Iron in PDB 9gmc: Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla

The structure of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla, PDB code: 9gmc was solved by E.De La Mora, J.Ruel, A.Usclat, L.Martin, P.Amara, B.Morinaka, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.51 / 1.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.692, 62.467, 113.138, 90, 117.33, 90
R / Rfree (%)	17.8 / 21.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla (pdb code 9gmc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla, PDB code: 9gmc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:17.8 occ:1.00 FE1 A:SF41001 0.0 17.8 1.0 OXT A:SAH1003 2.2 18.6 1.0 S4 A:SF41001 2.3 17.6 1.0 S3 A:SF41001 2.3 16.9 1.0 S2 A:SF41001 2.4 16.8 1.0 N A:SAH1003 2.5 16.2 1.0 FE3 A:SF41001 2.8 15.6 1.0 FE2 A:SF41001 2.8 16.8 1.0 FE4 A:SF41001 2.8 16.1 1.0 C A:SAH1003 3.1 17.6 1.0 SD A:SAH1003 3.2 16.5 1.0 CA A:SAH1003 3.2 16.6 1.0 CG A:SAH1003 3.7 16.3 1.0 CB A:SAH1003 4.0 16.1 1.0 S1 A:SF41001 4.0 16.5 1.0 NH2 A:ARG141 4.1 15.8 1.0 O A:SAH1003 4.2 17.2 1.0 SG A:CYS18 4.6 16.4 1.0 C2' A:SAH1003 4.6 19.0 1.0 O A:GLY73 4.7 12.8 1.0 C3' A:SAH1003 4.8 18.9 1.0 CB A:ASN107 4.8 14.0 1.0 C5' A:SAH1003 4.8 18.0 1.0 SG A:CYS22 4.8 17.0 1.0 NH1 A:ARG141 4.9 13.6 1.0 SG A:CYS25 4.9 18.2 1.0 CZ A:ARG141 4.9 15.6 1.0

Iron binding site 2 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:16.8 occ:1.00 FE2 A:SF41001 0.0 16.8 1.0 SG A:CYS22 2.2 17.0 1.0 S4 A:SF41001 2.3 17.6 1.0 S3 A:SF41001 2.3 16.9 1.0 S1 A:SF41001 2.3 16.5 1.0 FE3 A:SF41001 2.7 15.6 1.0 FE4 A:SF41001 2.8 16.1 1.0 FE1 A:SF41001 2.8 17.8 1.0 CB A:CYS22 3.1 17.2 1.0 NH2 A:ARG141 3.8 15.8 1.0 S2 A:SF41001 3.9 16.8 1.0 N A:CYS22 4.0 17.7 1.0 CZ A:ARG141 4.1 15.6 1.0 CA A:CYS22 4.1 17.8 1.0 NH1 A:ARG141 4.2 13.6 1.0 OXT A:SAH1003 4.3 18.6 1.0 CB A:LEU20 4.3 16.8 1.0 SG A:CYS18 4.6 16.4 1.0 SG A:CYS25 4.7 18.2 1.0 CB A:CYS25 4.7 17.7 1.0 CD1 A:LEU20 5.0 17.5 1.0 NE A:ARG141 5.0 15.1 1.0 C A:LEU20 5.0 16.2 1.0

Iron binding site 3 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:15.6 occ:1.00 FE3 A:SF41001 0.0 15.6 1.0 S1 A:SF41001 2.3 16.5 1.0 S2 A:SF41001 2.3 16.8 1.0 SG A:CYS18 2.3 16.4 1.0 S4 A:SF41001 2.3 17.6 1.0 FE4 A:SF41001 2.7 16.1 1.0 FE2 A:SF41001 2.7 16.8 1.0 FE1 A:SF41001 2.8 17.8 1.0 CB A:CYS18 3.3 15.4 1.0 S3 A:SF41001 3.9 16.9 1.0 N A:SAH1003 3.9 16.2 1.0 CE2 A:TYR28 4.1 17.3 1.0 O A:LEU20 4.3 15.9 1.0 O A:HOH1125 4.5 17.8 1.0 CB A:LEU20 4.5 16.8 1.0 ND2 A:ASN107 4.6 14.0 1.0 C A:LEU20 4.6 16.2 1.0 CD2 A:TYR28 4.7 16.2 1.0 SG A:CYS25 4.7 18.2 1.0 CA A:CYS18 4.7 14.8 1.0 SG A:CYS22 4.7 17.0 1.0 N A:LEU20 4.8 17.3 1.0 OXT A:SAH1003 4.8 18.6 1.0 CA A:LEU20 4.9 16.4 1.0 C A:GLY73 4.9 14.3 1.0

Iron binding site 4 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:16.1 occ:1.00 FE4 A:SF41001 0.0 16.1 1.0 SG A:CYS25 2.2 18.2 1.0 S2 A:SF41001 2.3 16.8 1.0 S1 A:SF41001 2.3 16.5 1.0 S3 A:SF41001 2.3 16.9 1.0 FE3 A:SF41001 2.7 15.6 1.0 FE2 A:SF41001 2.8 16.8 1.0 FE1 A:SF41001 2.8 17.8 1.0 CB A:CYS25 3.2 17.7 1.0 S4 A:SF41001 3.9 17.6 1.0 CD2 A:TYR28 4.1 16.2 1.0 CE2 A:TYR28 4.1 17.3 1.0 CE A:MET27 4.3 15.7 0.3 CA A:CYS25 4.4 17.3 1.0 SD A:SAH1003 4.4 16.5 1.0 CB A:CYS22 4.7 17.2 1.0 CE A:MET27 4.7 18.1 0.7 SG A:CYS22 4.7 17.0 1.0 N A:SAH1003 4.8 16.2 1.0 C8 A:SAH1003 4.8 17.4 1.0 SG A:CYS18 4.9 16.4 1.0 OXT A:SAH1003 5.0 18.6 1.0

Iron binding site 5 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:20.2 occ:1.00 FE1 A:SF41002 0.0 20.2 1.0 S4 A:SF41002 2.3 19.9 1.0 S3 A:SF41002 2.3 19.8 1.0 SG A:CYS327 2.3 24.4 1.0 S2 A:SF41002 2.3 20.6 1.0 FE2 A:SF41002 2.7 18.8 1.0 FE4 A:SF41002 2.7 19.9 1.0 FE3 A:SF41002 2.8 19.6 1.0 CB A:CYS327 3.1 26.1 1.0 S1 A:SF41002 3.9 19.7 1.0 CG2 A:VAL329 3.9 26.2 1.0 O A:HOH1382 4.4 46.7 1.0 CA A:CYS327 4.6 26.7 1.0 CA A:CYS324 4.6 23.1 1.0 CB A:CYS333 4.7 19.0 1.0 N A:VAL330 4.7 23.8 1.0 SG A:CYS333 4.7 18.8 1.0 CD2 A:PHE358 4.7 24.1 1.0 SG A:CYS354 4.8 18.3 1.0 SG A:CYS324 4.8 19.6 1.0 C A:VAL329 5.0 24.9 1.0 CA A:VAL330 5.0 23.5 1.0

Iron binding site 6 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:18.8 occ:1.00 FE2 A:SF41002 0.0 18.8 1.0 S3 A:SF41002 2.3 19.8 1.0 SG A:CYS333 2.3 18.8 1.0 S4 A:SF41002 2.3 19.9 1.0 S1 A:SF41002 2.3 19.7 1.0 FE1 A:SF41002 2.7 20.2 1.0 FE3 A:SF41002 2.8 19.6 1.0 FE4 A:SF41002 2.8 19.9 1.0 CB A:CYS333 3.1 19.0 1.0 S2 A:SF41002 3.9 20.6 1.0 N A:GLY335 4.0 20.2 1.0 CA A:GLY335 4.1 21.7 1.0 CA A:CYS333 4.5 19.9 1.0 CB A:MET357 4.6 18.7 1.0 C A:GLY335 4.6 22.2 1.0 N A:GLY336 4.7 22.6 1.0 CG2 A:THR351 4.7 15.8 1.0 C A:CYS333 4.7 19.9 1.0 SG A:CYS324 4.7 19.6 1.0 CG2 A:VAL329 4.8 26.2 1.0 N A:GLY334 4.9 20.1 1.0 SG A:CYS354 4.9 18.3 1.0 SG A:CYS327 4.9 24.4 1.0

Iron binding site 7 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:19.6 occ:1.00 FE3 A:SF41002 0.0 19.6 1.0 SG A:CYS324 2.3 19.6 1.0 S1 A:SF41002 2.3 19.7 1.0 S2 A:SF41002 2.3 20.6 1.0 S4 A:SF41002 2.3 19.9 1.0 FE4 A:SF41002 2.7 19.9 1.0 FE2 A:SF41002 2.8 18.8 1.0 FE1 A:SF41002 2.8 20.2 1.0 CB A:CYS324 3.2 21.8 1.0 CA A:CYS324 3.5 23.1 1.0 S3 A:SF41002 3.9 19.8 1.0 CG A:GLN350 4.1 21.5 0.8 CB A:GLN350 4.1 18.8 0.2 N A:CYS324 4.1 23.9 1.0 CA A:GLY335 4.2 21.7 1.0 CB A:GLN350 4.5 19.1 0.8 N A:GLY335 4.5 20.2 1.0 CA A:GLN350 4.6 17.1 0.2 CA A:GLN350 4.6 17.2 0.8 SG A:CYS354 4.7 18.3 1.0 CB A:CYS327 4.7 26.1 1.0 C A:CYS324 4.8 24.3 1.0 SG A:CYS333 4.8 18.8 1.0 SG A:CYS327 4.8 24.4 1.0 C A:THR323 4.9 25.8 1.0

Iron binding site 8 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:19.9 occ:1.00 FE4 A:SF41002 0.0 19.9 1.0 S2 A:SF41002 2.3 20.6 1.0 SG A:CYS354 2.3 18.3 1.0 S1 A:SF41002 2.3 19.7 1.0 S3 A:SF41002 2.3 19.8 1.0 FE3 A:SF41002 2.7 19.6 1.0 FE1 A:SF41002 2.7 20.2 1.0 FE2 A:SF41002 2.8 18.8 1.0 CB A:CYS354 3.2 16.8 1.0 CA A:CYS354 3.7 17.5 1.0 S4 A:SF41002 3.9 19.9 1.0 O A:CYS354 4.0 19.1 1.0 C A:CYS354 4.2 18.8 1.0 NE2 A:GLN350 4.2 28.4 0.8 CB A:GLN350 4.4 18.8 0.2 CG A:GLN350 4.5 21.5 0.8 OE1 A:GLN350 4.5 25.3 0.2 CB A:GLN350 4.6 19.1 0.8 SG A:CYS327 4.8 24.4 1.0 SG A:CYS324 4.8 19.6 1.0 SG A:CYS333 4.9 18.8 1.0 CD A:GLN350 4.9 25.2 0.8

Iron binding site 9 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1001 b:19.0 occ:1.00 FE1 C:SF41001 0.0 19.0 1.0 SG C:CYS22 2.2 17.7 1.0 S4 C:SF41001 2.3 18.7 1.0 S2 C:SF41001 2.3 18.8 1.0 S3 C:SF41001 2.3 19.5 1.0 FE4 C:SF41001 2.7 18.6 1.0 FE3 C:SF41001 2.7 19.0 1.0 FE2 C:SF41001 2.8 21.5 1.0 CB C:CYS22 3.1 19.0 1.0 NH2 C:ARG141 3.8 19.3 1.0 S1 C:SF41001 3.9 19.7 1.0 N C:CYS22 4.0 18.6 1.0 CZ C:ARG141 4.1 20.6 1.0 OXT C:SAH1003 4.1 21.3 1.0 NH1 C:ARG141 4.1 18.1 1.0 CA C:CYS22 4.2 18.9 1.0 CB C:LEU20 4.3 18.8 1.0 SG C:CYS18 4.6 19.3 1.0 CB C:CYS25 4.7 15.9 1.0 SG C:CYS25 4.7 17.9 1.0 NE C:ARG141 4.9 19.6 1.0 N C:SAH1003 5.0 18.3 1.0 CD1 C:LEU20 5.0 20.3 1.0

Iron binding site 10 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the R3A Mutant of Chla within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1001 b:21.5 occ:1.00 FE2 C:SF41001 0.0 21.5 1.0 OXT C:SAH1003 2.0 21.3 1.0 S3 C:SF41001 2.3 19.5 1.0 S4 C:SF41001 2.4 18.7 1.0 S1 C:SF41001 2.4 19.7 1.0 N C:SAH1003 2.4 18.3 1.0 FE4 C:SF41001 2.8 18.6 1.0 FE1 C:SF41001 2.8 19.0 1.0 FE3 C:SF41001 2.8 19.0 1.0 C C:SAH1003 2.9 19.6 1.0 CA C:SAH1003 3.1 18.8 1.0 SD C:SAH1003 3.3 19.6 1.0 CG C:SAH1003 3.6 19.8 1.0 CB C:SAH1003 3.9 18.7 1.0 S2 C:SF41001 4.0 18.8 1.0 NH2 C:ARG141 4.1 19.3 1.0 O C:SAH1003 4.1 19.4 1.0 SG C:CYS18 4.5 19.3 1.0 O C:GLY73 4.7 19.1 1.0 C2' C:SAH1003 4.7 18.7 1.0 C3' C:SAH1003 4.8 19.0 1.0 CB C:ASN107 4.8 17.4 1.0 C5' C:SAH1003 4.8 19.5 1.0 SG C:CYS22 4.9 17.7 1.0 NH1 C:ARG141 4.9 18.1 1.0 CZ C:ARG141 4.9 20.6 1.0 SG C:CYS25 5.0 17.9 1.0 ND2 C:ASN107 5.0 18.6 1.0

J.Ruel, T.Q.N.Nguyen, Y.Morishita, A.Usclat, L.Martin, P.Amara, S.Kieffer-Jaquinod, M.C.Stefanoiu, E.De La Mora, B.I.Morinaka, Y.Nicolet. Peptide Recognition and Mechanism of the Radical S -Adenosyl-L-Methionine Multiple Cyclophane Synthase Chlb. J.Am.Chem.Soc. V. 147 16850 2025.
ISSN: ESSN 1520-5126
PubMed: 40354606
DOI: 10.1021/JACS.4C16004