Iron in PDB 7tom: X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound

The structure of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound, PDB code: 7tom was solved by C.T.Lloyd, S.J.Booker, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.54 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.609, 77.158, 112.817, 90, 90, 90
R / Rfree (%)	15 / 19.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound (pdb code 7tom). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound, PDB code: 7tom:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:22.1 occ:1.00 ND1 A:HIS36 2.1 26.5 1.0 SG A:CYS12 2.3 22.3 1.0 SG A:CYS9 2.3 19.1 1.0 SG A:CYS33 2.4 22.1 1.0 CE1 A:HIS36 3.0 29.4 1.0 CB A:CYS9 3.1 19.7 1.0 CG A:HIS36 3.2 30.1 1.0 CB A:CYS33 3.4 20.9 1.0 CB A:CYS12 3.6 26.4 1.0 CB A:HIS36 3.6 23.7 1.0 N A:CYS12 3.8 20.2 1.0 O A:HOH735 4.0 28.6 1.0 N A:HIS36 4.1 26.9 1.0 NE2 A:HIS36 4.1 27.0 1.0 CD2 A:HIS36 4.2 28.5 1.0 CA A:CYS12 4.3 21.3 1.0 CB A:ILE11 4.4 24.2 1.0 CA A:HIS36 4.5 18.3 1.0 CA A:CYS9 4.5 20.6 1.0 CB A:GLU35 4.7 25.6 1.0 C A:ILE11 4.8 27.2 1.0 CA A:CYS33 4.8 18.3 1.0 CA A:ILE11 4.9 25.7 1.0 N A:ILE11 4.9 25.5 1.0 C A:CYS12 5.0 16.1 1.0 CG2 A:ILE11 5.0 29.4 1.0

Iron binding site 2 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:14.8 occ:0.97 FE1 A:SF4602 0.0 14.8 1.0 SG A:CYS98 2.3 15.2 1.0 S4 A:SF4602 2.3 18.0 1.0 S2 A:SF4602 2.3 13.3 0.9 S3 A:SF4602 2.3 13.4 0.9 FE2 A:SF4602 2.6 17.4 1.0 FE3 A:SF4602 2.7 10.8 0.8 FE4 A:SF4602 2.9 7.6 0.7 CB A:CYS98 3.3 13.7 1.0 N A:MET606 3.8 17.0 0.9 S1 A:SF4602 3.9 14.4 0.9 CB A:ALA109 4.3 24.2 1.0 CB A:LEU100 4.4 19.2 1.0 O A:LEU100 4.5 21.2 1.0 SG A:CYS102 4.6 18.1 1.0 CA A:CYS98 4.7 15.8 1.0 ND2 A:ASN173 4.8 10.9 1.0 C A:LEU100 4.8 22.5 1.0 SG A:CYS105 4.8 15.7 1.0 O A:MET606 4.9 14.9 0.9 N A:LEU100 4.9 15.6 1.0 C A:GLY145 4.9 11.9 1.0 CA A:LEU100 5.0 16.7 1.0 N A:GLU146 5.0 12.8 1.0

Iron binding site 3 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:17.4 occ:1.00 FE2 A:SF4602 0.0 17.4 1.0 S3 A:SF4602 2.2 13.4 0.9 S4 A:SF4602 2.3 18.0 1.0 SG A:CYS102 2.3 18.1 1.0 S1 A:SF4602 2.3 14.4 0.9 FE1 A:SF4602 2.6 14.8 1.0 FE3 A:SF4602 2.7 10.8 0.8 FE4 A:SF4602 2.9 7.6 0.7 CB A:CYS102 3.2 17.1 1.0 S2 A:SF4602 3.8 13.3 0.9 NE2 A:GLN197 3.9 16.8 1.0 NH1 A:ARG210 4.1 17.9 1.0 N A:CYS102 4.1 23.2 1.0 O A:MET606 4.2 14.9 0.9 CA A:CYS102 4.3 16.6 1.0 CB A:LEU100 4.4 19.2 1.0 SG A:CYS98 4.5 15.2 1.0 CD1 A:LEU100 4.6 14.2 1.0 CB A:CYS105 4.6 13.1 1.0 SG A:CYS105 4.7 15.7 1.0 O A:ILE104 4.8 16.3 1.0 N A:MET606 4.8 17.0 0.9

Iron binding site 4 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:10.8 occ:0.79 FE3 A:SF4602 0.0 10.8 0.8 S2 A:SF4602 2.2 13.3 0.9 S1 A:SF4602 2.3 14.4 0.9 SG A:CYS105 2.3 15.7 1.0 S4 A:SF4602 2.4 18.0 1.0 FE2 A:SF4602 2.7 17.4 1.0 FE1 A:SF4602 2.7 14.8 1.0 FE4 A:SF4602 2.8 7.6 0.7 CB A:CYS105 3.2 13.1 1.0 S3 A:SF4602 3.8 13.4 0.9 CE A:MET606 3.9 14.1 0.9 CA A:CYS105 4.1 19.1 1.0 CB A:ALA109 4.1 24.2 1.0 SD A:MET606 4.2 15.2 0.9 SG A:CYS102 4.7 18.1 1.0 NH2 A:ARG275 4.7 16.7 1.0 N A:MET606 4.7 17.0 0.9 CB A:CYS102 4.8 17.1 1.0 N A:ALA109 4.8 22.8 1.0 C A:CYS105 4.9 20.0 1.0 SG A:CYS98 4.9 15.2 1.0 O A:MET606 4.9 14.9 0.9 O A:ILE104 5.0 16.3 1.0

Iron binding site 5 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:7.6 occ:0.69 FE4 A:SF4602 0.0 7.6 0.7 S1 A:SF4602 2.3 14.4 0.9 O A:MET606 2.3 14.9 0.9 N A:MET606 2.3 17.0 0.9 S3 A:SF4602 2.4 13.4 0.9 S2 A:SF4602 2.4 13.3 0.9 SD A:MET606 2.7 15.2 0.9 FE3 A:SF4602 2.8 10.8 0.8 FE1 A:SF4602 2.9 14.8 1.0 FE2 A:SF4602 2.9 17.4 1.0 C A:MET606 3.0 18.2 0.9 CA A:MET606 3.1 12.0 0.9 CG A:MET606 3.5 11.5 0.9 CE A:MET606 3.7 14.1 0.9 CB A:MET606 3.9 10.0 0.9 NE2 A:GLN197 4.1 16.8 1.0 S4 A:SF4602 4.1 18.0 1.0 OXT A:MET606 4.2 15.4 0.9 O A:GLY145 4.6 11.3 1.0 SG A:CYS98 4.7 15.2 1.0 SG A:CYS105 4.9 15.7 1.0 C2' A:5AD605 4.9 13.9 1.0 SG A:CYS102 5.0 18.1 1.0

Iron binding site 6 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:11.8 occ:1.00 FE1 A:SF4603 0.0 11.8 1.0 SG A:CYS77 2.3 14.2 1.0 S2 A:SF4603 2.3 12.5 1.0 S3 A:SF4603 2.3 11.8 1.0 S4 A:SF4603 2.3 12.0 1.0 FE2 A:SF4603 2.7 14.9 1.0 FE4 A:SF4603 2.7 12.8 1.0 FE3 A:SF4603 2.7 13.6 1.0 CB A:CYS77 3.3 7.5 1.0 CA A:CYS77 3.5 9.8 1.0 N A:CYS77 3.6 10.2 1.0 S1 A:SF4603 3.9 14.6 1.0 CD A:PRO468 4.3 8.7 1.0 C A:ASP76 4.3 16.6 1.0 CG A:PRO468 4.3 10.4 1.0 ND1 A:HIS83 4.4 9.8 1.0 SG A:CYS73 4.7 14.8 1.0 N A:ASP76 4.8 11.9 1.0 CA A:PRO74 4.8 17.4 1.0 O A:ASP76 4.8 18.1 1.0 C A:PRO74 4.8 16.6 1.0 O A:PRO74 4.9 17.3 1.0 O A:HOH707 4.9 31.1 1.0 CG2 A:THR471 4.9 11.3 1.0 OG1 A:THR471 4.9 12.0 1.0 SG A:CYS80 4.9 13.6 1.0 C A:CYS77 4.9 11.3 1.0

Iron binding site 7 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:14.9 occ:1.00 FE2 A:SF4603 0.0 14.9 1.0 ND1 A:HIS83 2.0 9.8 1.0 S1 A:SF4603 2.3 14.6 1.0 S4 A:SF4603 2.3 12.0 1.0 S3 A:SF4603 2.4 11.8 1.0 FE4 A:SF4603 2.7 12.8 1.0 FE3 A:SF4603 2.7 13.6 1.0 FE1 A:SF4603 2.7 11.8 1.0 CE1 A:HIS83 3.0 11.7 1.0 CG A:HIS83 3.0 14.4 1.0 CB A:HIS83 3.4 9.5 1.0 S2 A:SF4603 3.8 12.5 1.0 CA A:HIS83 3.8 13.6 1.0 NE2 A:HIS83 4.1 9.8 1.0 CD2 A:HIS83 4.1 10.0 1.0 CG A:PRO468 4.3 10.4 1.0 CA A:MET453 4.4 12.8 1.0 N A:HIS83 4.4 13.2 1.0 O A:VAL452 4.5 9.8 1.0 SG A:CYS80 4.6 13.6 1.0 O A:MET453 4.6 11.2 1.0 SG A:CYS73 4.8 14.8 1.0 SG A:CYS77 4.8 14.2 1.0 C A:MET453 4.9 6.4 1.0 CD A:PRO468 4.9 8.7 1.0 CG A:MET453 5.0 16.7 1.0

Iron binding site 8 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:13.6 occ:1.00 FE3 A:SF4603 0.0 13.6 1.0 S1 A:SF4603 2.2 14.6 1.0 SG A:CYS73 2.3 14.8 1.0 S4 A:SF4603 2.3 12.0 1.0 S2 A:SF4603 2.3 12.5 1.0 FE2 A:SF4603 2.7 14.9 1.0 FE1 A:SF4603 2.7 11.8 1.0 FE4 A:SF4603 2.8 12.8 1.0 CB A:CYS73 3.1 13.6 1.0 CA A:CYS73 3.8 11.3 1.0 S3 A:SF4603 4.0 11.8 1.0 CA A:PRO74 4.1 17.4 1.0 CG A:MET453 4.2 16.7 1.0 ND1 A:HIS83 4.5 9.8 1.0 SG A:CYS77 4.6 14.2 1.0 CG1 A:VAL452 4.7 10.3 1.0 SG A:CYS80 4.8 13.6 1.0 C A:CYS73 4.8 15.6 1.0 N A:PRO74 4.8 15.4 1.0 CB A:PRO74 4.8 21.1 1.0 N A:CYS73 4.8 15.4 1.0 CA A:MET453 4.9 12.8 1.0 C A:PRO74 4.9 16.6 1.0

Iron binding site 9 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:12.8 occ:1.00 FE4 A:SF4603 0.0 12.8 1.0 S2 A:SF4603 2.2 12.5 1.0 SG A:CYS80 2.3 13.6 1.0 S3 A:SF4603 2.3 11.8 1.0 S1 A:SF4603 2.3 14.6 1.0 FE2 A:SF4603 2.7 14.9 1.0 FE1 A:SF4603 2.7 11.8 1.0 FE3 A:SF4603 2.8 13.6 1.0 CB A:CYS80 3.4 13.4 1.0 S4 A:SF4603 3.9 12.0 1.0 N A:CYS80 4.0 12.6 1.0 CA A:CYS80 4.2 10.7 1.0 O A:HOH899 4.2 15.5 1.0 N A:HIS83 4.4 13.2 1.0 ND1 A:HIS83 4.4 9.8 1.0 CB A:HIS83 4.5 9.5 1.0 C A:ASP76 4.6 16.6 1.0 O A:ASP76 4.6 18.1 1.0 CB A:ASP76 4.6 13.7 1.0 N A:CYS77 4.6 10.2 1.0 C A:CYS80 4.7 12.5 1.0 CA A:HIS83 4.7 13.6 1.0 O A:CYS80 4.7 12.9 1.0 CA A:CYS77 4.8 9.8 1.0 SG A:CYS77 4.8 14.2 1.0 SG A:CYS73 4.9 14.8 1.0 C A:ASN82 4.9 16.0 1.0 CB A:CYS73 4.9 13.6 1.0 CG A:HIS83 4.9 14.4 1.0

Iron binding site 10 out of 13 in the X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of X-Ray Crystal Structure of Glycerol Dibiphytanyl Glycerol Tetraether - Macrocyclic Archaeol Synthase (Gdgt-Mas) From Methanocaldococcus Jannaschii with Bacterial Lipid Substrate Analog, 5'Deoxyadenosine, and Methionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe604 b:13.9 occ:0.83 FE1 A:SF4604 0.0 13.9 0.8 S A:SCN607 2.2 34.0 0.8 S4 A:SF4604 2.2 15.2 1.0 S2 A:SF4604 2.3 15.4 1.0 S3 A:SF4604 2.3 16.2 1.0 FE2 A:SF4604 2.6 14.5 1.0 FE4 A:SF4604 2.7 15.3 1.0 FE3 A:SF4604 2.8 15.0 1.0 C A:SCN607 3.1 34.3 0.8 S1 A:SF4604 3.8 14.2 1.0 CD1 A:PHE441 4.1 19.0 1.0 CE1 A:PHE441 4.1 28.8 1.0 N A:SCN607 4.1 37.4 0.8 CG1 A:ILE457 4.3 12.6 0.5 CD1 A:ILE457 4.4 9.4 0.5 CB A:CYS338 4.4 11.9 1.0 SG A:CYS338 4.6 12.7 1.0 SG A:CYS470 4.7 12.4 1.0 SG A:CYS455 4.7 11.6 1.0 CG1 A:ILE457 4.8 13.4 0.5 CB A:ILE457 4.9 8.0 0.5 CB A:ILE457 5.0 8.1 0.5

C.T.Lloyd, D.F.Iwig, B.Wang, M.Cossu, W.W.Metcalf, A.K.Boal, S.J.Booker. Discovery, Structure and Mechanism of A Tetraether Lipid Synthase. Nature V. 609 197 2022.
ISSN: ESSN 1476-4687
PubMed: 35882349
DOI: 10.1038/S41586-022-05120-2