Iron in PDB 8j83: Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1

All present enzymatic activity of Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1:
1.17.1.9; 1.2.1.2;

The structure of Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1, PDB code: 8j83 was solved by A.Kobayashi, M.Taketa, K.Sowa, K.Kano, Y.Higuchi, H.Ogata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	232.86, 73.95, 95.74, 90, 106.72, 90
R / Rfree (%)	21.9 / 25.9

The structure of Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1 also contains other interesting chemical elements:

Tungsten

(W)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1 (pdb code 8j83). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1, PDB code: 8j83:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:37.6 occ:1.00 FE1 A:FES1004 0.0 37.6 1.0 S2 A:FES1004 2.2 38.8 1.0 S1 A:FES1004 2.2 39.3 1.0 SG A:CYS102 2.2 40.2 1.0 SG A:CYS115 2.3 39.5 1.0 CB A:CYS115 3.2 39.5 1.0 FE2 A:FES1004 3.2 37.3 1.0 CB A:CYS102 3.3 39.3 1.0 N A:CYS115 3.4 41.0 1.0 N A:CYS102 3.4 39.1 1.0 CA A:CYS115 3.7 40.0 1.0 CA A:CYS102 3.8 39.0 1.0 N A:ARG116 3.8 41.0 1.0 N A:HIS103 4.1 39.5 1.0 C A:CYS102 4.1 39.8 1.0 C A:CYS115 4.2 41.1 1.0 N A:ASN114 4.2 40.9 1.0 SG A:CYS132 4.4 40.8 1.0 CA A:GLY113 4.4 41.4 1.0 C A:ASN114 4.5 40.2 1.0 N A:LEU101 4.5 40.6 1.0 N A:ALA117 4.6 42.3 1.0 C A:GLY113 4.6 41.5 1.0 C A:LEU101 4.6 39.2 1.0 N A:GLY113 4.7 41.9 1.0 CA A:ARG116 4.8 41.4 1.0 CA A:ASN114 5.0 40.9 1.0 O A:CYS102 5.0 39.3 1.0 CB A:HIS103 5.0 40.1 1.0

Iron binding site 2 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:37.3 occ:1.00 FE2 A:FES1004 0.0 37.3 1.0 S1 A:FES1004 2.2 39.3 1.0 SG A:CYS118 2.2 41.2 1.0 S2 A:FES1004 2.2 38.8 1.0 SG A:CYS132 2.4 40.8 1.0 CB A:CYS118 3.2 42.6 1.0 FE1 A:FES1004 3.2 37.6 1.0 CB A:CYS132 3.3 41.5 1.0 N A:CYS132 4.0 43.5 1.0 CB A:ALA130 4.0 42.7 1.0 N A:CYS118 4.2 43.4 1.0 CA A:CYS132 4.2 42.9 1.0 CA A:CYS118 4.3 43.7 1.0 SG A:CYS115 4.6 39.5 1.0 CA A:GLY113 4.7 41.4 1.0 CA A:ALA130 4.7 44.1 1.0 N A:SER131 4.8 43.3 1.0 C A:ALA130 4.8 43.8 1.0 CB A:HIS103 4.8 40.1 1.0 C A:CYS118 4.9 44.2 1.0 SG A:CYS102 4.9 40.2 1.0 N A:ALA117 4.9 42.3 1.0 N A:ARG116 5.0 41.0 1.0

Iron binding site 3 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:40.6 occ:1.00 FE1 A:SF41005 0.0 40.6 1.0 S2 A:SF41005 2.1 40.5 1.0 S4 A:SF41005 2.1 40.6 1.0 S3 A:SF41005 2.1 41.4 1.0 SG A:CYS216 2.3 38.8 1.0 FE4 A:SF41005 3.0 38.2 1.0 FE3 A:SF41005 3.0 38.3 1.0 FE2 A:SF41005 3.1 41.2 1.0 N A:CYS216 3.3 40.0 1.0 CB A:CYS216 3.4 39.5 1.0 N A:ASN217 3.7 40.1 1.0 CA A:CYS216 3.7 40.0 1.0 S1 A:SF41005 3.7 40.7 1.0 C A:CYS216 3.9 40.5 1.0 N A:LEU218 4.1 40.1 1.0 CD A:PRO267 4.2 39.9 1.0 CG1 A:ILE214 4.3 40.8 1.0 C A:GLN215 4.3 40.2 1.0 N A:GLN215 4.4 41.3 1.0 CB A:LEU218 4.5 39.4 1.0 CA A:ASN217 4.6 40.8 1.0 CA A:GLN215 4.6 41.0 1.0 CG A:PRO267 4.8 39.8 1.0 C A:ASN217 4.8 40.3 1.0 SG A:CYS219 4.8 38.8 1.0 N A:CYS219 4.8 40.1 1.0 N A:ILE214 4.9 41.4 1.0 SG A:CYS213 4.9 40.8 1.0 CA A:LEU218 4.9 40.0 1.0 O A:CYS216 4.9 41.2 1.0 SG A:CYS266 5.0 40.1 1.0 C A:ILE214 5.0 40.2 1.0

Iron binding site 4 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:41.2 occ:1.00 FE2 A:SF41005 0.0 41.2 1.0 S1 A:SF41005 2.1 40.7 1.0 S4 A:SF41005 2.1 40.6 1.0 S3 A:SF41005 2.1 41.4 1.0 SG A:CYS213 2.3 40.8 1.0 FE4 A:SF41005 2.9 38.2 1.0 FE3 A:SF41005 3.0 38.3 1.0 FE1 A:SF41005 3.1 40.6 1.0 CB A:CYS213 3.1 42.3 1.0 CA A:CYS213 3.5 42.1 1.0 S2 A:SF41005 3.6 40.5 1.0 N A:ILE214 3.9 41.4 1.0 N A:GLN215 3.9 41.3 1.0 C A:CYS213 4.1 42.6 1.0 CG2 A:VAL243 4.1 41.1 1.0 CB A:ALA270 4.4 40.7 1.0 CA A:GLN215 4.4 41.0 1.0 CD2 A:LEU210 4.5 41.3 1.0 N A:CYS213 4.7 42.5 1.0 N A:CYS216 4.7 40.0 1.0 C A:ILE214 4.8 40.2 1.0 OG1 A:THR268 4.9 39.9 1.0 CA A:ILE214 4.9 41.7 1.0 SG A:CYS219 5.0 38.8 1.0

Iron binding site 5 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:38.3 occ:1.00 FE3 A:SF41005 0.0 38.3 1.0 S2 A:SF41005 2.1 40.5 1.0 S4 A:SF41005 2.1 40.6 1.0 S1 A:SF41005 2.1 40.7 1.0 SG A:CYS266 2.2 40.1 1.0 FE2 A:SF41005 3.0 41.2 1.0 FE4 A:SF41005 3.0 38.2 1.0 FE1 A:SF41005 3.0 40.6 1.0 CB A:CYS266 3.3 39.5 1.0 OG1 A:THR268 3.7 39.9 1.0 S3 A:SF41005 3.7 41.4 1.0 CA A:CYS266 3.9 39.9 1.0 CB A:ALA270 4.0 40.7 1.0 CD A:PRO267 4.0 39.9 1.0 CG A:LEU271 4.4 39.5 1.0 N A:PRO267 4.5 40.8 1.0 C A:CYS266 4.5 39.9 1.0 CD1 A:LEU271 4.6 39.5 1.0 N A:LEU271 4.7 40.1 1.0 SG A:CYS216 4.8 38.8 1.0 CB A:THR268 4.9 40.8 1.0 CA A:ALA270 4.9 40.5 1.0 CG2 A:THR268 4.9 40.7 1.0 N A:ALA270 4.9 40.3 1.0 N A:THR268 4.9 40.9 1.0

Iron binding site 6 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1005 b:38.2 occ:1.00 FE4 A:SF41005 0.0 38.2 1.0 S3 A:SF41005 2.1 41.4 1.0 S2 A:SF41005 2.1 40.5 1.0 S1 A:SF41005 2.1 40.7 1.0 SG A:CYS219 2.3 38.8 1.0 FE2 A:SF41005 2.9 41.2 1.0 FE1 A:SF41005 3.0 40.6 1.0 FE3 A:SF41005 3.0 38.3 1.0 CB A:CYS219 3.2 39.1 1.0 S4 A:SF41005 3.6 40.6 1.0 CG2 A:VAL243 3.8 41.1 1.0 N A:CYS219 3.8 40.1 1.0 CA A:CYS219 4.1 39.6 1.0 CD1 A:LEU271 4.5 39.5 1.0 N A:ASN217 4.7 40.1 1.0 CG1 A:VAL243 4.7 40.8 1.0 N A:LEU218 4.8 40.1 1.0 CB A:VAL243 4.8 41.1 1.0 SG A:CYS213 4.8 40.8 1.0 CA A:ASN217 4.8 40.8 1.0 SG A:CYS216 5.0 38.8 1.0

Iron binding site 7 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:38.1 occ:1.00 FE1 A:SF41006 0.0 38.1 1.0 S2 A:SF41006 2.1 40.1 1.0 S4 A:SF41006 2.1 39.6 1.0 S3 A:SF41006 2.1 39.8 1.0 SG A:CYS262 2.2 37.4 1.0 FE2 A:SF41006 3.0 40.4 1.0 FE4 A:SF41006 3.0 39.1 1.0 FE3 A:SF41006 3.1 40.5 1.0 CB A:CYS262 3.1 38.9 1.0 S1 A:SF41006 3.7 38.4 1.0 N A:CYS262 3.7 38.1 1.0 CA A:CYS262 4.0 38.8 1.0 CD1 A:ILE232 4.3 39.8 1.0 CE A:MET251 4.5 42.8 1.0 N A:GLU261 4.6 39.2 1.0 SG A:CYS259 4.8 36.7 1.0 N A:GLY260 4.8 38.7 1.0 CG1 A:ILE232 4.9 40.0 1.0 C A:GLU261 4.9 38.7 1.0 SG A:CYS223 4.9 38.9 1.0 CB A:CYS223 4.9 39.3 1.0 SG A:CYS256 5.0 37.9 1.0

Iron binding site 8 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:40.4 occ:1.00 FE2 A:SF41006 0.0 40.4 1.0 S3 A:SF41006 2.1 39.8 1.0 S1 A:SF41006 2.1 38.4 1.0 S4 A:SF41006 2.1 39.6 1.0 SG A:CYS256 2.3 37.9 1.0 FE4 A:SF41006 3.0 39.1 1.0 FE1 A:SF41006 3.0 38.1 1.0 FE3 A:SF41006 3.0 40.5 1.0 CB A:CYS256 3.3 39.3 1.0 S2 A:SF41006 3.6 40.1 1.0 CA A:CYS256 3.8 39.3 1.0 N A:ALA258 3.9 39.5 1.0 N A:VAL257 4.0 38.3 1.0 C A:CYS256 4.3 39.2 1.0 CA A:ALA258 4.4 39.3 1.0 CE A:MET251 4.5 42.8 1.0 N A:CYS259 4.6 39.0 1.0 CB A:VAL231 4.8 40.1 1.0 CG1 A:VAL231 4.8 40.0 1.0 C A:VAL257 4.8 38.3 1.0 CG2 A:VAL231 4.8 39.7 1.0 CE A:MET206 4.9 40.4 1.0 SG A:CYS262 4.9 37.4 1.0 CA A:VAL257 5.0 38.9 1.0

Iron binding site 9 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:40.5 occ:1.00 FE3 A:SF41006 0.0 40.5 1.0 S2 A:SF41006 2.1 40.1 1.0 S1 A:SF41006 2.1 38.4 1.0 S4 A:SF41006 2.2 39.6 1.0 SG A:CYS259 2.2 36.7 1.0 FE4 A:SF41006 3.0 39.1 1.0 FE2 A:SF41006 3.0 40.4 1.0 FE1 A:SF41006 3.1 38.1 1.0 CB A:CYS259 3.3 39.3 1.0 N A:CYS259 3.3 39.0 1.0 N A:GLY260 3.7 38.7 1.0 CA A:CYS259 3.7 39.2 1.0 ND2 A:ASN229 3.7 39.4 1.0 S3 A:SF41006 3.7 39.8 1.0 C A:CYS259 4.1 38.5 1.0 N A:GLU261 4.2 39.2 1.0 C A:ALA258 4.4 39.9 1.0 N A:ALA258 4.5 39.5 1.0 CG2 A:VAL257 4.6 38.5 1.0 CA A:GLY260 4.7 38.5 1.0 CA A:ALA258 4.7 39.3 1.0 CB A:GLU261 4.7 38.4 1.0 CG A:ASN229 4.8 40.3 1.0 C A:GLY260 4.9 38.9 1.0 SG A:CYS223 5.0 38.9 1.0 SG A:CYS256 5.0 37.9 1.0 N A:CYS262 5.0 38.1 1.0

Iron binding site 10 out of 20 in the Crystal Structure of Formate Dehydrogenase From Methylorubrum Extorquens AM1


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 Formate Dehydrogenase From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1006 b:39.1 occ:1.00 FE4 A:SF41006 0.0 39.1 1.0 S2 A:SF41006 2.1 40.1 1.0 S3 A:SF41006 2.1 39.8 1.0 S1 A:SF41006 2.1 38.4 1.0 SG A:CYS223 2.3 38.9 1.0 FE2 A:SF41006 3.0 40.4 1.0 FE1 A:SF41006 3.0 38.1 1.0 FE3 A:SF41006 3.0 40.5 1.0 CB A:CYS223 3.3 39.3 1.0 S4 A:SF41006 3.7 39.6 1.0 CB A:VAL231 3.9 40.1 1.0 CA A:CYS223 4.1 39.5 1.0 CG2 A:VAL231 4.2 39.7 1.0 CB A:ASN229 4.4 40.4 1.0 CG1 A:ILE232 4.5 40.0 1.0 ND2 A:ASN229 4.6 39.4 1.0 CG1 A:VAL231 4.7 40.0 1.0 N A:VAL231 4.7 40.5 1.0 CD1 A:ILE232 4.7 39.8 1.0 CA A:VAL231 4.8 40.4 1.0 N A:ILE232 4.8 40.4 1.0 SG A:CYS259 4.8 36.7 1.0

A.Kobayashi, M.Taketa, K.Sowa, K.Kano, Y.Higuchi, H.Ogata. Structure and Function Relationship of Formate Dehydrogenases: An Overview of Recent Progress. Iucrj V. 10 544 2023.
ISSN: ESSN 2052-2525
PubMed: 37668215
DOI: 10.1107/S2052252523006437