Iron in PDB 2vpw: Polysulfide Reductase with Bound Menaquinone

The structure of Polysulfide Reductase with Bound Menaquinone, PDB code: 2vpw was solved by M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.82 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.377, 163.580, 238.891, 90.00, 90.00, 90.00
R / Rfree (%)	27.1 / 27.5

The structure of Polysulfide Reductase with Bound Menaquinone also contains other interesting chemical elements:

Molybdenum

(Mo)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Iron atom in the Polysulfide Reductase with Bound Menaquinone (pdb code 2vpw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 40 binding sites of Iron where determined in the Polysulfide Reductase with Bound Menaquinone, PDB code: 2vpw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1764 b:50.0 occ:1.00 FE1 A:SF41764 0.0 50.0 1.0 SG A:CYS51 2.1 59.0 1.0 S2 A:SF41764 2.2 48.3 1.0 S4 A:SF41764 2.3 46.4 1.0 S3 A:SF41764 2.3 46.3 1.0 FE3 A:SF41764 2.7 44.7 1.0 FE2 A:SF41764 2.7 46.0 1.0 FE4 A:SF41764 2.7 45.5 1.0 CB A:CYS51 3.3 63.4 1.0 N A:CYS51 3.8 63.1 1.0 S1 A:SF41764 3.8 44.2 1.0 CB A:ASN216 4.1 57.1 1.0 CB A:TRP49 4.1 59.4 1.0 CA A:CYS51 4.2 61.9 1.0 SG A:CYS44 4.2 52.2 1.0 CD1 A:TRP49 4.4 58.4 1.0 CB A:CYS44 4.4 58.9 1.0 CG A:TRP49 4.7 58.8 1.0 SG A:CYS47 4.7 59.0 1.0 N A:ASN216 4.7 56.1 1.0 N A:ARG50 4.8 61.4 1.0 ND2 A:ASN216 4.8 57.5 1.0 C A:ARG50 5.0 63.6 1.0 CG A:ASN216 5.0 57.8 1.0

Iron binding site 2 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1764 b:46.0 occ:1.00 FE2 A:SF41764 0.0 46.0 1.0 S1 A:SF41764 2.2 44.2 1.0 S3 A:SF41764 2.3 46.3 1.0 S4 A:SF41764 2.3 46.4 1.0 SG A:CYS79 2.5 54.3 1.0 FE1 A:SF41764 2.7 50.0 1.0 FE3 A:SF41764 2.7 44.7 1.0 FE4 A:SF41764 2.7 45.5 1.0 CB A:CYS79 3.5 55.6 1.0 NH2 A:ARG81 3.6 48.5 1.0 S2 A:SF41764 3.8 48.3 1.0 N A:GLY82 3.9 54.0 1.0 CZ A:ARG81 4.1 49.4 1.0 CA A:GLY82 4.2 54.5 1.0 N A:CYS79 4.3 55.8 1.0 CA A:CYS79 4.4 54.3 1.0 O A:THR214 4.4 53.3 1.0 CB A:ARG81 4.5 51.6 1.0 SG A:CYS51 4.5 59.0 1.0 NH1 A:ARG81 4.5 49.5 1.0 NE A:ARG81 4.6 49.6 1.0 N A:ASN216 4.6 56.1 1.0 C A:ARG81 4.7 53.7 1.0 CB A:ASN216 4.7 57.1 1.0 C A:CYS79 4.7 53.0 1.0 SG A:CYS47 4.7 59.0 1.0 SG A:CYS44 4.7 52.2 1.0 O A:CYS79 4.7 51.8 1.0 CA A:ARG81 5.0 52.5 1.0 N A:ARG81 5.0 52.1 1.0

Iron binding site 3 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1764 b:44.7 occ:1.00 FE3 A:SF41764 0.0 44.7 1.0 S2 A:SF41764 2.2 48.3 1.0 S4 A:SF41764 2.3 46.4 1.0 S1 A:SF41764 2.3 44.2 1.0 SG A:CYS47 2.4 59.0 1.0 FE1 A:SF41764 2.7 50.0 1.0 FE2 A:SF41764 2.7 46.0 1.0 FE4 A:SF41764 2.7 45.5 1.0 CB A:CYS47 3.4 64.6 1.0 N A:CYS47 3.5 63.8 1.0 S3 A:SF41764 3.8 46.3 1.0 NH1 A:ARG81 3.9 49.5 1.0 CA A:CYS47 3.9 64.1 1.0 NH2 A:ARG81 3.9 48.5 1.0 CB A:TRP49 4.0 59.4 1.0 C A:GLY46 4.1 63.3 1.0 CZ A:ARG81 4.2 49.4 1.0 C A:CYS47 4.2 65.1 1.0 SG A:CYS44 4.3 52.2 1.0 O A:CYS47 4.3 65.2 1.0 N A:TRP49 4.4 62.1 1.0 CA A:GLY46 4.5 62.7 1.0 SG A:CYS51 4.6 59.0 1.0 CA A:TRP49 4.8 60.9 1.0 O A:GLY46 4.8 63.6 1.0 CD2 A:HIS215 4.8 55.3 1.0 SG A:CYS79 4.8 54.3 1.0 N A:PHE48 4.9 64.4 1.0 N A:ARG50 4.9 61.4 1.0

Iron binding site 4 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1764 b:45.5 occ:1.00 FE4 A:SF41764 0.0 45.5 1.0 SG A:CYS44 2.1 52.2 1.0 S3 A:SF41764 2.2 46.3 1.0 S1 A:SF41764 2.3 44.2 1.0 S2 A:SF41764 2.3 48.3 1.0 FE3 A:SF41764 2.7 44.7 1.0 FE2 A:SF41764 2.7 46.0 1.0 FE1 A:SF41764 2.7 50.0 1.0 CB A:CYS44 3.3 58.9 1.0 CA A:GLY82 3.4 54.5 1.0 CA A:GLY46 3.8 62.7 1.0 N A:GLY82 3.8 54.0 1.0 S4 A:SF41764 3.9 46.4 1.0 N A:GLY46 4.1 61.2 1.0 N A:CYS47 4.3 63.8 1.0 C A:GLY46 4.3 63.3 1.0 C A:ARG81 4.4 53.7 1.0 CA A:CYS44 4.6 58.7 1.0 O A:HOH2233 4.6 72.5 1.0 SG A:CYS51 4.6 59.0 1.0 SG A:CYS79 4.7 54.3 1.0 C A:CYS44 4.8 59.3 1.0 O A:ARG81 4.8 55.9 1.0 C A:GLY82 4.8 54.9 1.0 O A:CYS44 4.9 59.8 1.0 SG A:CYS47 4.9 59.0 1.0

Iron binding site 5 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1194 b:80.1 occ:1.00 FE1 B:SF41194 0.0 80.1 1.0 S2 B:SF41194 2.2 79.8 1.0 S4 B:SF41194 2.3 79.4 1.0 S3 B:SF41194 2.3 80.6 1.0 FE3 B:SF41194 2.7 78.5 1.0 FE2 B:SF41194 2.7 79.1 1.0 FE4 B:SF41194 2.7 80.1 1.0 SG B:CYS135 2.8 74.1 1.0 OG1 B:THR137 3.7 74.9 1.0 SG B:CYS139 3.8 71.8 1.0 S1 B:SF41194 3.8 81.3 1.0 CB B:CYS135 4.0 73.3 1.0 SG B:CYS16 4.4 70.5 1.0 CA B:CYS135 4.5 71.1 1.0 CD B:PRO136 4.5 68.2 1.0 SG B:CYS13 4.6 72.8 1.0 CG2 B:THR137 4.7 73.1 1.0 CB B:THR137 4.8 72.6 1.0 CD B:ARG140 4.8 65.0 1.0 N B:THR137 4.9 71.0 1.0 SG B:CYS19 4.9 70.3 1.0 C B:CYS135 5.0 70.7 1.0

Iron binding site 6 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1194 b:79.1 occ:1.00 FE2 B:SF41194 0.0 79.1 1.0 S1 B:SF41194 2.2 81.3 1.0 S3 B:SF41194 2.3 80.6 1.0 S4 B:SF41194 2.3 79.4 1.0 SG B:CYS13 2.3 72.8 1.0 FE1 B:SF41194 2.7 80.1 1.0 FE3 B:SF41194 2.7 78.5 1.0 FE4 B:SF41194 2.7 80.1 1.0 CB B:CYS13 3.7 68.6 1.0 S2 B:SF41194 3.8 79.8 1.0 N B:GLY15 3.9 57.2 1.0 CA B:CYS13 4.1 65.3 1.0 N B:VAL14 4.1 61.5 1.0 SG B:CYS139 4.3 71.8 1.0 CG B:PRO55 4.3 52.0 1.0 CA B:GLY15 4.3 57.3 1.0 C B:CYS13 4.5 64.0 1.0 N B:CYS16 4.6 61.1 1.0 SG B:CYS16 4.6 70.5 1.0 SG B:CYS19 4.6 70.3 1.0 O B:CYS16 4.7 66.4 1.0 CD B:PRO55 4.9 52.7 1.0 CD1 B:ILE38 4.9 51.0 1.0 C B:GLY15 4.9 58.3 1.0 C B:VAL14 5.0 57.5 1.0

Iron binding site 7 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1194 b:78.5 occ:1.00 FE3 B:SF41194 0.0 78.5 1.0 S2 B:SF41194 2.2 79.8 1.0 S4 B:SF41194 2.3 79.4 1.0 S1 B:SF41194 2.3 81.3 1.0 SG B:CYS16 2.4 70.5 1.0 O B:CYS16 2.5 66.4 1.0 FE1 B:SF41194 2.7 80.1 1.0 FE2 B:SF41194 2.7 79.1 1.0 FE4 B:SF41194 2.7 80.1 1.0 N B:ALA18 3.5 57.5 1.0 C B:CYS16 3.5 64.2 1.0 N B:CYS16 3.7 61.1 1.0 S3 B:SF41194 3.8 80.6 1.0 CB B:CYS16 4.0 67.2 1.0 CA B:CYS16 4.1 63.7 1.0 CB B:ALA18 4.1 56.6 1.0 SG B:CYS19 4.2 70.3 1.0 CA B:ALA18 4.3 57.9 1.0 C B:ALA17 4.3 57.3 1.0 N B:CYS19 4.3 61.2 1.0 CA B:ALA17 4.4 58.5 1.0 N B:ALA17 4.5 61.7 1.0 C B:GLY15 4.6 58.3 1.0 N B:GLY15 4.7 57.2 1.0 CA B:GLY15 4.8 57.3 1.0 SG B:CYS13 4.9 72.8 1.0 CD B:PRO136 4.9 68.2 1.0 CB B:CYS19 4.9 65.6 1.0 C B:ALA18 4.9 59.1 1.0

Iron binding site 8 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1194 b:80.1 occ:1.00 FE4 B:SF41194 0.0 80.1 1.0 S3 B:SF41194 2.2 80.6 1.0 SG B:CYS19 2.3 70.3 1.0 S1 B:SF41194 2.3 81.3 1.0 S2 B:SF41194 2.3 79.8 1.0 FE3 B:SF41194 2.7 78.5 1.0 FE2 B:SF41194 2.7 79.1 1.0 FE1 B:SF41194 2.7 80.1 1.0 CB B:CYS19 3.0 65.6 1.0 NH1 B:ARG140 3.6 64.0 1.0 S4 B:SF41194 3.9 79.4 1.0 N B:CYS19 3.9 61.2 1.0 CA B:CYS19 4.1 62.1 1.0 CG B:PRO55 4.3 52.0 1.0 CD B:ARG140 4.4 65.0 1.0 CD1 B:ILE38 4.5 51.0 1.0 O B:CYS16 4.5 66.4 1.0 N B:ALA18 4.6 57.5 1.0 SG B:CYS13 4.7 72.8 1.0 CZ B:ARG140 4.7 64.2 1.0 SG B:CYS135 4.8 74.1 1.0 CB B:PRO55 4.8 51.4 1.0 O B:HOH2103 4.9 0.8 1.0

Iron binding site 9 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1195 b:68.6 occ:1.00 FE1 B:SF41195 0.0 68.6 1.0 S2 B:SF41195 2.2 68.1 1.0 S4 B:SF41195 2.3 66.1 1.0 SG B:CYS131 2.3 72.1 1.0 S3 B:SF41195 2.3 67.7 1.0 FE3 B:SF41195 2.7 65.4 1.0 FE2 B:SF41195 2.7 66.7 1.0 FE4 B:SF41195 2.7 66.2 1.0 CB B:CYS131 3.3 73.2 1.0 N B:CYS131 3.3 71.3 1.0 S1 B:SF41195 3.8 67.1 1.0 CA B:CYS131 3.8 72.1 1.0 SG B:CYS119 3.9 70.1 1.0 CB B:PRO129 4.1 73.6 1.0 CB B:CYS23 4.3 59.4 1.0 N B:ALA130 4.3 70.3 1.0 C B:ALA130 4.4 70.1 1.0 SG B:CYS23 4.6 60.8 1.0 CB B:ALA130 4.6 67.1 1.0 CA B:ALA130 4.7 69.3 1.0 C B:PRO129 4.7 72.0 1.0 CD2 B:LEU36 4.9 50.2 1.0 CA B:PRO129 5.0 73.2 1.0 SG B:CYS116 5.0 68.5 1.0 CA B:CYS23 5.0 57.3 1.0

Iron binding site 10 out of 40 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1195 b:66.7 occ:1.00 FE2 B:SF41195 0.0 66.7 1.0 S1 B:SF41195 2.2 67.1 1.0 S3 B:SF41195 2.3 67.7 1.0 S4 B:SF41195 2.3 66.1 1.0 SG B:CYS116 2.3 68.5 1.0 FE1 B:SF41195 2.7 68.6 1.0 FE3 B:SF41195 2.7 65.4 1.0 FE4 B:SF41195 2.7 66.2 1.0 OE1 B:GLN57 3.5 57.6 1.0 CB B:CYS116 3.7 67.8 1.0 S2 B:SF41195 3.8 68.1 1.0 SG B:CYS131 3.9 72.1 1.0 CD B:GLN57 4.3 57.0 1.0 N B:PHE118 4.3 64.2 1.0 CA B:CYS116 4.4 64.5 1.0 CA B:PHE118 4.5 66.1 1.0 O B:HOH2044 4.5 99.3 1.0 N B:THR117 4.6 64.5 1.0 SG B:CYS23 4.7 60.8 1.0 CD1 B:PHE118 4.7 68.4 1.0 NE2 B:GLN57 4.8 57.6 1.0 C B:CYS116 4.9 65.3 1.0 N B:CYS119 4.9 68.7 1.0

M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata. Molecular Mechanism of Energy Conservation in Polysulfide Respiration. Nat.Struct.Mol.Biol. V. 15 730 2008.
ISSN: ISSN 1545-9993
PubMed: 18536726
DOI: 10.1038/NSMB.1434