Iron in PDB 9ktr: Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+

All present enzymatic activity of Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+:
1.17.1.9;

The structure of Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ 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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ (pdb code 9ktr). 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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+, PDB code: 9ktr:
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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:23.6 occ:1.00 FE1 A:FES1004 0.0 23.6 1.0 S2 A:FES1004 2.2 19.1 1.0 S1 A:FES1004 2.2 10.9 1.0 SG A:CYS68 2.3 14.8 1.0 SG A:CYS57 2.3 15.2 1.0 FE2 A:FES1004 2.7 34.5 1.0 CB A:CYS68 3.4 7.9 1.0 N A:CYS68 3.5 12.7 1.0 N A:ARG69 3.6 12.0 1.0 CB A:CYS57 3.7 7.8 1.0 CA A:CYS68 3.9 6.6 1.0 N A:CYS57 3.9 11.6 1.0 C A:CYS68 4.2 9.4 1.0 N A:SER67 4.2 12.2 1.0 CA A:CYS57 4.3 10.8 1.0 N A:ALA58 4.3 12.3 1.0 N A:LEU70 4.4 10.2 1.0 SG A:CYS85 4.5 23.0 1.0 SG A:CYS71 4.5 15.7 1.0 C A:SER67 4.5 8.8 1.0 N A:LEU56 4.5 13.0 1.0 CA A:ARG69 4.6 8.4 1.0 C A:CYS57 4.7 13.2 1.0 CA A:GLY66 4.8 9.8 1.0 C A:GLY66 4.8 9.8 1.0 N A:CYS71 4.9 13.2 1.0 CB A:CYS71 4.9 14.2 1.0 CA A:SER67 4.9 7.6 1.0 CB A:ALA58 5.0 13.6 1.0

Iron binding site 2 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:34.5 occ:1.00 FE2 A:FES1004 0.0 34.5 1.0 S2 A:FES1004 2.2 19.1 1.0 S1 A:FES1004 2.2 10.9 1.0 SG A:CYS71 2.3 15.7 1.0 SG A:CYS85 2.3 23.0 1.0 FE1 A:FES1004 2.7 23.6 1.0 CB A:CYS85 3.1 15.6 1.0 CB A:CYS71 3.4 14.2 1.0 N A:CYS85 4.1 15.9 1.0 SG A:CYS57 4.2 15.2 1.0 CA A:CYS85 4.2 15.8 1.0 OG A:SER83 4.3 17.1 1.0 N A:CYS71 4.4 13.2 1.0 CB A:SER83 4.4 14.0 1.0 CA A:CYS71 4.5 16.4 1.0 SG A:CYS68 4.5 14.8 1.0 CB A:ALA58 4.7 13.6 1.0 CA A:GLY66 4.8 9.8 1.0

Iron binding site 3 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:26.2 occ:1.00 FE1 A:SF41005 0.0 26.2 1.0 SG A:CYS130 2.3 10.4 1.0 S2 A:SF41005 2.3 8.0 1.0 S3 A:SF41005 2.3 10.4 1.0 S4 A:SF41005 2.3 8.7 1.0 FE3 A:SF41005 2.7 23.3 1.0 FE2 A:SF41005 2.7 22.1 1.0 FE4 A:SF41005 2.7 29.8 1.0 CB A:CYS130 3.2 8.8 1.0 CE1 A:HIS117 3.8 12.4 1.0 S1 A:SF41005 3.9 12.7 1.0 CB A:GLN133 4.0 8.6 1.0 N A:GLN133 4.2 10.6 1.0 CD2 A:LEU132 4.5 8.7 1.0 CG2 A:THR236 4.5 8.7 1.0 NE2 A:HIS117 4.5 9.1 1.0 ND1 A:HIS117 4.6 8.4 1.0 SG A:CYS124 4.6 8.6 1.0 CA A:GLN133 4.6 6.5 1.0 CB A:LEU132 4.7 7.8 1.0 CA A:CYS130 4.7 10.0 1.0 SG A:CYS121 4.7 17.7 1.0 CB A:THR236 4.8 8.2 1.0 CB A:ALA126 4.9 7.6 1.0 CA A:THR236 4.9 6.2 1.0 CG A:GLN133 5.0 8.3 1.0

Iron binding site 4 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:22.1 occ:1.00 FE2 A:SF41005 0.0 22.1 1.0 SG A:CYS121 2.3 17.7 1.0 S3 A:SF41005 2.3 10.4 1.0 S4 A:SF41005 2.3 8.7 1.0 S1 A:SF41005 2.3 12.7 1.0 FE3 A:SF41005 2.7 23.3 1.0 FE1 A:SF41005 2.7 26.2 1.0 FE4 A:SF41005 2.7 29.8 1.0 CB A:CYS121 3.4 10.5 1.0 CA A:CYS121 3.4 11.4 1.0 S2 A:SF41005 3.9 8.0 1.0 N A:CYS121 4.0 17.2 1.0 CE1 A:HIS117 4.1 12.4 1.0 ND1 A:HIS117 4.3 8.4 1.0 CB A:GLN133 4.5 8.6 1.0 NE2 A:GLN133 4.5 12.1 1.0 CD2 B:LEU122 4.5 6.8 1.0 CG A:GLN133 4.6 8.3 1.0 C A:ASP120 4.6 13.0 1.0 CD1 B:LEU122 4.7 6.4 1.0 SG A:CYS124 4.7 8.6 1.0 CB A:CYS124 4.7 9.0 1.0 C A:CYS121 4.7 9.4 1.0 CG B:LEU122 4.7 8.0 1.0 CD A:GLN133 4.8 7.8 1.0 SG A:CYS130 4.8 10.4 1.0 O A:PRO118 4.9 14.2 1.0 O A:ASP120 4.9 15.5 1.0 O A:CYS121 5.0 11.4 1.0

Iron binding site 5 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:23.3 occ:1.00 FE3 A:SF41005 0.0 23.3 1.0 SG A:CYS124 2.3 8.6 1.0 S2 A:SF41005 2.3 8.0 1.0 S4 A:SF41005 2.3 8.7 1.0 S1 A:SF41005 2.3 12.7 1.0 FE1 A:SF41005 2.7 26.2 1.0 FE2 A:SF41005 2.7 22.1 1.0 FE4 A:SF41005 2.7 29.8 1.0 CB A:CYS124 3.2 9.0 1.0 S3 A:SF41005 3.9 10.4 1.0 CE1 A:HIS117 3.9 12.4 1.0 CD A:LYS181 4.0 8.6 1.0 CE A:LYS181 4.1 8.7 1.0 NZ A:LYS181 4.4 8.6 1.0 CB A:ALA237 4.5 11.1 1.0 CA A:CYS121 4.6 11.4 1.0 CG A:LYS181 4.6 8.2 1.0 O A:ASP120 4.6 15.5 1.0 CA A:CYS124 4.6 7.5 1.0 SG A:CYS130 4.7 10.4 1.0 ND1 A:HIS117 4.8 8.4 1.0 NE2 A:HIS117 4.8 9.1 1.0 CB A:ALA126 4.8 7.6 1.0 SG A:CYS121 4.8 17.7 1.0 C A:ASP120 4.9 13.0 1.0 N A:ALA237 5.0 10.1 1.0 N A:CYS121 5.0 17.2 1.0

Iron binding site 6 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:29.8 occ:1.00 FE4 A:SF41005 0.0 29.8 1.0 CE1 A:HIS117 1.4 12.4 1.0 ND1 A:HIS117 2.1 8.4 1.0 S1 A:SF41005 2.3 12.7 1.0 S3 A:SF41005 2.3 10.4 1.0 S2 A:SF41005 2.3 8.0 1.0 NE2 A:HIS117 2.6 9.1 1.0 FE2 A:SF41005 2.7 22.1 1.0 FE1 A:SF41005 2.7 26.2 1.0 FE3 A:SF41005 2.7 23.3 1.0 CG A:HIS117 3.4 6.8 1.0 CD2 A:HIS117 3.6 7.2 1.0 S4 A:SF41005 3.9 8.7 1.0 CD2 A:LEU132 4.0 8.7 1.0 O A:PRO118 4.2 14.2 1.0 CG A:LYS181 4.3 8.2 1.0 CD A:LYS181 4.6 8.6 1.0 CB A:HIS117 4.6 8.7 1.0 CB A:LYS181 4.7 8.2 1.0 SG A:CYS130 4.7 10.4 1.0 SG A:CYS121 4.8 17.7 1.0 SG A:CYS124 4.9 8.6 1.0 CD1 B:LEU122 5.0 6.4 1.0 CE A:LYS181 5.0 8.7 1.0

Iron binding site 7 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:24.3 occ:1.00 FE1 A:SF41006 0.0 24.3 1.0 SG A:CYS185 2.3 10.3 1.0 S3 A:SF41006 2.3 17.9 1.0 S2 A:SF41006 2.3 10.6 1.0 S4 A:SF41006 2.3 9.6 1.0 FE2 A:SF41006 2.7 29.9 1.0 FE4 A:SF41006 2.7 37.6 1.0 FE3 A:SF41006 2.7 27.6 1.0 N A:CYS185 3.6 12.2 1.0 CB A:CYS185 3.8 11.9 1.0 CD A:PRO235 3.9 6.5 1.0 S1 A:SF41006 3.9 8.2 1.0 N A:MET186 3.9 18.1 1.0 CA A:CYS185 4.1 11.7 1.0 CB A:CYS234 4.2 13.8 1.0 N A:ARG187 4.2 13.0 1.0 C A:CYS185 4.3 14.7 1.0 CG A:ARG187 4.4 15.4 1.0 CG1 A:ILE183 4.4 7.3 1.0 CB A:ARG187 4.5 10.9 1.0 SG A:CYS182 4.5 8.2 1.0 CG A:PRO235 4.6 8.1 1.0 N A:VAL184 4.7 9.1 1.0 SG A:CYS234 4.7 6.5 1.0 C A:VAL184 4.7 9.1 1.0 CA A:VAL184 4.9 7.5 1.0 CA A:CYS234 4.9 10.5 1.0 CA A:MET186 4.9 13.5 1.0 N A:ILE183 4.9 5.9 1.0 CD1 A:ILE183 5.0 7.1 1.0 N A:PRO235 5.0 6.1 1.0

Iron binding site 8 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:29.9 occ:1.00 FE2 A:SF41006 0.0 29.9 1.0 SG A:CYS182 2.3 8.2 1.0 S3 A:SF41006 2.3 17.9 1.0 S4 A:SF41006 2.3 9.6 1.0 S1 A:SF41006 2.3 8.2 1.0 FE1 A:SF41006 2.7 24.3 1.0 FE4 A:SF41006 2.7 37.6 1.0 FE3 A:SF41006 2.7 27.6 1.0 CB A:CYS182 3.4 5.1 1.0 CA A:CYS182 3.7 4.8 1.0 CG2 A:THR238 3.8 7.0 1.0 S2 A:SF41006 3.9 10.6 1.0 CB A:THR238 3.9 7.3 1.0 N A:ILE183 4.0 5.9 1.0 OG1 A:THR238 4.1 6.9 1.0 N A:VAL184 4.3 9.1 1.0 C A:CYS182 4.4 6.2 1.0 CG1 A:ILE212 4.4 10.0 1.0 CA A:VAL184 4.7 7.5 1.0 OG1 A:THR236 4.8 10.9 1.0 SG A:CYS185 4.8 10.3 1.0 N A:CYS185 4.9 12.2 1.0 SG A:CYS234 4.9 6.5 1.0 N A:CYS182 4.9 6.9 1.0

Iron binding site 9 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:27.6 occ:1.00 FE3 A:SF41006 0.0 27.6 1.0 S2 A:SF41006 2.3 10.6 1.0 S1 A:SF41006 2.3 8.2 1.0 S4 A:SF41006 2.3 9.6 1.0 SG A:CYS234 2.3 6.5 1.0 CB A:CYS234 2.6 13.8 1.0 FE1 A:SF41006 2.7 24.3 1.0 FE4 A:SF41006 2.7 37.6 1.0 FE2 A:SF41006 2.7 29.9 1.0 CA A:CYS234 3.9 10.5 1.0 S3 A:SF41006 3.9 17.9 1.0 CB A:THR238 4.0 7.3 1.0 CD A:PRO235 4.2 6.5 1.0 OG1 A:THR236 4.2 10.9 1.0 C A:CYS234 4.4 9.6 1.0 CD1 A:LEU239 4.4 6.8 1.0 OG1 A:THR238 4.5 6.9 1.0 N A:PRO235 4.5 6.1 1.0 N A:LEU239 4.6 7.9 1.0 CG2 A:THR238 4.6 7.0 1.0 SG A:CYS185 4.7 10.3 1.0 CB A:LEU239 4.7 8.0 1.0 CG A:LEU239 4.9 7.4 1.0 N A:THR236 5.0 7.1 1.0 CA A:THR238 5.0 7.8 1.0 SG A:CYS182 5.0 8.2 1.0

Iron binding site 10 out of 48 in the Cryo-Em Structure of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+


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 Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:37.6 occ:1.00 FE4 A:SF41006 0.0 37.6 1.0 S2 A:SF41006 2.3 10.6 1.0 S1 A:SF41006 2.3 8.2 1.0 S3 A:SF41006 2.3 17.9 1.0 FE2 A:SF41006 2.7 29.9 1.0 FE1 A:SF41006 2.7 24.3 1.0 FE3 A:SF41006 2.7 27.6 1.0 S4 A:SF41006 3.9 9.6 1.0 CG1 A:ILE212 4.0 10.0 1.0 N A:ARG187 4.0 13.0 1.0 CB A:CYS234 4.4 13.8 1.0 CD1 A:LEU239 4.4 6.8 1.0 N A:MET186 4.4 18.1 1.0 SG A:CYS182 4.5 8.2 1.0 CG2 A:ILE212 4.5 9.5 1.0 N A:CYS188 4.6 17.3 1.0 CB A:ILE212 4.6 8.8 1.0 CA A:MET186 4.7 13.5 1.0 CD1 A:ILE212 4.7 8.6 1.0 SG A:CYS185 4.8 10.3 1.0 C A:MET186 4.8 10.3 1.0 SG A:CYS234 4.8 6.5 1.0 CA A:ARG187 4.9 11.1 1.0 CB A:ARG187 5.0 10.9 1.0

K.Zhang, L.Zhang. Mechanistic Understanding on the Catalytic Preference of Formate Dehydrogenase From Rhodobacter Aestuarii Towards Carbon Dioxide Reduction To Be Published.