Iron in PDB 9ktl: Cryo-Em Structure of Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh

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

The structure of Cryo-Em Structure of Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh 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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh (pdb code 9ktl). 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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh, PDB code: 9ktl:
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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:18.0 occ:1.00 FE1 A:FES1004 0.0 18.0 1.0 S2 A:FES1004 2.2 8.5 1.0 S1 A:FES1004 2.2 10.3 1.0 SG A:CYS68 2.3 10.1 1.0 SG A:CYS57 2.3 13.6 1.0 FE2 A:FES1004 2.7 28.0 1.0 CB A:CYS68 3.3 5.5 1.0 N A:CYS68 3.4 9.8 1.0 CB A:CYS57 3.6 5.7 1.0 N A:ARG69 3.7 9.3 1.0 CA A:CYS68 3.8 6.2 1.0 N A:CYS57 3.8 7.4 1.0 C A:CYS68 4.2 8.7 1.0 CA A:CYS57 4.2 6.4 1.0 N A:SER67 4.2 9.6 1.0 N A:ALA58 4.2 8.2 1.0 C A:SER67 4.4 7.2 1.0 SG A:CYS85 4.4 11.4 1.0 N A:LEU56 4.4 8.3 1.0 SG A:CYS71 4.5 9.2 1.0 N A:LEU70 4.6 9.4 1.0 C A:CYS57 4.6 8.8 1.0 CA A:ARG69 4.7 8.5 1.0 C A:GLY66 4.8 9.4 1.0 CA A:GLY66 4.8 8.3 1.0 CA A:SER67 4.9 6.6 1.0 CB A:CYS71 5.0 8.3 1.0 N A:CYS71 5.0 10.7 1.0 C A:LEU56 5.0 6.8 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:28.0 occ:1.00 FE2 A:FES1004 0.0 28.0 1.0 S1 A:FES1004 2.2 10.3 1.0 S2 A:FES1004 2.2 8.5 1.0 SG A:CYS71 2.3 9.2 1.0 SG A:CYS85 2.3 11.4 1.0 FE1 A:FES1004 2.7 18.0 1.0 CB A:CYS85 3.1 7.6 1.0 CB A:CYS71 3.4 8.3 1.0 N A:CYS85 4.1 9.2 1.0 CA A:CYS85 4.2 7.9 1.0 SG A:CYS57 4.2 13.6 1.0 OG A:SER83 4.3 11.8 1.0 SG A:CYS68 4.4 10.1 1.0 N A:CYS71 4.4 10.7 1.0 CB A:SER83 4.5 10.6 1.0 CA A:CYS71 4.5 10.6 1.0 CB A:ALA58 4.7 10.5 1.0 CA A:GLY66 4.8 8.3 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:17.8 occ:1.00 FE1 A:SF41005 0.0 17.8 1.0 SG A:CYS130 2.2 4.8 1.0 S3 A:SF41005 2.3 5.1 1.0 S2 A:SF41005 2.3 3.3 1.0 S4 A:SF41005 2.3 2.7 1.0 FE3 A:SF41005 2.7 21.2 1.0 FE2 A:SF41005 2.7 14.9 1.0 FE4 A:SF41005 2.7 21.4 1.0 CB A:CYS130 3.1 5.2 1.0 CE1 A:HIS117 3.8 7.5 1.0 S1 A:SF41005 3.9 3.8 1.0 CB A:GLN133 4.1 5.5 1.0 N A:GLN133 4.2 6.4 1.0 CD2 A:LEU132 4.5 4.6 1.0 NE2 A:HIS117 4.5 4.7 1.0 CB A:LEU132 4.5 4.2 1.0 CA A:CYS130 4.6 6.7 1.0 SG A:CYS124 4.7 5.7 1.0 CA A:GLN133 4.7 4.8 1.0 ND1 A:HIS117 4.7 6.3 1.0 SG A:CYS121 4.7 4.7 1.0 CG2 A:THR236 4.8 3.5 1.0 CB A:THR236 4.8 3.8 1.0 CA A:THR236 4.9 3.1 1.0 CG A:LEU132 4.9 5.2 1.0 CB A:ALA126 4.9 4.5 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:14.9 occ:1.00 FE2 A:SF41005 0.0 14.9 1.0 SG A:CYS121 2.3 4.7 1.0 S3 A:SF41005 2.3 5.1 1.0 S4 A:SF41005 2.3 2.7 1.0 S1 A:SF41005 2.3 3.8 1.0 FE3 A:SF41005 2.7 21.2 1.0 FE1 A:SF41005 2.7 17.8 1.0 FE4 A:SF41005 2.7 21.4 1.0 CB A:CYS121 3.4 4.6 1.0 CA A:CYS121 3.4 5.7 1.0 S2 A:SF41005 3.9 3.3 1.0 N A:CYS121 3.9 7.6 1.0 CE1 A:HIS117 4.0 7.5 1.0 ND1 A:HIS117 4.3 6.3 1.0 NE2 A:GLN133 4.4 7.1 1.0 CB A:GLN133 4.5 5.5 1.0 CD1 B:LEU122 4.5 4.4 1.0 CD2 B:LEU122 4.5 4.5 1.0 C A:ASP120 4.6 8.0 1.0 SG A:CYS124 4.7 5.7 1.0 CG B:LEU122 4.7 4.6 1.0 CG A:GLN133 4.7 5.7 1.0 CB A:CYS124 4.7 5.8 1.0 C A:CYS121 4.7 5.3 1.0 CD A:GLN133 4.7 5.6 1.0 SG A:CYS130 4.8 4.8 1.0 O A:PRO118 4.8 9.4 1.0 O A:CYS121 5.0 6.1 1.0 O A:ASP120 5.0 8.0 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:21.2 occ:1.00 FE3 A:SF41005 0.0 21.2 1.0 SG A:CYS124 2.3 5.7 1.0 S1 A:SF41005 2.3 3.8 1.0 S2 A:SF41005 2.3 3.3 1.0 S4 A:SF41005 2.3 2.7 1.0 FE2 A:SF41005 2.7 14.9 1.0 FE1 A:SF41005 2.7 17.8 1.0 FE4 A:SF41005 2.8 21.4 1.0 CB A:CYS124 3.1 5.8 1.0 S3 A:SF41005 3.9 5.1 1.0 CE1 A:HIS117 3.9 7.5 1.0 CD A:LYS181 4.1 4.3 1.0 CE A:LYS181 4.2 4.5 1.0 NZ A:LYS181 4.3 3.8 1.0 CB A:ALA237 4.5 5.3 1.0 CA A:CYS121 4.5 5.7 1.0 CA A:CYS124 4.6 4.8 1.0 CG A:LYS181 4.7 4.5 1.0 SG A:CYS130 4.7 4.8 1.0 O A:ASP120 4.7 8.0 1.0 NE2 A:HIS117 4.8 4.7 1.0 CB A:ALA126 4.8 4.5 1.0 SG A:CYS121 4.8 4.7 1.0 ND1 A:HIS117 4.8 6.3 1.0 C A:ASP120 4.9 8.0 1.0 N A:CYS121 5.0 7.6 1.0 CB A:CYS130 5.0 5.2 1.0 N A:ALA237 5.0 4.5 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:21.4 occ:1.00 FE4 A:SF41005 0.0 21.4 1.0 CE1 A:HIS117 1.4 7.5 1.0 ND1 A:HIS117 2.2 6.3 1.0 S1 A:SF41005 2.3 3.8 1.0 S2 A:SF41005 2.3 3.3 1.0 S3 A:SF41005 2.3 5.1 1.0 NE2 A:HIS117 2.5 4.7 1.0 FE2 A:SF41005 2.7 14.9 1.0 FE1 A:SF41005 2.7 17.8 1.0 FE3 A:SF41005 2.8 21.2 1.0 CG A:HIS117 3.4 5.7 1.0 CD2 A:HIS117 3.5 5.3 1.0 S4 A:SF41005 3.9 2.7 1.0 CD2 A:LEU132 4.0 4.6 1.0 O A:PRO118 4.2 9.4 1.0 CG A:LYS181 4.3 4.5 1.0 CB A:LYS181 4.7 5.1 1.0 CD A:LYS181 4.7 4.3 1.0 SG A:CYS130 4.7 4.8 1.0 CB A:HIS117 4.7 5.7 1.0 SG A:CYS121 4.8 4.7 1.0 SG A:CYS124 4.9 5.7 1.0 CD1 B:LEU122 4.9 4.4 1.0 CG A:PRO118 5.0 5.8 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:12.3 occ:1.00 FE1 A:SF41006 0.0 12.3 1.0 SG A:CYS185 2.3 5.5 1.0 S2 A:SF41006 2.3 5.3 1.0 S3 A:SF41006 2.3 5.1 1.0 S4 A:SF41006 2.3 4.9 1.0 FE3 A:SF41006 2.7 20.8 1.0 FE2 A:SF41006 2.7 17.5 1.0 FE4 A:SF41006 2.7 24.0 1.0 N A:CYS185 3.5 5.6 1.0 CB A:CYS185 3.7 5.0 1.0 N A:MET186 3.9 7.4 1.0 CD A:PRO235 3.9 3.7 1.0 S1 A:SF41006 3.9 2.6 1.0 CA A:CYS185 4.0 5.5 1.0 N A:ARG187 4.0 4.8 1.0 C A:CYS185 4.2 6.4 1.0 CG1 A:ILE183 4.4 4.7 1.0 CB A:ARG187 4.4 6.1 1.0 N A:VAL184 4.4 4.6 1.0 C A:VAL184 4.5 4.3 1.0 CG A:PRO235 4.6 4.7 1.0 SG A:CYS182 4.7 7.6 1.0 SG A:CYS234 4.7 2.3 1.0 CA A:VAL184 4.7 3.9 1.0 CA A:MET186 4.7 6.0 1.0 CA A:ARG187 4.8 4.7 1.0 C A:MET186 4.9 5.0 1.0 N A:ILE183 4.9 4.0 1.0 C A:ILE183 5.0 4.2 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:17.5 occ:1.00 FE2 A:SF41006 0.0 17.5 1.0 SG A:CYS182 2.2 7.6 1.0 S3 A:SF41006 2.3 5.1 1.0 S4 A:SF41006 2.3 4.9 1.0 S1 A:SF41006 2.3 2.6 1.0 FE3 A:SF41006 2.7 20.8 1.0 FE4 A:SF41006 2.7 24.0 1.0 FE1 A:SF41006 2.7 12.3 1.0 CB A:CYS182 3.5 3.3 1.0 CA A:CYS182 3.8 3.2 1.0 S2 A:SF41006 3.9 5.3 1.0 N A:VAL184 4.0 4.6 1.0 N A:ILE183 4.1 4.0 1.0 CG2 A:THR238 4.2 4.9 1.0 CG1 A:ILE212 4.2 5.2 1.0 C A:CYS182 4.3 4.3 1.0 CB A:THR238 4.3 3.9 1.0 CA A:VAL184 4.4 3.9 1.0 OG1 A:THR238 4.5 4.0 1.0 N A:CYS185 4.7 5.6 1.0 SG A:CYS234 4.8 2.3 1.0 SG A:CYS185 4.9 5.5 1.0 C A:ILE183 4.9 4.2 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:20.8 occ:1.00 FE3 A:SF41006 0.0 20.8 1.0 SG A:CYS234 2.2 2.3 1.0 S1 A:SF41006 2.3 2.6 1.0 S2 A:SF41006 2.3 5.3 1.0 S4 A:SF41006 2.3 4.9 1.0 FE2 A:SF41006 2.7 17.5 1.0 FE4 A:SF41006 2.7 24.0 1.0 FE1 A:SF41006 2.7 12.3 1.0 CB A:CYS234 3.4 4.4 1.0 CA A:CYS234 3.9 5.0 1.0 S3 A:SF41006 3.9 5.1 1.0 CB A:THR238 3.9 3.9 1.0 CD A:PRO235 4.0 3.7 1.0 OG1 A:THR236 4.1 4.1 1.0 OG1 A:THR238 4.3 4.0 1.0 CG2 A:THR238 4.5 4.9 1.0 CD1 A:LEU239 4.5 3.7 1.0 N A:PRO235 4.6 3.7 1.0 N A:LEU239 4.6 4.1 1.0 C A:CYS234 4.6 5.1 1.0 SG A:CYS185 4.7 5.5 1.0 CB A:LEU239 4.8 4.2 1.0 SG A:CYS182 4.8 7.6 1.0 CG A:LEU239 4.9 4.4 1.0 CA A:THR238 5.0 4.3 1.0

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


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 Reduced Form of Formate Dehydrogenase From Rhodobacter Aestuarii (Rafdh) with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:24.0 occ:1.00 FE4 A:SF41006 0.0 24.0 1.0 S2 A:SF41006 2.3 5.3 1.0 S3 A:SF41006 2.3 5.1 1.0 S1 A:SF41006 2.3 2.6 1.0 FE3 A:SF41006 2.7 20.8 1.0 FE2 A:SF41006 2.7 17.5 1.0 FE1 A:SF41006 2.7 12.3 1.0 S4 A:SF41006 3.9 4.9 1.0 CG1 A:ILE212 3.9 5.2 1.0 N A:CYS188 4.0 7.8 1.0 N A:ARG187 4.1 4.8 1.0 CD1 A:LEU239 4.3 3.7 1.0 CB A:CYS188 4.5 12.5 1.0 N A:MET186 4.6 7.4 1.0 CG2 A:ILE212 4.6 5.7 1.0 CB A:ILE212 4.7 5.1 1.0 SG A:CYS182 4.7 7.6 1.0 CA A:MET186 4.7 6.0 1.0 SG A:CYS185 4.7 5.5 1.0 CD1 A:ILE212 4.7 4.5 1.0 SG A:CYS234 4.7 2.3 1.0 C A:MET186 4.8 5.0 1.0 CA A:CYS188 4.8 7.6 1.0 C A:ARG187 4.9 6.9 1.0 CA A:ARG187 4.9 4.7 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.