Iron in PDB 8ahx: Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii (pdb code 8ahx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, PDB code: 8ahx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:107.7 occ:1.00 FE1 A:FES201 0.0 107.7 1.0 S1 A:FES201 2.2 102.8 1.0 S2 A:FES201 2.2 113.4 1.0 SG E:CYS122 2.3 113.4 1.0 SG A:CYS25 2.3 102.8 1.0 FE2 A:FES201 2.7 101.0 1.0 CB A:CYS25 3.1 82.0 1.0 CB E:CYS122 3.2 103.6 1.0 N E:CYS122 3.9 98.4 1.0 CA E:CYS122 4.1 100.8 1.0 SG A:CYS113 4.2 96.9 1.0 N A:CYS25 4.2 74.1 1.0 N E:ALA37 4.2 87.4 1.0 CA A:CYS25 4.2 73.5 1.0 SG E:CYS39 4.5 101.1 1.0 O E:THR120 4.6 119.0 1.0 CA E:ALA37 4.7 78.6 1.0 N E:LEU38 4.7 72.4 1.0 CD A:PRO26 4.9 78.0 1.0 O A:ASN112 5.0 104.1 1.0

Iron binding site 2 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:101.0 occ:1.00 FE2 A:FES201 0.0 101.0 1.0 S1 A:FES201 2.2 102.8 1.0 S2 A:FES201 2.2 113.4 1.0 SG A:CYS113 2.3 96.9 1.0 SG E:CYS39 2.3 101.1 1.0 FE1 A:FES201 2.7 107.7 1.0 CB A:CYS113 3.3 74.4 1.0 CB E:CYS39 3.5 85.8 1.0 O A:ASN112 3.8 104.1 1.0 SG A:CYS25 4.3 102.8 1.0 N E:CYS39 4.3 76.5 1.0 N A:GLY23 4.4 81.2 1.0 SG E:CYS122 4.5 113.4 1.0 C A:ASN112 4.5 94.1 1.0 N A:LEU24 4.5 76.2 1.0 CA A:CYS113 4.6 74.0 1.0 CA E:CYS39 4.6 73.9 1.0 O E:THR120 4.6 119.0 1.0 CA A:GLY23 4.7 78.7 1.0 N A:CYS113 4.7 81.9 1.0 N A:CYS25 4.9 74.1 1.0

Iron binding site 3 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:117.5 occ:1.00 FE1 B:SF4201 0.0 117.5 1.0 SG B:CYS119 2.3 126.0 1.0 S4 B:SF4201 2.3 146.7 1.0 S2 B:SF4201 2.3 138.2 1.0 S3 B:SF4201 2.3 142.6 1.0 FE2 B:SF4201 2.7 144.6 1.0 FE3 B:SF4201 2.7 162.3 1.0 FE4 B:SF4201 2.7 152.5 1.0 OG1 B:THR121 3.3 128.8 1.0 CB B:ALA123 3.5 107.0 1.0 CB B:CYS119 3.9 125.4 1.0 S1 B:SF4201 3.9 143.6 1.0 CD1 B:ILE124 4.0 104.1 1.0 CA B:CYS119 4.6 123.7 1.0 O B:THR121 4.6 131.9 1.0 CB B:THR121 4.6 123.0 1.0 SG B:CYS145 4.7 126.1 1.0 SG B:CYS142 4.7 140.4 1.0 CA B:ALA123 4.8 100.4 1.0 CA B:CYS139 4.8 102.1 1.0 SG B:CYS139 4.8 104.3 1.0 CB B:CYS139 4.8 100.1 1.0 CG2 B:THR121 4.9 124.2 1.0 N B:ALA123 4.9 95.4 1.0

Iron binding site 4 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:144.6 occ:1.00 FE2 B:SF4201 0.0 144.6 1.0 SG B:CYS145 2.3 126.1 1.0 S1 B:SF4201 2.3 143.6 1.0 S3 B:SF4201 2.3 142.6 1.0 S4 B:SF4201 2.3 146.7 1.0 FE1 B:SF4201 2.7 117.5 1.0 FE4 B:SF4201 2.7 152.5 1.0 FE3 B:SF4201 2.7 162.3 1.0 CB B:CYS145 3.5 133.3 1.0 S2 B:SF4201 3.9 138.2 1.0 N B:CYS145 4.0 131.4 1.0 CD1 B:ILE124 4.3 104.1 1.0 SG B:CYS119 4.3 126.0 1.0 CA B:CYS145 4.4 133.8 1.0 N B:LYS144 4.5 127.4 1.0 CB B:ALA102 4.5 104.3 1.0 SG B:CYS139 4.6 104.3 1.0 N B:GLY143 4.6 114.2 1.0 SG B:CYS142 4.9 140.4 1.0 CA B:GLY143 4.9 115.1 1.0 C B:LYS144 4.9 130.5 1.0 C B:GLY143 4.9 117.0 1.0

Iron binding site 5 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:162.3 occ:1.00 FE3 B:SF4201 0.0 162.3 1.0 SG B:CYS142 2.3 140.4 1.0 S4 B:SF4201 2.3 146.7 1.0 S1 B:SF4201 2.3 143.6 1.0 S2 B:SF4201 2.3 138.2 1.0 FE4 B:SF4201 2.7 152.5 1.0 FE1 B:SF4201 2.7 117.5 1.0 FE2 B:SF4201 2.7 144.6 1.0 N B:CYS142 3.7 134.0 1.0 CB B:CYS142 3.8 131.4 1.0 N B:GLY143 3.8 114.2 1.0 S3 B:SF4201 3.9 142.6 1.0 N B:LYS144 4.0 127.4 1.0 CA B:CYS142 4.1 134.3 1.0 C B:CYS142 4.3 132.3 1.0 CG B:LYS144 4.4 126.4 1.0 SG B:CYS119 4.4 126.0 1.0 CB B:LYS144 4.5 128.2 1.0 N B:GLY141 4.6 119.9 1.0 C B:GLY141 4.7 124.6 1.0 OG1 B:THR140 4.7 102.8 1.0 CA B:GLY143 4.7 115.1 1.0 SG B:CYS145 4.8 126.1 1.0 SG B:CYS139 4.8 104.3 1.0 CA B:LYS144 4.8 130.3 1.0 N B:THR140 4.8 106.0 1.0 OG1 B:THR121 4.8 128.8 1.0 C B:GLY143 4.9 117.0 1.0 CA B:GLY141 4.9 121.0 1.0

Iron binding site 6 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:152.5 occ:1.00 FE4 B:SF4201 0.0 152.5 1.0 SG B:CYS139 2.3 104.3 1.0 S3 B:SF4201 2.3 142.6 1.0 S1 B:SF4201 2.3 143.6 1.0 S2 B:SF4201 2.3 138.2 1.0 FE3 B:SF4201 2.7 162.3 1.0 FE2 B:SF4201 2.7 144.6 1.0 FE1 B:SF4201 2.7 117.5 1.0 CB B:CYS139 3.0 100.1 1.0 CA B:CYS139 3.4 102.1 1.0 N B:THR140 3.5 106.0 1.0 N B:GLY141 3.7 119.9 1.0 S4 B:SF4201 3.9 146.7 1.0 C B:CYS139 3.9 100.7 1.0 CA B:GLY141 4.4 121.0 1.0 CB B:ALA102 4.4 104.3 1.0 C B:THR140 4.6 101.9 1.0 N B:CYS142 4.6 134.0 1.0 CA B:THR140 4.6 103.6 1.0 SG B:CYS142 4.6 140.4 1.0 CB B:ALA123 4.6 107.0 1.0 N B:CYS139 4.7 105.0 1.0 SG B:CYS145 4.8 126.1 1.0 OG1 B:THR121 4.9 128.8 1.0 N B:ALA102 4.9 108.6 1.0 OG1 B:THR140 4.9 102.8 1.0 C B:GLY141 4.9 124.6 1.0

Iron binding site 7 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:166.2 occ:1.00 FE1 B:SF4202 0.0 166.2 1.0 SG B:CYS109 2.3 148.2 1.0 S2 B:SF4202 2.3 152.4 1.0 S4 B:SF4202 2.3 167.9 1.0 S3 B:SF4202 2.3 159.9 1.0 FE3 B:SF4202 2.7 173.7 1.0 FE2 B:SF4202 2.7 175.3 1.0 FE4 B:SF4202 2.7 152.5 1.0 CB B:CYS109 2.9 142.5 1.0 CA B:CYS109 3.1 140.0 1.0 N B:ILE110 3.6 134.6 1.0 C B:CYS109 3.8 138.5 1.0 N B:GLY111 3.8 133.9 1.0 S1 B:SF4202 3.9 166.7 1.0 CG2 B:VAL133 4.1 129.5 1.0 N B:CYS112 4.3 135.5 1.0 N B:CYS109 4.4 140.8 1.0 CA B:GLY111 4.4 137.4 1.0 O B:GLN108 4.5 146.2 1.0 C B:ILE110 4.7 134.2 1.0 SG B:CYS149 4.7 160.1 1.0 SG B:CYS115 4.8 132.1 1.0 CA B:ILE110 4.8 136.6 1.0 O B:CYS109 4.8 134.0 1.0 CB B:CYS153 4.8 154.2 1.0 SG B:CYS153 4.8 161.8 1.0 SG B:CYS112 4.9 146.8 1.0 C B:GLY111 4.9 134.1 1.0 C B:GLN108 4.9 147.1 1.0

Iron binding site 8 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:175.3 occ:1.00 FE2 B:SF4202 0.0 175.3 1.0 SG B:CYS112 2.3 146.8 1.0 S3 B:SF4202 2.3 159.9 1.0 S1 B:SF4202 2.3 166.7 1.0 S4 B:SF4202 2.3 167.9 1.0 FE4 B:SF4202 2.7 152.5 1.0 FE3 B:SF4202 2.7 173.7 1.0 FE1 B:SF4202 2.7 166.2 1.0 N B:CYS112 3.2 135.5 1.0 CB B:CYS112 3.2 143.0 1.0 N B:THR113 3.4 136.0 1.0 CA B:CYS112 3.5 139.5 1.0 C B:CYS112 3.6 140.7 1.0 S2 B:SF4202 3.9 152.4 1.0 N B:ARG114 3.9 135.8 1.0 C B:GLY111 4.3 134.1 1.0 O B:CYS112 4.3 145.3 1.0 CA B:THR113 4.4 140.8 1.0 SG B:CYS149 4.4 160.1 1.0 CB B:ARG114 4.5 135.8 1.0 N B:GLY111 4.6 133.9 1.0 C B:THR113 4.7 141.7 1.0 N B:CYS115 4.7 122.1 1.0 SG B:CYS115 4.7 132.1 1.0 CA B:GLY111 4.7 137.4 1.0 CA B:ARG114 4.7 135.6 1.0 CD B:PRO150 4.8 155.9 1.0 SG B:CYS109 4.8 148.2 1.0 N B:ILE110 4.9 134.6 1.0

Iron binding site 9 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:173.7 occ:1.00 FE3 B:SF4202 0.0 173.7 1.0 SG B:CYS115 2.3 132.1 1.0 S1 B:SF4202 2.3 166.7 1.0 S2 B:SF4202 2.3 152.4 1.0 S4 B:SF4202 2.3 167.9 1.0 FE1 B:SF4202 2.7 166.2 1.0 FE2 B:SF4202 2.7 175.3 1.0 FE4 B:SF4202 2.7 152.5 1.0 CB B:CYS115 3.1 122.5 1.0 N B:CYS115 3.7 122.1 1.0 CG2 B:VAL133 3.7 129.5 1.0 S3 B:SF4202 3.9 159.9 1.0 CA B:CYS115 4.0 120.4 1.0 SG B:CYS109 4.5 148.2 1.0 N B:ARG114 4.5 135.8 1.0 N B:THR113 4.6 136.0 1.0 SG B:CYS112 4.7 146.8 1.0 C B:ARG114 4.8 134.8 1.0 CA B:THR113 4.9 140.8 1.0 SG B:CYS149 4.9 160.1 1.0

Iron binding site 10 out of 18 in the Cryo-Em Structure of the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii


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 the Nitrogen-Fixation Associated Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:152.5 occ:1.00 FE4 B:SF4202 0.0 152.5 1.0 SG B:CYS149 2.3 160.1 1.0 S3 B:SF4202 2.3 159.9 1.0 S1 B:SF4202 2.3 166.7 1.0 S2 B:SF4202 2.3 152.4 1.0 FE2 B:SF4202 2.7 175.3 1.0 FE1 B:SF4202 2.7 166.2 1.0 FE3 B:SF4202 2.7 173.7 1.0 CB B:CYS149 3.0 153.1 1.0 CB B:CYS153 3.6 154.2 1.0 CA B:CYS149 3.8 154.1 1.0 S4 B:SF4202 3.9 167.9 1.0 O B:GLN108 4.3 146.2 1.0 SG B:CYS112 4.3 146.8 1.0 CA B:CYS109 4.6 140.0 1.0 SG B:CYS153 4.6 161.8 1.0 N B:CYS153 4.7 154.9 1.0 CA B:CYS153 4.8 155.5 1.0 CB B:CYS109 4.8 142.5 1.0 SG B:CYS115 4.8 132.1 1.0 C B:CYS149 4.8 154.2 1.0 N B:CYS149 4.9 150.8 1.0 SG B:CYS109 4.9 148.2 1.0 CD B:PRO150 4.9 155.9 1.0 CB B:CYS115 4.9 122.5 1.0

L.Zhang, O.Einsle. Architecture of the Nadh:Ferredoxin Oxidoreductase Rnf That Drives Biological Nitrogen Fixation To Be Published.