Iron in PDB 9gzq: Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)

The structure of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641), PDB code: 9gzq was solved by P.Arnoux, M.V.Cherrier, Y.Nicolet, P.Legrand, M.Broc, F.Seduk, R.Arias-Cartin, A.Magalon, A.Walburger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.06 / 3.63
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	215.909, 215.909, 215.528, 90, 90, 90
R / Rfree (%)	28 / 32

The structure of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) also contains other interesting chemical elements:

Molybdenum

(Mo)

1 atom

Pages:

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

Binding sites:

The binding sites of Iron atom in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) (pdb code 9gzq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641), PDB code: 9gzq:
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 Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1000 b:145.8 occ:1.00 FE1 A:FES1000 0.0 145.8 1.0 SG A:CYS48 2.2 152.2 1.0 S2 A:FES1000 2.2 140.8 1.0 S1 A:FES1000 2.2 144.7 1.0 SG A:CYS37 2.3 139.1 1.0 FE2 A:FES1000 2.7 154.5 1.0 CB A:CYS48 3.3 137.5 1.0 N A:CYS48 3.4 135.6 1.0 CB A:CYS37 3.4 124.1 1.0 N A:CYS37 3.6 114.7 1.0 CA A:CYS48 3.7 136.6 1.0 N A:ASP49 3.8 136.3 1.0 CA A:CYS37 3.8 120.1 1.0 N A:TYR38 4.1 123.2 1.0 N A:THR47 4.1 127.2 1.0 C A:CYS37 4.2 122.3 1.0 C A:CYS48 4.2 138.5 1.0 SG A:CYS51 4.4 138.0 1.0 OG1 A:THR50 4.5 132.6 1.0 N A:THR50 4.5 124.7 1.0 SG A:CYS63 4.5 164.1 1.0 C A:THR47 4.5 133.9 1.0 CA A:GLU46 4.6 142.8 1.0 N A:GLU46 4.6 138.6 1.0 C A:GLU46 4.7 145.9 1.0 N A:VAL36 4.7 111.9 1.0 CA A:ASP49 4.8 134.4 1.0 C A:VAL36 4.8 116.8 1.0 CA A:THR47 4.9 126.1 1.0 O A:CYS37 5.0 124.4 1.0

Iron binding site 2 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1000 b:154.5 occ:1.00 FE2 A:FES1000 0.0 154.5 1.0 S1 A:FES1000 2.2 144.7 1.0 S2 A:FES1000 2.2 140.8 1.0 SG A:CYS51 2.2 138.0 1.0 SG A:CYS63 2.3 164.1 1.0 FE1 A:FES1000 2.7 145.8 1.0 CB A:CYS63 3.3 149.0 1.0 CB A:CYS51 3.8 124.4 1.0 CG A:ARG61 4.0 134.5 1.0 CB A:ARG61 4.3 131.7 1.0 SG A:CYS48 4.3 152.2 1.0 SG A:CYS37 4.3 139.1 1.0 N A:CYS63 4.4 148.2 1.0 CD A:ARG61 4.4 131.0 1.0 CA A:CYS63 4.4 145.0 1.0 N A:CYS51 4.6 130.4 1.0 CA A:GLU46 4.6 142.8 1.0 N A:GLU46 4.8 138.6 1.0 CA A:CYS51 4.8 124.3 1.0 N A:ASP49 4.9 136.3 1.0 CB A:TYR38 5.0 122.1 1.0

Iron binding site 3 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:96.5 occ:1.00 FE1 A:SF41001 0.0 96.5 1.0 SG A:CYS99 2.2 133.8 1.0 S3 A:SF41001 2.3 133.5 1.0 S2 A:SF41001 2.3 130.3 1.0 S4 A:SF41001 2.3 121.0 1.0 FE4 A:SF41001 2.8 93.0 1.0 FE2 A:SF41001 2.8 105.9 1.0 FE3 A:SF41001 2.8 117.7 1.0 CB A:CYS99 3.2 121.7 1.0 N A:CYS99 3.4 116.6 1.0 CA A:CYS99 3.4 118.6 1.0 CG A:LEU97 3.9 114.9 1.0 CB A:HIS112 3.9 120.8 1.0 CD1 A:LEU97 3.9 118.5 1.0 S1 A:SF41001 4.0 146.6 1.0 N A:TYR98 4.1 115.4 1.0 CA A:LEU97 4.3 122.2 1.0 C A:TYR98 4.4 112.9 1.0 C A:LEU97 4.5 126.5 1.0 CB A:LEU97 4.7 114.5 1.0 CG A:HIS112 4.7 117.7 1.0 CB A:CYS102 4.8 116.9 1.0 SG A:CYS109 4.8 125.1 1.0 SG A:CYS102 4.8 115.0 1.0 ND1 A:HIS112 4.8 113.2 1.0 CA A:HIS112 4.8 117.6 1.0 CA A:TYR98 4.9 111.1 1.0 CD2 A:LEU97 4.9 129.6 1.0 C A:CYS99 4.9 125.7 1.0 NE2 A:HIS95 5.0 117.3 1.0

Iron binding site 4 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:105.9 occ:1.00 FE2 A:SF41001 0.0 105.9 1.0 SG A:CYS102 2.2 115.0 1.0 S4 A:SF41001 2.3 121.0 1.0 S1 A:SF41001 2.3 146.6 1.0 S3 A:SF41001 2.3 133.5 1.0 FE3 A:SF41001 2.8 117.7 1.0 FE1 A:SF41001 2.8 96.5 1.0 FE4 A:SF41001 2.8 93.0 1.0 CB A:CYS102 3.0 116.9 1.0 S2 A:SF41001 4.0 130.3 1.0 CB A:TYR104 4.0 112.2 1.0 OD1 A:ASN204 4.2 113.2 1.0 CA A:CYS99 4.3 118.6 1.0 C A:TYR104 4.3 121.0 1.0 N A:ASN105 4.3 128.2 1.0 N A:TYR104 4.4 113.4 1.0 CA A:CYS102 4.4 111.8 1.0 CA A:TYR104 4.4 109.4 1.0 N A:CYS99 4.4 116.6 1.0 CG A:ASN204 4.5 103.6 1.0 NE2 A:HIS95 4.7 117.3 1.0 SG A:CYS109 4.7 125.1 1.0 SG A:CYS99 4.7 133.8 1.0 CD1 A:TYR98 4.7 113.8 1.0 C A:CYS102 4.8 113.3 1.0 CB A:ASN204 4.8 98.3 1.0 CB A:CYS99 4.8 121.7 1.0 O A:TYR104 4.8 129.2 1.0 C A:TYR98 4.8 112.9 1.0 CE1 A:TYR98 4.9 117.7 1.0 N A:TYR98 4.9 115.4 1.0 CB A:ASN105 5.0 115.4 1.0

Iron binding site 5 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:117.7 occ:1.00 FE3 A:SF41001 0.0 117.7 1.0 SG A:CYS109 2.1 125.1 1.0 S1 A:SF41001 2.3 146.6 1.0 S2 A:SF41001 2.3 130.3 1.0 S4 A:SF41001 2.3 121.0 1.0 FE4 A:SF41001 2.8 93.0 1.0 FE2 A:SF41001 2.8 105.9 1.0 FE1 A:SF41001 2.8 96.5 1.0 CB A:CYS109 3.0 106.3 1.0 CB A:HIS112 3.6 120.8 1.0 S3 A:SF41001 4.0 133.5 1.0 O A:TYR104 4.2 129.2 1.0 N A:HIS112 4.2 110.5 1.0 CB A:TYR104 4.3 112.2 1.0 C A:TYR104 4.4 121.0 1.0 CA A:CYS109 4.4 105.8 1.0 CA A:HIS112 4.5 117.6 1.0 CG A:HIS112 4.6 117.7 1.0 SG A:CYS99 4.6 133.8 1.0 SG A:CYS102 4.7 115.0 1.0 N A:ASN105 4.8 128.2 1.0 CB A:CYS203 4.8 134.2 1.0 CD1 A:TYR104 4.8 117.0 1.0 NE2 A:HIS95 4.8 117.3 1.0 CB A:ILE111 4.9 106.8 1.0 O A:CYS109 4.9 126.5 1.0 C A:CYS109 4.9 115.6 1.0 CA A:CYS203 4.9 115.7 1.0 CA A:TYR104 5.0 109.4 1.0 CG A:TYR104 5.0 114.2 1.0

Iron binding site 6 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:93.0 occ:1.00 FE4 A:SF41001 0.0 93.0 1.0 NE2 A:HIS95 2.3 117.3 1.0 S2 A:SF41001 2.3 130.3 1.0 S3 A:SF41001 2.3 133.5 1.0 S1 A:SF41001 2.3 146.6 1.0 FE3 A:SF41001 2.8 117.7 1.0 FE1 A:SF41001 2.8 96.5 1.0 FE2 A:SF41001 2.8 105.9 1.0 CD2 A:HIS95 3.0 109.2 1.0 CE1 A:HIS95 3.4 116.9 1.0 S4 A:SF41001 4.0 121.0 1.0 NE2 A:GLN147 4.0 124.3 1.0 OD1 A:ASN204 4.0 113.2 1.0 CD1 A:LEU97 4.1 118.5 1.0 CG A:HIS95 4.2 101.5 1.0 CA A:LEU97 4.2 122.2 1.0 SG A:CYS109 4.2 125.1 1.0 ND1 A:HIS95 4.4 109.0 1.0 CB A:CYS203 4.5 134.2 1.0 CG A:LEU97 4.6 114.9 1.0 CG2 A:ILE111 4.7 100.4 1.0 N A:LEU97 4.7 124.7 1.0 SG A:CYS102 4.8 115.0 1.0 CB A:LEU97 4.8 114.5 1.0 N A:TYR98 4.8 115.4 1.0 SG A:CYS99 4.9 133.8 1.0 CB A:ILE111 4.9 106.8 1.0 CG A:ASN204 5.0 103.6 1.0

Iron binding site 7 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:113.2 occ:1.00 FE1 A:SF41002 0.0 113.2 1.0 SG A:CYS151 2.2 124.7 1.0 S4 A:SF41002 2.3 148.3 1.0 S3 A:SF41002 2.3 120.8 1.0 S2 A:SF41002 2.3 115.7 1.0 FE2 A:SF41002 2.8 132.8 1.0 FE3 A:SF41002 2.8 118.0 1.0 FE4 A:SF41002 2.8 104.6 1.0 CB A:CYS151 3.6 125.2 1.0 CD A:PRO202 3.7 104.0 1.0 N A:CYS151 3.8 120.2 1.0 S1 A:SF41002 4.0 129.6 1.0 CG1 A:ILE149 4.1 107.8 1.0 N A:GLY152 4.1 114.6 1.0 CA A:CYS151 4.1 121.9 1.0 SG A:CYS201 4.4 129.9 1.0 CG A:PRO202 4.4 112.9 1.0 C A:CYS151 4.5 122.9 1.0 N A:ARG153 4.6 102.6 1.0 N A:LEU150 4.6 108.6 1.0 N A:ILE149 4.7 100.6 1.0 CD1 A:ILE149 4.7 112.4 1.0 SG A:CYS148 4.7 135.9 1.0 C A:LEU150 4.8 122.1 1.0 C A:ILE149 4.9 112.9 1.0 CA A:CYS201 5.0 95.8 1.0 CB A:CYS201 5.0 95.2 1.0

Iron binding site 8 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:132.8 occ:1.00 FE2 A:SF41002 0.0 132.8 1.0 SG A:CYS148 2.1 135.9 1.0 S4 A:SF41002 2.3 148.3 1.0 S3 A:SF41002 2.3 120.8 1.0 S1 A:SF41002 2.3 129.6 1.0 FE3 A:SF41002 2.8 118.0 1.0 FE1 A:SF41002 2.8 113.2 1.0 FE4 A:SF41002 2.8 104.6 1.0 CB A:CYS148 3.2 118.8 1.0 CA A:CYS148 3.5 108.4 1.0 N A:ILE149 3.5 100.6 1.0 N A:LEU150 3.8 108.6 1.0 C A:CYS148 3.9 110.1 1.0 S2 A:SF41002 4.0 115.7 1.0 CB A:ALA205 4.1 110.7 1.0 CG2 A:VAL178 4.2 117.4 1.0 CA A:LEU150 4.4 114.7 1.0 C A:ILE149 4.5 112.9 1.0 CA A:ILE149 4.5 108.8 1.0 CE1 A:TYR143 4.6 112.7 1.0 N A:CYS151 4.6 120.2 1.0 CG1 A:ILE149 4.8 107.8 1.0 N A:CYS148 4.8 106.8 1.0 OH A:TYR143 4.8 114.5 1.0 SG A:CYS151 4.9 124.7 1.0 O A:CYS148 4.9 126.0 1.0

Iron binding site 9 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:118.0 occ:1.00 FE3 A:SF41002 0.0 118.0 1.0 S1 A:SF41002 2.3 129.6 1.0 S4 A:SF41002 2.3 148.3 1.0 S2 A:SF41002 2.3 115.7 1.0 SG A:CYS201 2.7 129.9 1.0 FE2 A:SF41002 2.8 132.8 1.0 FE4 A:SF41002 2.8 104.6 1.0 FE1 A:SF41002 2.8 113.2 1.0 CB A:CYS201 3.4 95.2 1.0 CB A:ALA205 3.7 110.7 1.0 S3 A:SF41002 4.0 120.8 1.0 N A:MET206 4.0 98.0 1.0 CB A:MET206 4.0 105.2 1.0 CA A:CYS201 4.2 95.8 1.0 CE A:MET206 4.5 115.2 1.0 CD A:PRO202 4.5 104.0 1.0 SG A:CYS154 4.6 116.8 1.0 C A:ALA205 4.6 121.9 1.0 CA A:MET206 4.6 103.9 1.0 CA A:ALA205 4.7 113.8 1.0 SG A:CYS148 4.7 135.9 1.0 SG A:CYS151 4.8 124.7 1.0 CB A:CYS154 4.8 114.1 1.0

Iron binding site 10 out of 18 in the Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Force Lacking the Helical Membrane Plug-in (Hmp; DUF1641) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:104.6 occ:1.00 FE4 A:SF41002 0.0 104.6 1.0 S2 A:SF41002 2.3 115.7 1.0 S3 A:SF41002 2.3 120.8 1.0 S1 A:SF41002 2.3 129.6 1.0 SG A:CYS154 2.6 116.8 1.0 FE3 A:SF41002 2.8 118.0 1.0 FE1 A:SF41002 2.8 113.2 1.0 FE2 A:SF41002 2.8 132.8 1.0 CB A:CYS154 3.6 114.1 1.0 CG2 A:VAL178 3.8 117.4 1.0 S4 A:SF41002 4.0 148.3 1.0 N A:CYS154 4.0 107.6 1.0 N A:GLY152 4.1 114.6 1.0 SG A:CYS151 4.2 124.7 1.0 SG A:CYS148 4.3 135.9 1.0 CA A:GLY152 4.4 121.6 1.0 CA A:CYS154 4.4 104.6 1.0 N A:ARG153 4.4 102.6 1.0 CE A:MET206 4.7 115.2 1.0 C A:GLY152 4.8 119.5 1.0 CB A:VAL178 4.9 110.0 1.0 N A:CYS151 5.0 120.2 1.0

M.Broc, M.V.Cherrier, A.Uzel, R.Arias-Cartin, P.Arnoux, G.Brasseur, F.Seduk, B.Guigliarelli, P.Legrand, F.Pierrel, G.Schoehn, M.J.Mate, L.Martin, S.Grimaldi, Y.Nicolet, A.Magalon, A.Walburger. A Scaffold For Quinone Channeling Between Membrane and Soluble Bacterial Oxidoreductases. Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985
PubMed: 40855134
DOI: 10.1038/S41594-025-01607-4