Iron in PDB 6tg9: Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus

All present enzymatic activity of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus:
1.2.1.2;

The structure of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus 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; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus (pdb code 6tg9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus, PDB code: 6tg9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:6.0 occ:1.00 FE1 A:FES1004 0.0 6.0 1.0 S2 A:FES1004 2.2 6.0 1.0 S1 A:FES1004 2.2 6.0 1.0 SG A:CYS68 2.3 3.2 1.0 SG A:CYS57 2.3 3.6 1.0 FE2 A:FES1004 3.1 6.0 1.0 CB A:CYS68 3.6 3.2 1.0 CB A:CYS57 3.6 3.6 1.0 O A:VAL65 3.8 2.6 1.0 N A:CYS68 3.8 3.2 1.0 N A:CYS57 3.9 3.6 1.0 N A:ARG69 4.1 4.1 1.0 CA A:CYS57 4.2 3.6 1.0 CA A:CYS68 4.3 3.2 1.0 N A:SER67 4.3 3.0 1.0 N A:ALA58 4.3 3.2 1.0 C A:CYS57 4.4 3.6 1.0 SG A:CYS71 4.5 6.3 1.0 SG A:CYS85 4.5 7.9 1.0 C A:CYS68 4.7 3.2 1.0 CB A:ALA58 4.7 3.2 1.0 N A:LEU56 4.7 3.5 1.0 CA A:GLY66 4.8 2.8 1.0 C A:SER67 4.9 3.0 1.0 C A:VAL65 4.9 2.6 1.0 N A:LEU70 4.9 4.5 1.0 C A:GLY66 4.9 2.8 1.0 CB A:CYS85 5.0 7.9 1.0

Iron binding site 2 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:6.0 occ:1.00 FE2 A:FES1004 0.0 6.0 1.0 S1 A:FES1004 2.2 6.0 1.0 S2 A:FES1004 2.2 6.0 1.0 CB A:CYS85 2.3 7.9 1.0 SG A:CYS85 2.3 7.9 1.0 SG A:CYS71 2.4 6.3 1.0 FE1 A:FES1004 3.1 6.0 1.0 CA A:CYS85 3.5 7.9 1.0 CB A:CYS71 3.6 6.3 1.0 N A:CYS85 3.6 7.9 1.0 CB A:ALA58 4.4 3.2 1.0 CB A:THR83 4.5 7.1 1.0 C A:CYS85 4.6 7.9 1.0 CG2 A:THR83 4.6 7.1 1.0 SG A:CYS57 4.7 3.6 1.0 SG A:CYS68 4.7 3.2 1.0 CD2 A:LEU43 4.8 10.2 1.0 O A:VAL65 4.8 2.6 1.0 C A:SER84 4.8 8.9 1.0 CA A:CYS71 4.8 6.3 1.0 N A:SER84 4.9 8.9 1.0 N A:THR86 4.9 9.7 1.0 N A:CYS71 5.0 6.3 1.0

Iron binding site 3 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:16.3 occ:1.00 FE1 A:SF41005 0.0 16.3 1.0 S3 A:SF41005 2.3 16.3 1.0 S2 A:SF41005 2.3 16.3 1.0 S4 A:SF41005 2.3 16.3 1.0 SG A:CYS130 2.4 3.2 1.0 FE4 A:SF41005 2.7 16.3 1.0 FE2 A:SF41005 2.7 16.3 1.0 FE3 A:SF41005 2.7 16.3 1.0 CB A:CYS130 2.9 3.2 1.0 S1 A:SF41005 3.9 16.3 1.0 CA A:CYS130 4.3 3.2 1.0 O A:ALA126 4.3 4.8 1.0 CA A:THR236 4.6 7.0 1.0 CB A:GLN133 4.6 2.6 1.0 NE2 A:HIS117 4.8 4.0 1.0 SG A:CYS121 4.8 16.3 1.0 SG A:CYS124 4.8 4.7 1.0 C A:THR236 4.9 7.0 1.0 CB A:ALA126 4.9 4.8 1.0 N A:GLN133 4.9 2.6 1.0 O A:PRO235 4.9 4.9 1.0 CB A:THR236 5.0 7.0 1.0

Iron binding site 4 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:16.3 occ:1.00 FE2 A:SF41005 0.0 16.3 1.0 S3 A:SF41005 2.3 16.3 1.0 SG A:CYS121 2.3 16.3 1.0 S1 A:SF41005 2.3 16.3 1.0 S4 A:SF41005 2.3 16.3 1.0 FE3 A:SF41005 2.7 16.3 1.0 FE4 A:SF41005 2.7 16.3 1.0 FE1 A:SF41005 2.7 16.3 1.0 CB A:CYS121 3.3 16.3 1.0 CA A:CYS121 3.5 16.3 1.0 N A:CYS121 3.8 16.3 1.0 S2 A:SF41005 3.9 16.3 1.0 OE1 A:GLN133 4.1 2.6 1.0 CB A:CYS124 4.5 4.7 1.0 CD A:GLN133 4.6 2.6 1.0 C A:ASP120 4.7 6.7 1.0 NE2 A:HIS117 4.7 4.0 1.0 SG A:CYS124 4.8 4.7 1.0 SG A:CYS130 4.9 3.2 1.0 C A:CYS121 5.0 16.3 1.0

Iron binding site 5 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:16.3 occ:1.00 FE3 A:SF41005 0.0 16.3 1.0 S2 A:SF41005 2.3 16.3 1.0 S1 A:SF41005 2.3 16.3 1.0 S4 A:SF41005 2.3 16.3 1.0 SG A:CYS124 2.4 4.7 1.0 FE2 A:SF41005 2.7 16.3 1.0 FE4 A:SF41005 2.7 16.3 1.0 FE1 A:SF41005 2.7 16.3 1.0 CB A:CYS124 2.9 4.7 1.0 S3 A:SF41005 3.9 16.3 1.0 CB A:ALA237 4.1 16.3 1.0 NZ A:LYS181 4.1 7.3 1.0 CA A:CYS124 4.4 4.7 1.0 CE A:LYS181 4.4 7.3 1.0 CD A:LYS181 4.5 7.3 1.0 CA A:CYS121 4.8 16.3 1.0 CB A:ALA126 4.9 4.8 1.0 N A:ALA126 4.9 4.8 1.0 SG A:CYS121 4.9 16.3 1.0 NE2 A:HIS117 4.9 4.0 1.0 C A:CYS124 4.9 4.7 1.0 N A:CYS121 4.9 16.3 1.0 O A:THR236 4.9 7.0 1.0 SG A:CYS130 4.9 3.2 1.0 O A:ALA126 5.0 4.8 1.0

Iron binding site 6 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:16.3 occ:1.00 FE4 A:SF41005 0.0 16.3 1.0 S2 A:SF41005 2.3 16.3 1.0 S1 A:SF41005 2.3 16.3 1.0 S3 A:SF41005 2.3 16.3 1.0 NE2 A:HIS117 2.3 4.0 1.0 FE2 A:SF41005 2.7 16.3 1.0 FE1 A:SF41005 2.7 16.3 1.0 FE3 A:SF41005 2.7 16.3 1.0 CD2 A:HIS117 3.2 4.0 1.0 CE1 A:HIS117 3.3 4.0 1.0 S4 A:SF41005 3.9 16.3 1.0 CG A:HIS117 4.4 4.0 1.0 ND1 A:HIS117 4.4 4.0 1.0 SG A:CYS130 4.5 3.2 1.0 SG A:CYS121 4.5 16.3 1.0 CD A:LYS181 4.6 7.3 1.0 O A:PRO118 4.7 4.7 1.0 CG A:LYS181 4.7 7.3 1.0 O A:THR236 4.8 7.0 1.0 CB A:LYS181 4.8 7.3 1.0 CE A:LYS181 4.8 7.3 1.0 SG A:CYS124 4.9 4.7 1.0

Iron binding site 7 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:16.3 occ:1.00 FE1 A:SF41006 0.0 16.3 1.0 S2 A:SF41006 2.3 16.3 1.0 S4 A:SF41006 2.3 16.3 1.0 S3 A:SF41006 2.3 16.3 1.0 SG A:CYS185 2.3 4.9 1.0 FE3 A:SF41006 2.7 16.3 1.0 FE4 A:SF41006 2.7 16.3 1.0 FE2 A:SF41006 2.7 16.3 1.0 O A:ILE183 3.1 4.4 1.0 N A:MET186 3.8 4.4 1.0 S1 A:SF41006 3.9 16.3 1.0 CB A:CYS185 3.9 4.9 1.0 N A:CYS185 4.0 4.9 1.0 C A:ILE183 4.2 4.4 1.0 CA A:CYS185 4.3 4.9 1.0 N A:ARG187 4.5 4.7 1.0 C A:CYS185 4.5 4.9 1.0 CG1 A:ILE183 4.6 4.4 1.0 CD A:PRO235 4.6 4.9 1.0 CA A:MET186 4.7 4.4 1.0 SG A:CYS182 4.7 5.8 1.0 C A:VAL184 4.7 3.7 1.0 SG A:CYS234 4.7 16.3 1.0 SG A:CYS188 4.8 5.1 1.0 CA A:VAL184 4.9 3.7 1.0 N A:VAL184 4.9 3.7 1.0

Iron binding site 8 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:16.3 occ:1.00 FE2 A:SF41006 0.0 16.3 1.0 S4 A:SF41006 2.3 16.3 1.0 S3 A:SF41006 2.3 16.3 1.0 S1 A:SF41006 2.3 16.3 1.0 SG A:CYS182 2.3 5.8 1.0 FE3 A:SF41006 2.7 16.3 1.0 FE1 A:SF41006 2.7 16.3 1.0 FE4 A:SF41006 2.7 16.3 1.0 O A:ILE183 2.9 4.4 1.0 CB A:CYS182 3.5 5.8 1.0 CA A:CYS182 3.9 5.8 1.0 S2 A:SF41006 3.9 16.3 1.0 C A:ILE183 4.0 4.4 1.0 CG1 A:ILE212 4.2 3.4 1.0 N A:ILE183 4.2 4.4 1.0 C A:CYS182 4.4 5.8 1.0 CG2 A:THR238 4.7 7.1 1.0 OG1 A:THR238 4.8 7.1 1.0 CB A:THR238 4.8 7.1 1.0 SG A:CYS234 4.8 16.3 1.0 CA A:VAL184 4.8 3.7 1.0 CA A:ILE183 4.8 4.4 1.0 SG A:CYS188 4.9 5.1 1.0 N A:VAL184 4.9 3.7 1.0 SG A:CYS185 4.9 4.9 1.0

Iron binding site 9 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:16.3 occ:1.00 FE3 A:SF41006 0.0 16.3 1.0 S4 A:SF41006 2.3 16.3 1.0 S2 A:SF41006 2.3 16.3 1.0 S1 A:SF41006 2.3 16.3 1.0 SG A:CYS234 2.3 16.3 1.0 FE1 A:SF41006 2.7 16.3 1.0 FE2 A:SF41006 2.7 16.3 1.0 FE4 A:SF41006 2.7 16.3 1.0 CB A:CYS234 3.3 16.3 1.0 CA A:CYS234 3.8 16.3 1.0 S3 A:SF41006 3.9 16.3 1.0 CB A:THR238 4.3 7.1 1.0 OG1 A:THR236 4.3 7.0 1.0 CD A:PRO235 4.7 4.9 1.0 C A:CYS234 4.7 16.3 1.0 CG2 A:THR238 4.7 7.1 1.0 OG1 A:THR238 4.7 7.1 1.0 O A:ILE183 4.8 4.4 1.0 CD1 A:LEU239 4.8 5.9 1.0 SG A:CYS185 4.8 4.9 1.0 N A:CYS234 4.9 16.3 1.0 CB A:CYS188 4.9 5.1 1.0 N A:PRO235 4.9 4.9 1.0 N A:LEU239 4.9 5.9 1.0 SG A:CYS188 4.9 5.1 1.0 SG A:CYS182 5.0 5.8 1.0 CG A:LEU239 5.0 5.9 1.0

Iron binding site 10 out of 48 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:16.3 occ:1.00 FE4 A:SF41006 0.0 16.3 1.0 S2 A:SF41006 2.3 16.3 1.0 S3 A:SF41006 2.3 16.3 1.0 S1 A:SF41006 2.3 16.3 1.0 SG A:CYS188 2.4 5.1 1.0 FE1 A:SF41006 2.7 16.3 1.0 FE3 A:SF41006 2.7 16.3 1.0 FE2 A:SF41006 2.7 16.3 1.0 CB A:CYS188 3.0 5.1 1.0 S4 A:SF41006 3.9 16.3 1.0 N A:CYS188 3.9 5.1 1.0 CG1 A:ILE212 4.1 3.4 1.0 CA A:CYS188 4.1 5.1 1.0 CD1 A:ILE212 4.6 3.4 1.0 N A:MET186 4.6 4.4 1.0 CA A:MET186 4.6 4.4 1.0 N A:ARG187 4.7 4.7 1.0 SG A:CYS182 4.7 5.8 1.0 SG A:CYS185 4.7 4.9 1.0 O A:ILE183 4.8 4.4 1.0 CG2 A:ILE212 4.8 3.4 1.0 C A:MET186 4.8 4.4 1.0 SG A:CYS234 4.9 16.3 1.0 CB A:ILE212 4.9 3.4 1.0 CD1 A:LEU239 4.9 5.9 1.0

P.Wendler, C.Radon, G.Mittelstaedt, B.R.Duffus, J.Buerger, T.Mielke, S.Leimkuehler. Cryo-Em Structures Reveal Intricate Fe-S Cluster Arrangement and Charging in Rhodobacter Capsulatus Formate Dehydrogenase Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-15614-0