Iron in PDB 1tko: Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States

The structure of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States, PDB code: 1tko was solved by K.Zeth, S.Offermann, L.O.Essen, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.90
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.110, 91.110, 150.040, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 26.3

The structure of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Iron atom in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States (pdb code 1tko). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 38 binding sites of Iron where determined in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States, PDB code: 1tko:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:24.7 occ:0.75 OE2 A:GLU154 2.3 32.8 1.0 OE2 C:GLU154 2.4 32.7 1.0 FE A:FE304 2.9 51.6 0.8 O A:HOH346 2.9 36.8 1.0 FE C:FE309 2.9 48.9 0.8 FE C:FE303 3.0 39.6 0.8 CD A:GLU154 3.2 30.7 1.0 CD C:GLU154 3.2 29.6 1.0 OE1 C:GLU154 3.3 32.2 1.0 OE1 A:GLU154 3.3 35.1 1.0 O C:HOH503 3.7 6.3 1.0 CE1 A:HIS150 4.4 23.2 1.0 NE2 A:HIS150 4.4 20.9 1.0 FE A:FE320 4.4 38.7 0.8 CE1 C:HIS150 4.5 22.0 1.0 NE2 C:HIS150 4.5 20.5 1.0 CG A:GLU154 4.6 27.7 1.0 CG C:GLU154 4.6 25.9 1.0

Iron binding site 2 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe304 b:51.6 occ:0.75 O A:HOH346 2.6 36.8 1.0 OE1 A:GLU154 2.8 35.1 1.0 FE A:FE302 2.9 24.7 0.8 OE2 A:GLU154 3.0 32.8 1.0 CD A:GLU154 3.1 30.7 1.0 FE A:FE320 3.3 38.7 0.8 FE C:FE303 3.5 39.6 0.8 OE2 C:GLU154 3.9 32.7 1.0 FE C:FE309 3.9 48.9 0.8 CG A:GLU154 4.5 27.7 1.0 CB A:GLU154 4.9 22.9 1.0 CD C:GLU154 5.0 29.6 1.0

Iron binding site 3 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe306 b:41.6 occ:0.50 CE1 A:HIS164 2.5 38.3 1.0 NE2 C:GLN86 2.8 30.8 1.0 NE2 A:HIS164 2.9 39.2 1.0 CE1 A:HIS168 3.0 35.9 1.0 O D:TRP53 3.4 25.5 1.0 ND1 A:HIS164 3.7 38.6 1.0 CD C:GLN86 3.7 29.9 1.0 ND1 A:HIS168 3.8 34.5 1.0 NE2 A:HIS168 3.9 35.5 1.0 CB C:GLN86 4.2 25.4 1.0 CD2 A:HIS164 4.2 37.5 1.0 CG C:GLN86 4.3 28.0 1.0 O C:GLU83 4.4 27.7 1.0 OE1 C:GLN86 4.5 33.2 1.0 C D:TRP53 4.6 23.4 1.0 CG A:HIS164 4.6 35.5 1.0 N C:ALA87 4.8 25.5 1.0 C C:GLN86 4.8 26.2 1.0 CG A:HIS168 5.0 32.4 1.0 CD2 A:HIS168 5.0 34.0 1.0

Iron binding site 4 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe312 b:43.7 occ:0.50 OE1 B:GLU75 2.5 39.1 1.0 FE B:FE311 2.6 46.6 0.5 OE2 A:GLU75 2.8 36.0 1.0 FE A:FE325 3.2 45.5 0.5 OE1 A:GLU75 3.4 36.0 1.0 CD A:GLU75 3.4 34.1 1.0 CG B:GLU72 3.5 35.8 1.0 CD B:GLU75 3.7 37.1 1.0 CA B:GLU72 4.0 25.5 1.0 CB B:GLU72 4.0 28.2 1.0 O A:HOH348 4.2 18.3 1.0 OE2 B:GLU72 4.2 46.0 1.0 OE2 B:GLU75 4.3 37.6 1.0 CD B:GLU72 4.4 42.8 1.0 CB B:GLU75 4.7 29.0 1.0 N B:GLU72 4.8 25.1 1.0 CG B:GLU75 4.8 33.4 1.0 CG A:GLU75 4.9 30.8 1.0 O B:GLU72 4.9 22.8 1.0 C B:GLU72 5.0 23.9 1.0

Iron binding site 5 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe314 b:32.5 occ:0.50 OE1 B:GLU56 2.4 38.0 1.0 OE1 A:GLN86 2.8 31.2 1.0 NE2 A:GLN86 3.4 28.5 1.0 CD A:GLN86 3.4 29.4 1.0 CD B:GLU56 3.5 36.5 1.0 O A:GLN86 3.9 26.4 1.0 CG B:GLU56 4.1 34.0 1.0 OE2 B:GLU56 4.4 36.5 1.0 CG A:GLN86 4.9 27.3 1.0 C A:GLN86 4.9 25.4 1.0

Iron binding site 6 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe316 b:52.8 occ:0.50 OE1 A:GLU80 2.6 42.5 1.0 OE2 A:GLU83 2.8 38.9 1.0 CD A:GLU80 3.4 39.7 1.0 OE2 A:GLU80 3.7 44.1 1.0 OD2 A:ASP79 3.8 26.4 1.0 CD A:GLU83 3.9 36.0 1.0 OE1 A:GLU83 4.4 36.5 1.0 CG A:GLU80 4.6 34.1 1.0 FE B:FE333 4.6 29.9 0.5 CA A:GLU80 4.9 23.7 1.0 FE A:FE332 4.9 28.6 0.5 CG A:ASP79 5.0 26.0 1.0

Iron binding site 7 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe320 b:38.7 occ:0.75 FE C:FE309 3.2 48.9 0.8 FE C:FE303 3.2 39.6 0.8 FE A:FE304 3.3 51.6 0.8 O A:HOH346 3.9 36.8 1.0 FE A:FE302 4.4 24.7 0.8

Iron binding site 8 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe322 b:68.6 occ:0.50 OD1 A:ASP172 3.0 40.4 1.0 OD2 A:ASP172 3.3 42.1 1.0 CG A:ASP172 3.6 39.5 1.0 NH2 C:ARG8 3.7 37.6 1.0 OE1 A:GLU171 4.1 37.0 1.0 CZ C:ARG8 4.1 38.5 1.0 NH1 C:ARG8 4.1 38.2 1.0 NE C:ARG8 5.0 38.3 1.0 O C:ARG8 5.0 35.8 1.0

Iron binding site 9 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe325 b:45.5 occ:0.50 O A:HOH348 2.7 18.3 1.0 FE B:FE311 2.8 46.6 0.5 FE A:FE312 3.2 43.7 0.5 OE1 A:GLU75 4.0 36.0 1.0 CD A:GLU75 4.2 34.1 1.0 OE2 A:GLU75 4.2 36.0 1.0 OE2 B:GLU72 4.4 46.0 1.0 CG A:GLU72 4.5 35.9 1.0 OE2 A:GLU76 4.5 46.7 1.0 CG A:GLU76 4.6 38.0 1.0 OE2 A:GLU72 5.0 47.3 1.0

Iron binding site 10 out of 38 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe332 b:28.6 occ:0.50 OD2 A:ASP79 2.2 26.4 1.0 NE2 B:HIS52 2.4 18.1 1.0 OE1 A:GLU83 2.5 36.5 1.0 OD1 A:ASP79 2.6 27.6 1.0 CG A:ASP79 2.7 26.0 1.0 CD2 B:HIS52 3.2 19.1 1.0 CE1 B:HIS52 3.5 19.1 1.0 CD A:GLU83 3.6 36.0 1.0 OE2 A:GLU83 4.1 38.9 1.0 CB A:ASP79 4.2 22.4 1.0 CG B:HIS52 4.4 20.0 1.0 FE B:FE333 4.5 29.9 0.5 ND1 B:HIS52 4.5 20.8 1.0 NZ B:LYS49 4.6 18.8 1.0 CG A:GLU83 4.7 30.9 1.0 NE1 B:TRP53 4.7 23.8 1.0 CD1 B:TRP53 4.8 23.6 1.0 CE1 B:HIS64 4.9 30.5 1.0 FE A:FE316 4.9 52.8 0.5 NE2 B:HIS64 5.0 32.5 1.0

K.Zeth, S.Offermann, L.O.Essen, D.Oesterhelt. Iron-Oxo Clusters Biomineralizing on Protein Surfaces: Structural Analysis of Halobacterium Salinarum Dpsa in Its Low- and High-Iron States. Proc.Natl.Acad.Sci.Usa V. 101 13780 2004.
ISSN: ISSN 0027-8424
PubMed: 15365182
DOI: 10.1073/PNAS.0401821101