Iron in PDB 6lkp: Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77

The structure of Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77, PDB code: 6lkp was solved by T.Minato, T.Teramoto, Y.Kakuta, S.Ogo, K.S.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.39 / 2.90
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.787, 92.787, 261.120, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 31.5

The structure of Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 (pdb code 6lkp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77, PDB code: 6lkp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:85.0 occ:1.00 O A:GLU100 2.4 84.6 1.0 O A:CYS102 2.9 0.9 1.0 O A:ALA99 3.3 0.7 1.0 C A:GLU100 3.5 0.4 1.0 N A:CYS102 3.6 0.8 1.0 C A:CYS102 3.8 0.1 1.0 CA A:CYS102 4.1 0.2 1.0 CB A:CYS102 4.2 0.3 1.0 CA A:GLU100 4.3 0.3 1.0 C A:ALA99 4.4 0.1 1.0 N A:LEU101 4.4 0.8 1.0 C A:LEU101 4.5 0.6 1.0 CA A:LEU101 4.7 0.5 1.0 N A:GLU100 4.8 0.6 1.0

Iron binding site 2 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:0.5 occ:1.00 OD1 A:ASN85 2.3 86.3 1.0 O A:ASN85 2.9 84.0 1.0 CG A:ASN85 3.2 80.1 1.0 NE2 D:HIS167 3.8 0.9 1.0 ND2 A:ASN85 3.9 75.8 1.0 C A:ASN85 3.9 82.6 1.0 CB A:ASN85 4.3 88.7 1.0 CA A:ASN85 4.4 86.8 1.0 CD2 D:HIS167 4.4 0.7 1.0 O A:GLY89 4.6 0.0 1.0 O A:GLY88 4.6 0.9 1.0 CE1 D:HIS167 4.7 0.7 1.0 CA A:GLY88 4.7 0.7 1.0 OE1 A:GLN9 4.7 0.2 1.0 C A:GLY88 4.8 0.0 1.0 N A:GLY88 4.9 0.1 1.0 N A:GLY86 5.0 92.2 1.0

Iron binding site 3 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:70.5 occ:1.00 O B:GLU100 2.5 94.6 1.0 O B:CYS102 2.9 93.5 1.0 O B:ALA99 3.3 83.1 1.0 C B:GLU100 3.5 91.3 1.0 C B:CYS102 4.0 93.9 1.0 N B:CYS102 4.0 85.3 1.0 CA B:GLU100 4.2 95.7 1.0 C B:ALA99 4.4 74.9 1.0 N B:LEU101 4.5 93.9 1.0 CA B:CYS102 4.5 78.9 1.0 C B:LEU101 4.5 77.2 1.0 CB B:CYS102 4.8 79.7 1.0 N B:GLU100 4.8 86.2 1.0 CA B:LEU101 4.8 84.3 1.0

Iron binding site 4 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:0.7 occ:1.00 OD1 B:ASN85 2.4 0.5 1.0 O B:ASN85 3.3 88.4 1.0 CG B:ASN85 3.5 0.4 1.0 CD B:LYS15 4.0 0.9 1.0 ND2 B:ASN85 4.1 0.6 1.0 C B:ASN85 4.2 98.5 1.0 OE1 C:GLU55 4.3 0.7 1.0 CE1 F:HIS167 4.3 0.7 1.0 NE2 F:HIS167 4.4 0.2 1.0 CG B:LYS15 4.5 0.2 1.0 NZ B:LYS15 4.6 0.3 1.0 CB B:ASN85 4.7 88.7 1.0 CE B:LYS15 4.7 0.5 1.0 CA B:ASN85 4.8 94.4 1.0 CD C:GLU55 4.8 0.1 1.0 CA B:GLY88 4.9 75.8 1.0 OE2 C:GLU55 4.9 0.1 1.0

Iron binding site 5 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe203 b:75.5 occ:1.00 O C:GLU100 2.4 76.9 1.0 O C:CYS102 3.1 0.9 1.0 O C:ALA99 3.2 94.1 1.0 C C:GLU100 3.4 88.9 1.0 CA C:GLU100 4.0 95.6 1.0 N C:CYS102 4.1 90.9 1.0 C C:CYS102 4.1 83.5 1.0 C C:ALA99 4.3 89.4 1.0 CA C:CYS102 4.4 82.1 1.0 N C:LEU101 4.5 95.9 1.0 CB C:CYS102 4.5 72.1 1.0 C C:LEU101 4.6 85.5 1.0 N C:GLU100 4.7 91.8 1.0 CA C:LEU101 4.9 90.9 1.0

Iron binding site 6 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe204 b:0.0 occ:1.00 O C:ASN85 2.2 95.6 1.0 OD1 C:ASN85 2.3 90.0 1.0 C C:ASN85 3.3 85.4 1.0 CG C:ASN85 3.4 57.4 1.0 CA C:ASN85 3.9 81.9 1.0 CA C:GLY88 4.1 83.6 1.0 CB C:ASN85 4.3 61.8 1.0 ND2 C:ASN85 4.3 90.9 1.0 N C:GLY88 4.3 78.6 1.0 CE1 A:HIS167 4.4 0.2 1.0 N C:GLY86 4.4 98.6 1.0 O C:GLY89 4.5 99.2 1.0 C C:GLY88 4.6 82.1 1.0 NE2 A:HIS167 4.6 0.4 1.0 CA C:GLY86 4.7 93.6 1.0 O C:GLY86 4.7 79.6 1.0 C C:GLY86 4.8 87.8 1.0 OE1 C:GLN9 4.9 98.5 1.0 N C:GLY89 5.0 95.4 1.0 OE2 B:GLU55 5.0 0.9 1.0

Iron binding site 7 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe204 b:96.1 occ:1.00 O D:GLU100 2.5 0.3 1.0 O D:CYS102 3.0 0.1 1.0 O D:ALA99 3.1 0.5 1.0 C D:GLU100 3.5 0.6 1.0 N D:CYS102 3.8 0.2 1.0 C D:CYS102 4.0 0.7 1.0 CA D:GLU100 4.2 0.1 1.0 C D:ALA99 4.2 98.8 1.0 CA D:CYS102 4.3 0.5 1.0 N D:LEU101 4.3 0.4 1.0 C D:LEU101 4.5 0.6 1.0 CB D:CYS102 4.5 0.4 1.0 CA D:LEU101 4.7 0.3 1.0 N D:GLU100 4.7 95.7 1.0

Iron binding site 8 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe205 b:0.8 occ:1.00 OD1 D:ASN85 2.7 98.5 1.0 CG D:ASN85 3.5 95.7 1.0 ND2 D:ASN85 3.7 77.7 1.0 O D:ASN85 3.8 96.5 1.0 NE2 C:HIS167 3.8 0.4 1.0 OE1 E:GLU55 4.3 0.3 1.0 CD2 C:HIS167 4.4 1.0 1.0 C D:ASN85 4.6 99.5 1.0 CD E:GLU55 4.6 0.9 1.0 CD D:LYS15 4.7 0.7 1.0 OE2 E:GLU55 4.7 1.0 1.0 NZ D:LYS15 4.7 0.7 1.0 CE1 C:HIS167 4.8 0.9 1.0 CB D:ASN85 4.8 84.1 1.0 CA D:ASN85 5.0 86.6 1.0

Iron binding site 9 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe204 b:99.8 occ:1.00 O E:GLU100 2.2 0.5 1.0 O E:CYS102 3.1 93.6 1.0 C E:GLU100 3.3 0.9 1.0 O E:ALA99 3.5 0.5 1.0 CA E:GLU100 3.9 0.3 1.0 N E:CYS102 4.0 90.0 1.0 C E:CYS102 4.2 98.3 1.0 N E:LEU101 4.3 0.2 1.0 C E:LEU101 4.5 0.9 1.0 C E:ALA99 4.5 0.5 1.0 CA E:CYS102 4.5 0.0 1.0 CA E:LEU101 4.6 0.9 1.0 CB E:CYS102 4.7 0.8 1.0 N E:GLU100 4.7 0.6 1.0 O E:PHE104 4.9 0.6 1.0

Iron binding site 10 out of 12 in the Crystal Structure of DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77


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 DPS1 From the Thermophilic Non-Heterocystous Filamentous Cyanobacterium Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe205 b:94.8 occ:1.00 OD1 E:ASN85 2.4 0.6 1.0 CG E:ASN85 3.5 0.5 1.0 O E:ASN85 3.5 95.6 1.0 OE1 D:GLU55 4.0 0.3 1.0 ND2 E:ASN85 4.1 0.4 1.0 C E:ASN85 4.4 87.5 1.0 CD D:GLU55 4.5 0.1 1.0 OE2 D:GLU55 4.6 0.4 1.0 CB E:ASN85 4.7 0.1 1.0 CA E:ASN85 4.9 80.7 1.0

T.Minato, T.Teramoto, Y.Kakuta, S.Ogo, K.S.Yoon. Biochemical and Structural Characterization of A Thermostable Dps Protein with His-Type Ferroxidase Centers and Outer Metal-Binding Sites. Febs Open Bio 2020.
ISSN: ESSN 2211-5463
PubMed: 32170832
DOI: 10.1002/2211-5463.12837