 CB B:GLU48 4.8 32.8 1.0 CD2 B:HIS51 4.9 48.8 1.0 CB B:GLU15 5.0 30.7 1.0 ND2 B:ASN97 5.0 47.6 1.0

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