Iron in PDB 9erl: Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State

All present enzymatic activity of Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State:
7.2.1.2;

The structure of Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State also contains other interesting chemical elements:

Sodium

(Na)

3 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 - 42;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State (pdb code 9erl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 42 binding sites of Iron where determined in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State, PDB code: 9erl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:18.3 occ:1.00 FE1 A:FES203 0.0 18.3 1.0 S1 A:FES203 2.2 18.3 1.0 S2 A:FES203 2.2 18.3 1.0 SG E:CYS108 2.3 10.2 1.0 SG A:CYS25 2.3 0.0 1.0 FE2 A:FES203 2.7 18.3 1.0 CB A:CYS25 3.2 0.0 1.0 CB E:CYS108 3.4 10.2 1.0 SG E:CYS25 4.1 5.0 1.0 N A:CYS25 4.3 0.0 1.0 N E:GLY23 4.3 6.8 1.0 CA A:CYS25 4.4 0.0 1.0 N E:MET24 4.5 10.0 1.0 CA E:GLY23 4.5 6.8 1.0 CA E:CYS108 4.6 10.2 1.0 SG A:CYS113 4.7 9.0 1.0 CG2 A:THR111 4.8 21.9 1.0 O A:THR111 4.8 21.9 1.0 N E:CYS108 4.8 10.2 1.0 C E:ASN107 5.0 11.1 1.0 C E:GLY23 5.0 6.8 1.0

Iron binding site 2 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:18.3 occ:1.00 FE2 A:FES203 0.0 18.3 1.0 S2 A:FES203 2.2 18.3 1.0 S1 A:FES203 2.2 18.3 1.0 SG E:CYS25 2.3 5.0 1.0 SG A:CYS113 2.3 9.0 1.0 FE1 A:FES203 2.7 18.3 1.0 CB A:CYS113 3.5 9.0 1.0 CB E:CYS25 3.7 5.0 1.0 O A:LEU22 3.8 5.3 1.0 O A:THR111 4.1 21.9 1.0 SG E:CYS108 4.5 10.2 1.0 N E:CYS25 4.5 5.0 1.0 SG A:CYS25 4.6 0.0 1.0 O A:ASN112 4.6 15.3 1.0 CA A:CYS113 4.7 9.0 1.0 C A:ASN112 4.7 15.3 1.0 N A:CYS113 4.8 9.0 1.0 CA E:CYS25 4.8 5.0 1.0 O E:VAL106 4.9 16.1 1.0 C A:LEU22 5.0 5.3 1.0

Iron binding site 3 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:12.5 occ:1.00 FE1 B:SF4401 0.0 12.5 1.0 SG B:CYS200 2.3 0.0 1.0 S2 B:SF4401 2.3 12.5 1.0 S4 B:SF4401 2.3 12.5 1.0 S3 B:SF4401 2.3 12.5 1.0 FE4 B:SF4401 2.7 12.5 1.0 FE2 B:SF4401 2.7 12.5 1.0 FE3 B:SF4401 2.7 12.5 1.0 CB B:CYS200 3.7 0.0 1.0 S1 B:SF4401 3.9 12.5 1.0 CA B:CYS200 4.0 0.0 1.0 N B:HIS201 4.3 0.0 1.0 CB B:ASN202 4.3 0.0 1.0 CA B:ALA216 4.5 7.8 1.0 O B:THR215 4.6 10.4 1.0 N B:ASN202 4.7 0.0 1.0 C B:CYS200 4.7 0.0 1.0 SG B:CYS106 4.8 0.0 1.0 SG B:CYS138 4.8 0.0 1.0 SG B:CYS213 4.8 6.7 1.0 O B:LYS199 4.9 0.0 1.0 CB B:ALA216 4.9 7.8 1.0

Iron binding site 4 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:12.5 occ:1.00 FE2 B:SF4401 0.0 12.5 1.0 SG B:CYS138 2.3 0.0 1.0 S4 B:SF4401 2.3 12.5 1.0 S1 B:SF4401 2.3 12.5 1.0 S3 B:SF4401 2.3 12.5 1.0 FE4 B:SF4401 2.7 12.5 1.0 FE3 B:SF4401 2.7 12.5 1.0 FE1 B:SF4401 2.7 12.5 1.0 CB B:CYS138 3.3 0.0 1.0 S2 B:SF4401 3.9 12.5 1.0 CA B:GLY141 4.3 0.0 1.0 N B:GLY141 4.4 0.0 1.0 CB B:CYS213 4.5 6.7 1.0 SG B:CYS213 4.7 6.7 1.0 C B:TYR140 4.7 0.0 1.0 SG B:CYS106 4.7 0.0 1.0 CA B:CYS138 4.8 0.0 1.0 ND2 B:ASN202 4.8 0.0 1.0 SG B:CYS200 4.8 0.0 1.0 CB B:ASN202 4.8 0.0 1.0

Iron binding site 5 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:12.5 occ:1.00 FE3 B:SF4401 0.0 12.5 1.0 SG B:CYS213 2.3 6.7 1.0 S4 B:SF4401 2.3 12.5 1.0 S1 B:SF4401 2.3 12.5 1.0 S2 B:SF4401 2.3 12.5 1.0 FE2 B:SF4401 2.7 12.5 1.0 FE1 B:SF4401 2.7 12.5 1.0 FE4 B:SF4401 2.7 12.5 1.0 CB B:CYS213 2.9 6.7 1.0 S3 B:SF4401 3.9 12.5 1.0 CA B:CYS213 4.4 6.7 1.0 OG1 B:THR215 4.7 10.4 1.0 CA B:GLY108 4.7 3.0 1.0 SG B:CYS138 4.7 0.0 1.0 SG B:CYS200 4.8 0.0 1.0 SG B:CYS106 4.8 0.0 1.0 N B:GLY108 4.8 3.0 1.0 CB B:ALA113 4.8 5.5 1.0 O B:THR215 4.8 10.4 1.0 C B:THR215 4.9 10.4 1.0 N B:ALA216 4.9 7.8 1.0 CA B:ALA216 4.9 7.8 1.0

Iron binding site 6 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:12.5 occ:1.00 FE4 B:SF4401 0.0 12.5 1.0 SG B:CYS106 2.3 0.0 1.0 S3 B:SF4401 2.3 12.5 1.0 S2 B:SF4401 2.3 12.5 1.0 S1 B:SF4401 2.3 12.5 1.0 FE1 B:SF4401 2.7 12.5 1.0 FE2 B:SF4401 2.7 12.5 1.0 FE3 B:SF4401 2.7 12.5 1.0 CB B:CYS106 3.8 0.0 1.0 S4 B:SF4401 3.9 12.5 1.0 CA B:CYS106 4.2 0.0 1.0 N B:GLN107 4.3 0.9 1.0 CA B:GLY141 4.3 0.0 1.0 N B:GLY108 4.4 3.0 1.0 C B:CYS106 4.8 0.0 1.0 SG B:CYS200 4.8 0.0 1.0 CA B:GLY108 4.8 3.0 1.0 SG B:CYS138 4.9 0.0 1.0 SG B:CYS213 4.9 6.7 1.0

Iron binding site 7 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:0.0 occ:1.00 FE1 B:SF4402 0.0 0.0 1.0 SG B:CYS142 2.3 0.0 1.0 S2 B:SF4402 2.3 0.0 1.0 S3 B:SF4402 2.3 0.0 1.0 S4 B:SF4402 2.3 0.0 1.0 FE3 B:SF4402 2.7 0.0 1.0 FE4 B:SF4402 2.7 0.0 1.0 FE2 B:SF4402 2.7 0.0 1.0 CB B:CYS142 3.7 0.0 1.0 S1 B:SF4402 3.9 0.0 1.0 CA B:CYS142 4.2 0.0 1.0 N B:LEU143 4.2 0.0 1.0 N B:GLY144 4.2 0.0 1.0 C B:CYS142 4.6 0.0 1.0 SG B:CYS125 4.7 0.0 1.0 CA B:GLY144 4.8 0.0 1.0 SG B:CYS182 4.8 0.0 1.0 SG B:CYS148 4.8 0.0 1.0 CD B:PRO165 4.9 3.0 1.0

Iron binding site 8 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:0.0 occ:1.00 FE2 B:SF4402 0.0 0.0 1.0 SG B:CYS182 2.3 0.0 1.0 S1 B:SF4402 2.3 0.0 1.0 S3 B:SF4402 2.3 0.0 1.0 S4 B:SF4402 2.3 0.0 1.0 FE4 B:SF4402 2.7 0.0 1.0 FE1 B:SF4402 2.7 0.0 1.0 FE3 B:SF4402 2.7 0.0 1.0 CB B:CYS182 3.5 0.0 1.0 S2 B:SF4402 3.9 0.0 1.0 CA B:CYS182 4.1 0.0 1.0 CD B:PRO183 4.4 0.0 1.0 SG B:CYS148 4.7 0.0 1.0 CG B:MET187 4.8 0.0 1.0 SG B:CYS125 4.8 0.0 1.0 SG B:CYS142 4.8 0.0 1.0 C B:CYS182 4.8 0.0 1.0 N B:PRO183 4.8 0.0 1.0 CB B:ILE186 4.9 0.0 1.0

Iron binding site 9 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:0.0 occ:1.00 FE3 B:SF4402 0.0 0.0 1.0 SG B:CYS125 2.3 0.0 1.0 S4 B:SF4402 2.3 0.0 1.0 S1 B:SF4402 2.3 0.0 1.0 S2 B:SF4402 2.3 0.0 1.0 FE1 B:SF4402 2.7 0.0 1.0 FE2 B:SF4402 2.7 0.0 1.0 FE4 B:SF4402 2.7 0.0 1.0 CB B:CYS125 3.6 0.0 1.0 S3 B:SF4402 3.9 0.0 1.0 N B:THR147 4.3 0.0 1.0 N B:GLY146 4.4 0.0 1.0 N B:GLY144 4.5 0.0 1.0 CB B:THR147 4.6 0.0 1.0 N B:TYR145 4.6 0.0 1.0 CD B:PRO183 4.7 0.0 1.0 SG B:CYS142 4.7 0.0 1.0 SG B:CYS148 4.8 0.0 1.0 SG B:CYS182 4.8 0.0 1.0 OG1 B:THR147 4.9 0.0 1.0 CA B:GLY146 4.9 0.0 1.0 CB B:LEU143 4.9 0.0 1.0 N B:LEU143 4.9 0.0 1.0 CA B:CYS125 4.9 0.0 1.0

Iron binding site 10 out of 42 in the Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State


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 Sodium Pumping Rnf Complex From Acetobacterium Woodii in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:0.0 occ:1.00 FE4 B:SF4402 0.0 0.0 1.0 SG B:CYS148 2.3 0.0 1.0 S2 B:SF4402 2.3 0.0 1.0 S1 B:SF4402 2.3 0.0 1.0 S3 B:SF4402 2.3 0.0 1.0 FE2 B:SF4402 2.7 0.0 1.0 FE1 B:SF4402 2.7 0.0 1.0 FE3 B:SF4402 2.7 0.0 1.0 CB B:CYS148 3.5 0.0 1.0 S4 B:SF4402 3.9 0.0 1.0 N B:CYS148 3.9 0.0 1.0 CA B:CYS148 4.4 0.0 1.0 N B:THR147 4.5 0.0 1.0 SG B:CYS182 4.7 0.0 1.0 CA B:GLY146 4.7 0.0 1.0 SG B:CYS142 4.8 0.0 1.0 SG B:CYS125 4.8 0.0 1.0 CG B:PRO165 4.8 3.0 1.0 N B:GLY146 4.9 0.0 1.0 SD B:MET187 4.9 0.0 1.0 CG B:MET187 5.0 0.0 1.0 C B:GLY146 5.0 0.0 1.0

A.Kumar, J.M.Schuller. Cryo-Em Structure of Sodium Pumping Rnf Complex From Acetobacterium Woodii Reduced with Low Potential Ferredoxin Nat Commun 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-57375-8