Iron in PDB 7b0c: [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment

The structure of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment, PDB code: 7b0c was solved by R.Rohac, J.C.Fontecilla-Camps, A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.45 / 3.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	118.81, 118.81, 89.53, 90, 90, 120
R / Rfree (%)	21.9 / 23.6

The binding sites of Iron atom in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment (pdb code 7b0c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment, PDB code: 7b0c:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:111.2 occ:1.00 FE1 A:SF4201 0.0 111.2 1.0 SG A:CYS93 2.3 132.9 1.0 S2 A:SF4201 2.3 121.9 1.0 S3 A:SF4201 2.3 107.2 1.0 S4 A:SF4201 2.3 110.5 1.0 FE2 A:SF4201 2.7 107.0 1.0 FE4 A:SF4201 2.7 110.4 1.0 FE3 A:SF4201 2.7 113.2 1.0 CB A:CYS93 3.3 124.1 1.0 S1 A:SF4201 3.9 109.3 1.0 CA A:CYS93 3.9 135.5 1.0 CG2 A:VAL91 4.1 113.8 1.0 OD1 B:ASP8 4.4 112.6 1.0 N A:CYS93 4.5 143.4 1.0 CB A:VAL91 4.6 114.9 1.0 CD A:ARG108 4.6 120.9 1.0 CG A:ARG108 4.6 112.1 1.0 CB A:CYS99 4.7 125.4 1.0 CB A:ARG108 4.7 111.5 1.0 SG A:CYS105 4.8 117.2 1.0 NE A:ARG108 4.8 117.3 1.0 SG A:CYS99 4.9 126.5 1.0

Iron binding site 2 out of 8 in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:107.0 occ:1.00 FE2 A:SF4201 0.0 107.0 1.0 OD1 B:ASP8 2.0 112.6 1.0 S1 A:SF4201 2.3 109.3 1.0 S3 A:SF4201 2.3 107.2 1.0 S4 A:SF4201 2.3 110.5 1.0 FE3 A:SF4201 2.7 113.2 1.0 FE4 A:SF4201 2.7 110.4 1.0 FE1 A:SF4201 2.7 111.2 1.0 CG B:ASP8 3.0 108.7 1.0 OD2 B:ASP8 3.5 116.2 1.0 CD2 A:LEU107 3.9 102.8 1.0 S2 A:SF4201 3.9 121.9 1.0 CB B:ASP8 4.3 105.7 1.0 NE B:ARG12 4.6 114.2 1.0 SG A:CYS105 4.6 117.2 1.0 CG A:LEU107 4.7 111.8 1.0 CB A:VAL91 4.7 114.9 1.0 CG2 A:VAL91 4.7 113.8 1.0 CG1 A:VAL91 4.8 106.5 1.0 SG A:CYS93 4.8 132.9 1.0 SG A:CYS99 4.8 126.5 1.0 CG B:ARG12 4.8 109.8 1.0 O B:ASP8 5.0 114.2 1.0

Iron binding site 3 out of 8 in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:113.2 occ:1.00 FE3 A:SF4201 0.0 113.2 1.0 S1 A:SF4201 2.3 109.3 1.0 S2 A:SF4201 2.3 121.9 1.0 S4 A:SF4201 2.3 110.5 1.0 SG A:CYS99 2.3 126.5 1.0 FE2 A:SF4201 2.7 107.0 1.0 FE4 A:SF4201 2.7 110.4 1.0 FE1 A:SF4201 2.7 111.2 1.0 CB A:CYS99 2.8 125.4 1.0 NE B:ARG12 3.9 114.2 1.0 S3 A:SF4201 3.9 107.2 1.0 OD1 B:ASP8 4.1 112.6 1.0 CZ B:ARG12 4.2 122.7 1.0 CB A:LEU101 4.3 119.2 1.0 CD B:ARG12 4.4 112.1 1.0 CA A:CYS99 4.4 131.3 1.0 OD2 B:ASP8 4.4 116.2 1.0 NH2 B:ARG12 4.4 116.5 1.0 CG B:ARG12 4.6 109.8 1.0 SG A:CYS93 4.7 132.9 1.0 CG B:ASP8 4.7 108.7 1.0 SG A:CYS105 4.8 117.2 1.0 CB A:CYS93 4.8 124.1 1.0 CD1 A:LEU101 4.8 120.4 1.0 NH1 B:ARG12 4.9 131.2 1.0 CA A:CYS93 5.0 135.5 1.0 N A:LEU101 5.0 128.9 1.0

Iron binding site 4 out of 8 in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:110.4 occ:1.00 FE4 A:SF4201 0.0 110.4 1.0 SG A:CYS105 2.3 117.2 1.0 S2 A:SF4201 2.3 121.9 1.0 S1 A:SF4201 2.3 109.3 1.0 S3 A:SF4201 2.3 107.2 1.0 FE2 A:SF4201 2.7 107.0 1.0 FE1 A:SF4201 2.7 111.2 1.0 FE3 A:SF4201 2.7 113.2 1.0 CB A:CYS105 3.2 115.0 1.0 S4 A:SF4201 3.9 110.5 1.0 CB A:LEU101 4.3 119.2 1.0 N A:ARG108 4.4 107.5 1.0 CB A:LEU107 4.5 104.8 1.0 CB A:ARG108 4.5 111.5 1.0 SG A:CYS99 4.6 126.5 1.0 OD1 B:ASP8 4.6 112.6 1.0 CA A:CYS105 4.6 116.9 1.0 CD2 A:LEU107 4.6 102.8 1.0 O A:LEU101 4.8 122.4 1.0 SG A:CYS93 4.8 132.9 1.0 CD1 A:LEU101 4.9 120.4 1.0 CG A:LEU107 4.9 111.8 1.0 CA A:ARG108 4.9 108.9 1.0

Iron binding site 5 out of 8 in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:110.7 occ:1.00 FE1 B:SF4201 0.0 110.7 1.0 SG B:CYS93 2.3 131.1 1.0 S2 B:SF4201 2.3 124.7 1.0 S3 B:SF4201 2.3 106.9 1.0 S4 B:SF4201 2.3 110.1 1.0 FE2 B:SF4201 2.7 106.8 1.0 FE4 B:SF4201 2.7 109.9 1.0 FE3 B:SF4201 2.7 112.1 1.0 CB B:CYS93 3.3 128.9 1.0 S1 B:SF4201 3.9 108.9 1.0 CA B:CYS93 4.0 134.5 1.0 CG2 B:VAL91 4.1 114.0 1.0 OD1 A:ASP8 4.4 118.5 1.0 N B:CYS93 4.5 141.8 1.0 CD B:ARG108 4.6 122.3 1.0 CG B:ARG108 4.6 112.0 1.0 CB B:VAL91 4.6 116.9 1.0 CB B:CYS99 4.7 119.8 1.0 CB B:ARG108 4.7 111.1 1.0 SG B:CYS105 4.7 115.6 1.0 NE B:ARG108 4.9 119.2 1.0 SG B:CYS99 4.9 126.1 1.0

Iron binding site 6 out of 8 in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:106.8 occ:1.00 FE2 B:SF4201 0.0 106.8 1.0 OD1 A:ASP8 1.9 118.5 1.0 S3 B:SF4201 2.3 106.9 1.0 S1 B:SF4201 2.3 108.9 1.0 S4 B:SF4201 2.3 110.1 1.0 FE3 B:SF4201 2.7 112.1 1.0 FE1 B:SF4201 2.7 110.7 1.0 FE4 B:SF4201 2.7 109.9 1.0 CG A:ASP8 3.0 109.8 1.0 OD2 A:ASP8 3.4 115.5 1.0 S2 B:SF4201 3.9 124.7 1.0 CD2 B:LEU107 3.9 102.8 1.0 CB A:ASP8 4.3 103.9 1.0 NE A:ARG12 4.5 111.0 1.0 SG B:CYS105 4.7 115.6 1.0 CB B:VAL91 4.7 116.9 1.0 CG B:LEU107 4.8 110.8 1.0 CG2 B:VAL91 4.8 114.0 1.0 SG B:CYS93 4.8 131.1 1.0 SG B:CYS99 4.8 126.1 1.0 CG A:ARG12 4.8 109.3 1.0 CG1 B:VAL91 4.8 104.6 1.0 O A:ASP8 4.9 111.8 1.0

Iron binding site 7 out of 8 in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:112.1 occ:1.00 FE3 B:SF4201 0.0 112.1 1.0 S1 B:SF4201 2.3 108.9 1.0 S2 B:SF4201 2.3 124.7 1.0 S4 B:SF4201 2.3 110.1 1.0 SG B:CYS99 2.3 126.1 1.0 FE2 B:SF4201 2.7 106.8 1.0 FE1 B:SF4201 2.7 110.7 1.0 FE4 B:SF4201 2.7 109.9 1.0 CB B:CYS99 2.8 119.8 1.0 NE A:ARG12 3.9 111.0 1.0 S3 B:SF4201 3.9 106.9 1.0 OD1 A:ASP8 4.2 118.5 1.0 CZ A:ARG12 4.2 119.9 1.0 CB B:LEU101 4.3 118.2 1.0 CA B:CYS99 4.3 125.7 1.0 CD A:ARG12 4.4 111.5 1.0 OD2 A:ASP8 4.4 115.5 1.0 NH2 A:ARG12 4.4 117.1 1.0 SG B:CYS93 4.6 131.1 1.0 CG A:ARG12 4.7 109.3 1.0 CG A:ASP8 4.7 109.8 1.0 SG B:CYS105 4.8 115.6 1.0 CB B:CYS93 4.8 128.9 1.0 CD1 B:LEU101 4.8 122.8 1.0 NH1 A:ARG12 4.9 130.0 1.0 N B:LEU101 4.9 129.4 1.0 CA B:CYS93 5.0 134.5 1.0 C B:CYS99 5.0 131.5 1.0 CA B:LEU101 5.0 122.0 1.0

Iron binding site 8 out of 8 in the [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of [4FE-4S]-Nsrr Complexed to 23-Bp HMPA1 Operator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:109.9 occ:1.00 FE4 B:SF4201 0.0 109.9 1.0 SG B:CYS105 2.3 115.6 1.0 S1 B:SF4201 2.3 108.9 1.0 S2 B:SF4201 2.3 124.7 1.0 S3 B:SF4201 2.3 106.9 1.0 FE2 B:SF4201 2.7 106.8 1.0 FE1 B:SF4201 2.7 110.7 1.0 FE3 B:SF4201 2.7 112.1 1.0 CB B:CYS105 3.3 114.6 1.0 S4 B:SF4201 3.9 110.1 1.0 CB B:LEU101 4.3 118.2 1.0 CB B:LEU107 4.4 104.8 1.0 N B:ARG108 4.5 107.6 1.0 CD2 B:LEU107 4.5 102.8 1.0 OD1 A:ASP8 4.6 118.5 1.0 CB B:ARG108 4.6 111.1 1.0 SG B:CYS99 4.6 126.1 1.0 CA B:CYS105 4.7 116.6 1.0 O B:LEU101 4.8 121.5 1.0 SG B:CYS93 4.8 131.1 1.0 CG B:LEU107 4.8 110.8 1.0 CD1 B:LEU101 4.8 122.8 1.0 CA B:ARG108 5.0 108.7 1.0

R.Rohac, J.C.Crack, E.De Rosny, O.Gigarel, N.E.Le Brun, J.C.Fontecilla-Camps, A.Volbeda. Structural Determinants of Dna Recognition By the No Sensor Nsrr and Related RRF2-Type [Fes]-Transcription Factors. Commun Biol V. 5 769 2022.
ISSN: ESSN 2399-3642
PubMed: 35908109
DOI: 10.1038/S42003-022-03745-7