Iron in PDB 8vpo: X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis

The structure of X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis, PDB code: 8vpo was solved by T.L.Grove, J.C.Lachowicz, C.Zizola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.88 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.172, 74.348, 91.765, 90, 90, 90
R / Rfree (%)	16.5 / 19.2

The binding sites of Iron atom in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis (pdb code 8vpo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis, PDB code: 8vpo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis


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 Tige From Paramaledivibacter Caminithermalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:15.3 occ:1.00 FE1 A:SF4501 0.0 15.3 1.0 S4 A:SF4501 2.3 15.1 1.0 S3 A:SF4501 2.3 15.7 1.0 S2 A:SF4501 2.3 15.7 1.0 SG A:CYS423 2.3 15.0 1.0 FE3 A:SF4501 2.7 16.1 1.0 FE4 A:SF4501 2.7 16.4 1.0 FE2 A:SF4501 2.8 15.9 1.0 CB A:CYS423 3.2 15.6 1.0 S1 A:SF4501 3.9 16.9 1.0 ND2 A:ASN410 4.1 16.2 1.0 N A:GLY425 4.2 15.0 1.0 O A:CYS423 4.3 16.9 1.0 CA A:GLY425 4.3 15.2 1.0 C A:CYS423 4.3 15.8 1.0 CA A:CYS423 4.4 15.2 1.0 CB A:LEU419 4.5 17.9 1.0 CD2 A:TYR449 4.5 14.4 1.0 SG A:CYS446 4.6 18.6 1.0 SG A:CYS417 4.8 15.5 1.0 CD1 A:LEU419 4.8 16.8 1.0 SG A:CYS414 4.9 17.9 1.0 O A:LEU419 4.9 15.8 1.0

Iron binding site 2 out of 8 in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis


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 Tige From Paramaledivibacter Caminithermalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:15.9 occ:1.00 FE2 A:SF4501 0.0 15.9 1.0 S3 A:SF4501 2.2 15.7 1.0 S1 A:SF4501 2.3 16.9 1.0 S4 A:SF4501 2.3 15.1 1.0 SG A:CYS414 2.3 17.9 1.0 FE4 A:SF4501 2.7 16.4 1.0 FE3 A:SF4501 2.7 16.1 1.0 FE1 A:SF4501 2.8 15.3 1.0 CB A:CYS414 3.3 16.2 1.0 ND2 A:ASN410 3.8 16.2 1.0 CA A:CYS414 3.8 15.4 1.0 S2 A:SF4501 3.9 15.7 1.0 CG A:MET441 4.3 15.9 1.0 O A:HOH811 4.4 18.1 1.0 N A:CYS414 4.6 16.5 1.0 SD A:MET441 4.6 17.3 1.0 SG A:CYS417 4.7 15.5 1.0 CB A:CYS417 4.7 15.0 1.0 SG A:CYS446 4.7 18.6 1.0 CG A:ASN410 4.8 14.2 1.0 SG A:CYS423 4.9 15.0 1.0 CB A:ASN410 4.9 13.6 1.0

Iron binding site 3 out of 8 in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis


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 Tige From Paramaledivibacter Caminithermalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:16.1 occ:1.00 FE3 A:SF4501 0.0 16.1 1.0 S2 A:SF4501 2.3 15.7 1.0 S4 A:SF4501 2.3 15.1 1.0 SG A:CYS417 2.3 15.5 1.0 S1 A:SF4501 2.3 16.9 1.0 FE4 A:SF4501 2.7 16.4 1.0 FE2 A:SF4501 2.7 15.9 1.0 FE1 A:SF4501 2.7 15.3 1.0 CB A:CYS417 3.2 15.0 1.0 S3 A:SF4501 3.8 15.7 1.0 O A:HOH645 4.0 35.7 1.0 CB A:LEU419 4.3 17.9 1.0 CA A:CYS417 4.6 16.4 1.0 N A:LEU419 4.6 15.7 1.0 SG A:CYS414 4.8 17.9 1.0 CE A:LYS450 4.8 32.4 1.0 SG A:CYS423 4.8 15.0 1.0 CA A:LEU419 4.8 14.3 1.0 C A:LEU419 4.8 15.6 1.0 SG A:CYS446 4.8 18.6 1.0 CG A:LEU419 4.9 14.4 1.0 CD A:LYS450 4.9 26.6 1.0 CB A:CYS414 4.9 16.2 1.0 CD1 A:LEU419 4.9 16.8 1.0 N A:ILE420 5.0 14.7 1.0 CA A:CYS414 5.0 15.4 1.0

Iron binding site 4 out of 8 in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis


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 Tige From Paramaledivibacter Caminithermalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:16.4 occ:1.00 FE4 A:SF4501 0.0 16.4 1.0 S1 A:SF4501 2.2 16.9 1.0 S3 A:SF4501 2.3 15.7 1.0 S2 A:SF4501 2.3 15.7 1.0 SG A:CYS446 2.3 18.6 1.0 FE2 A:SF4501 2.7 15.9 1.0 FE3 A:SF4501 2.7 16.1 1.0 FE1 A:SF4501 2.7 15.3 1.0 CB A:CYS446 3.1 16.5 1.0 S4 A:SF4501 3.8 15.1 1.0 CA A:CYS446 3.9 16.6 1.0 O A:HOH1029 4.1 36.7 1.0 O A:HOH885 4.6 22.3 1.0 CG A:MET441 4.6 15.9 1.0 CB A:MET441 4.7 16.8 1.0 SG A:CYS423 4.7 15.0 1.0 SG A:CYS417 4.7 15.5 1.0 SG A:CYS414 4.8 17.9 1.0 O A:HOH645 4.9 35.7 1.0 N A:CYS446 4.9 16.5 1.0

Iron binding site 5 out of 8 in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis


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 Tige From Paramaledivibacter Caminithermalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:18.2 occ:1.00 FE1 A:SF4502 0.0 18.2 1.0 OH A:TYR339 2.0 20.1 1.0 S2 A:SF4502 2.3 17.3 1.0 S3 A:SF4502 2.3 17.8 1.0 S4 A:SF4502 2.3 18.7 1.0 FE2 A:SF4502 2.6 18.3 1.0 FE3 A:SF4502 2.7 17.4 1.0 FE4 A:SF4502 2.7 17.4 1.0 CZ A:TYR339 2.9 18.3 1.0 CE2 A:TYR339 3.6 20.3 1.0 O A:HOH763 3.8 33.6 1.0 S1 A:SF4502 3.8 17.5 1.0 O A:HOH633 3.8 32.0 1.0 CE1 A:TYR339 3.9 18.1 1.0 O A:HOH660 4.6 20.8 1.0 SG A:CYS378 4.7 17.6 1.0 O A:HOH873 4.7 28.4 1.0 O A:HOH874 4.7 36.9 1.0 CD2 A:TYR339 4.8 15.1 1.0 SG A:CYS427 4.8 19.6 1.0 SG A:CYS360 4.8 17.7 1.0

Iron binding site 6 out of 8 in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis


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 Tige From Paramaledivibacter Caminithermalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:18.3 occ:1.00 FE2 A:SF4502 0.0 18.3 1.0 S1 A:SF4502 2.3 17.5 1.0 S3 A:SF4502 2.3 17.8 1.0 S4 A:SF4502 2.3 18.7 1.0 SG A:CYS378 2.3 17.6 1.0 FE1 A:SF4502 2.6 18.2 1.0 FE3 A:SF4502 2.7 17.4 1.0 FE4 A:SF4502 2.7 17.4 1.0 CB A:CYS378 3.3 17.3 1.0 S2 A:SF4502 3.8 17.3 1.0 O A:HOH898 4.3 27.9 1.0 CB A:ALA362 4.4 18.0 1.0 CA A:GLY380 4.4 21.6 1.0 OH A:TYR339 4.4 20.1 1.0 O A:HOH874 4.5 36.9 1.0 N A:GLY380 4.5 19.4 1.0 NE2 A:GLN366 4.7 19.4 1.0 CA A:CYS378 4.7 18.1 1.0 SG A:CYS360 4.8 17.7 1.0 SG A:CYS427 4.9 19.6 1.0 C A:GLY380 4.9 23.0 1.0

Iron binding site 7 out of 8 in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis


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 Tige From Paramaledivibacter Caminithermalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:17.4 occ:1.00 FE3 A:SF4502 0.0 17.4 1.0 S1 A:SF4502 2.3 17.5 1.0 S4 A:SF4502 2.3 18.7 1.0 S2 A:SF4502 2.3 17.3 1.0 SG A:CYS360 2.4 17.7 1.0 FE1 A:SF4502 2.7 18.2 1.0 FE2 A:SF4502 2.7 18.3 1.0 FE4 A:SF4502 2.8 17.4 1.0 CB A:CYS360 3.4 15.4 1.0 O A:HOH893 3.8 21.6 1.0 CA A:CYS360 3.9 15.4 1.0 S3 A:SF4502 3.9 17.8 1.0 CB A:ALA362 4.0 18.0 1.0 N A:ALA362 4.4 16.2 1.0 C A:CYS360 4.5 17.7 1.0 OH A:TYR339 4.5 20.1 1.0 O A:HOH660 4.5 20.8 1.0 CG A:LEU428 4.6 19.2 1.0 N A:SER361 4.6 19.2 1.0 O A:HOH671 4.7 24.8 1.0 N A:LEU428 4.8 15.4 1.0 SG A:CYS378 4.8 17.6 1.0 SG A:CYS427 4.8 19.6 1.0 CA A:ALA362 4.9 13.6 1.0 CD1 A:LEU428 4.9 20.0 1.0

Iron binding site 8 out of 8 in the X-Ray Crystal Structure of Tige From Paramaledivibacter Caminithermalis


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 Tige From Paramaledivibacter Caminithermalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:17.4 occ:1.00 FE4 A:SF4502 0.0 17.4 1.0 S3 A:SF4502 2.3 17.8 1.0 S2 A:SF4502 2.3 17.3 1.0 S1 A:SF4502 2.3 17.5 1.0 SG A:CYS427 2.3 19.6 1.0 FE1 A:SF4502 2.7 18.2 1.0 FE2 A:SF4502 2.7 18.3 1.0 FE3 A:SF4502 2.8 17.4 1.0 CB A:CYS427 3.4 20.1 1.0 CA A:CYS427 3.9 15.7 1.0 S4 A:SF4502 3.9 18.7 1.0 N A:LEU428 4.1 15.4 1.0 C A:CYS427 4.4 17.0 1.0 OH A:TYR339 4.5 20.1 1.0 O A:HOH635 4.5 28.6 1.0 O A:GLY380 4.6 24.9 1.0 CA A:GLY380 4.7 21.6 1.0 O A:HOH893 4.7 21.6 1.0 SG A:CYS378 4.8 17.6 1.0 C A:GLY380 4.8 23.0 1.0 N A:GLY429 4.8 17.6 1.0 SG A:CYS360 4.9 17.7 1.0

Y.Lien, J.C.Lachowicz, A.Mendauletova, C.Zizola, T.Ngendahimana, A.Kostenko, S.S.Eaton, J.A.Latham, T.L.Grove. Structural, Biochemical, and Bioinformatic Basis For Identifying Radical Sam Cyclopropyl Synthases Acs Chem.Biol. 2024.
ISSN: ESSN 1554-8937
DOI: 10.1021/ACSCHEMBIO.3C00583