Iron in PDB 4m7s: Crystal Structure of Semet Btrn in An Open Conformation

The structure of Crystal Structure of Semet Btrn in An Open Conformation, PDB code: 4m7s was solved by P.J.Goldman, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.51 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.408, 42.058, 50.925, 90.00, 105.40, 90.00
R / Rfree (%)	17.1 / 21.8

The binding sites of Iron atom in the Crystal Structure of Semet Btrn in An Open Conformation (pdb code 4m7s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Semet Btrn in An Open Conformation, PDB code: 4m7s:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Semet Btrn in An Open Conformation


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 Semet Btrn in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:27.8 occ:1.00 FE1 A:SF4501 0.0 27.8 1.0 S2 A:SF4501 2.3 28.5 1.0 S3 A:SF4501 2.3 29.6 1.0 S4 A:SF4501 2.3 29.9 1.0 SG A:CYS235 2.5 36.0 1.0 FE3 A:SF4501 2.7 28.2 1.0 FE2 A:SF4501 2.7 28.2 1.0 FE4 A:SF4501 2.7 27.1 1.0 CB A:CYS235 3.1 30.4 1.0 S1 A:SF4501 3.9 27.6 1.0 CB A:ASN237 4.1 43.4 1.0 CG A:GLU189 4.3 46.2 1.0 CA A:CYS235 4.6 35.0 1.0 ND2 A:ASN237 4.7 48.2 1.0 SG A:CYS232 4.7 28.9 1.0 NH2 A:ARG226 4.8 33.6 1.0 CB A:GLU189 4.8 41.2 1.0 CA A:CYS232 4.8 27.1 1.0 SG A:CYS187 4.8 30.9 1.0 CB A:CYS232 4.8 26.3 1.0 SG A:CYS169 4.9 29.4 1.0 CG A:ASN237 5.0 46.6 1.0 N A:ASN237 5.0 44.6 1.0 CZ A:ARG226 5.0 37.4 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Semet Btrn in An Open Conformation


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 Semet Btrn in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:28.2 occ:1.00 FE2 A:SF4501 0.0 28.2 1.0 SG A:CYS232 2.3 28.9 1.0 S3 A:SF4501 2.3 29.6 1.0 S1 A:SF4501 2.3 27.6 1.0 S4 A:SF4501 2.3 29.9 1.0 FE4 A:SF4501 2.6 27.1 1.0 FE3 A:SF4501 2.7 28.2 1.0 FE1 A:SF4501 2.7 27.8 1.0 CB A:CYS232 3.1 26.3 1.0 CA A:CYS232 3.7 27.1 1.0 S2 A:SF4501 3.9 28.5 1.0 N A:CYS232 4.3 26.1 1.0 CD1 A:LEU221 4.5 36.1 1.0 CD1 A:LEU231 4.6 40.2 1.0 CB A:CYS235 4.6 30.4 1.0 CG A:LEU221 4.7 36.0 1.0 C A:LEU231 4.8 31.3 1.0 CZ A:PHE217 4.8 28.7 1.0 SG A:CYS235 4.9 36.0 1.0 SG A:CYS169 4.9 29.4 1.0 C A:CYS232 4.9 30.2 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Semet Btrn in An Open Conformation


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 Semet Btrn in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:28.2 occ:1.00 FE3 A:SF4501 0.0 28.2 1.0 S4 A:SF4501 2.3 29.9 1.0 S2 A:SF4501 2.3 28.5 1.0 S1 A:SF4501 2.3 27.6 1.0 SG A:CYS187 2.5 30.9 1.0 FE1 A:SF4501 2.7 27.8 1.0 FE4 A:SF4501 2.7 27.1 1.0 FE2 A:SF4501 2.7 28.2 1.0 CB A:CYS187 3.2 24.8 1.0 S3 A:SF4501 3.9 29.6 1.0 CG A:GLU189 3.9 46.2 1.0 CB A:GLU189 4.0 41.2 1.0 CA A:CYS187 4.7 22.7 1.0 SG A:CYS232 4.7 28.9 1.0 CD1 A:LEU231 4.8 40.2 1.0 CB A:VAL171 4.8 28.8 1.0 SG A:CYS169 4.8 29.4 1.0 SG A:CYS235 4.9 36.0 1.0 CG1 A:VAL171 4.9 19.3 1.0 N A:GLU189 5.0 30.3 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Semet Btrn in An Open Conformation


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 Semet Btrn in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:27.1 occ:1.00 FE4 A:SF4501 0.0 27.1 1.0 S3 A:SF4501 2.3 29.6 1.0 S2 A:SF4501 2.3 28.5 1.0 S1 A:SF4501 2.3 27.6 1.0 SG A:CYS169 2.5 29.4 1.0 FE2 A:SF4501 2.6 28.2 1.0 FE3 A:SF4501 2.7 28.2 1.0 FE1 A:SF4501 2.7 27.8 1.0 CB A:CYS169 3.3 31.6 1.0 S4 A:SF4501 3.9 29.9 1.0 ND2 A:ASN237 4.2 48.2 1.0 CG2 A:VAL171 4.3 28.1 1.0 CB A:VAL171 4.4 28.8 1.0 SG A:CYS232 4.6 28.9 1.0 CD A:PRO172 4.6 26.0 1.0 CA A:CYS169 4.7 32.8 1.0 SG A:CYS187 4.8 30.9 1.0 NH1 A:ARG226 4.9 38.4 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Semet Btrn in An Open Conformation


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 Semet Btrn in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:28.7 occ:1.00 FE1 A:SF4502 0.0 28.7 1.0 S2 A:SF4502 2.3 32.9 1.0 S3 A:SF4502 2.3 28.5 1.0 S4 A:SF4502 2.3 26.6 1.0 SG A:CYS16 2.4 31.9 1.0 FE2 A:SF4502 2.7 28.2 1.0 FE3 A:SF4502 2.7 31.0 1.0 FE4 A:SF4502 2.7 32.5 1.0 CB A:CYS16 3.2 35.2 1.0 O A:HOH623 3.6 32.5 1.0 S1 A:SF4502 3.9 29.6 1.0 ND2 A:ASN25 4.1 57.5 1.0 CB A:ARG18 4.2 39.4 1.0 O A:ARG18 4.5 33.4 1.0 ND2 A:ASN92 4.6 25.4 1.0 N A:ARG18 4.6 33.8 1.0 CA A:CYS16 4.7 36.0 1.0 CA A:ARG18 4.7 37.6 1.0 C A:ARG18 4.7 36.6 1.0 SG A:CYS20 4.8 34.0 1.0 O A:TYR62 4.9 35.2 1.0 SG A:CYS23 4.9 34.0 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Semet Btrn in An Open Conformation


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 Semet Btrn in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:28.2 occ:1.00 FE2 A:SF4502 0.0 28.2 1.0 S4 A:SF4502 2.3 26.6 1.0 S3 A:SF4502 2.3 28.5 1.0 S1 A:SF4502 2.3 29.6 1.0 SG A:CYS20 2.3 34.0 1.0 FE3 A:SF4502 2.7 31.0 1.0 FE1 A:SF4502 2.7 28.7 1.0 FE4 A:SF4502 2.7 32.5 1.0 CB A:CYS20 3.1 32.2 1.0 S2 A:SF4502 3.9 32.9 1.0 CB A:ARG18 4.0 39.4 1.0 CG A:HIS117 4.1 75.7 1.0 N A:CYS20 4.1 35.6 1.0 ND1 A:HIS117 4.2 78.9 1.0 CB A:HIS117 4.2 75.3 1.0 CA A:CYS20 4.2 36.1 1.0 CB A:CYS23 4.4 32.3 1.0 CD2 A:HIS117 4.5 73.2 1.0 CE1 A:HIS117 4.7 77.8 1.0 SG A:CYS16 4.7 31.9 1.0 SG A:CYS23 4.8 34.0 1.0 CD A:ARG18 4.8 43.3 1.0 NE2 A:HIS117 4.8 74.0 1.0 OH A:TYR22 4.9 66.8 1.0 C A:ARG18 4.9 36.6 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Semet Btrn in An Open Conformation


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 Semet Btrn in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.0 occ:1.00 FE3 A:SF4502 0.0 31.0 1.0 S1 A:SF4502 2.3 29.6 1.0 S2 A:SF4502 2.3 32.9 1.0 S4 A:SF4502 2.3 26.6 1.0 SG A:CYS23 2.4 34.0 1.0 FE2 A:SF4502 2.7 28.2 1.0 FE1 A:SF4502 2.7 28.7 1.0 FE4 A:SF4502 2.7 32.5 1.0 CB A:CYS23 3.0 32.3 1.0 ND2 A:ASN25 3.5 57.5 1.0 S3 A:SF4502 3.9 28.5 1.0 CG A:ASN25 4.5 56.1 1.0 CA A:CYS23 4.5 35.8 1.0 CB A:CYS20 4.5 32.2 1.0 CB A:ASN25 4.7 55.3 1.0 SG A:CYS20 4.7 34.0 1.0 O A:TYR62 4.9 35.2 1.0 SG A:CYS16 5.0 31.9 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Semet Btrn in An Open Conformation


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 Semet Btrn in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:32.5 occ:1.00 FE4 A:SF4502 0.0 32.5 1.0 S2 A:SF4502 2.3 32.9 1.0 S1 A:SF4502 2.3 29.6 1.0 S3 A:SF4502 2.3 28.5 1.0 FE1 A:SF4502 2.7 28.7 1.0 FE3 A:SF4502 2.7 31.0 1.0 FE2 A:SF4502 2.7 28.2 1.0 O A:HOH638 2.9 46.7 1.0 NE2 A:HIS117 3.6 74.0 1.0 CD2 A:HIS117 3.7 73.2 1.0 O A:HOH623 3.7 32.5 1.0 S4 A:SF4502 3.9 26.6 1.0 CE1 A:HIS117 4.0 77.8 1.0 CG A:HIS117 4.2 75.7 1.0 ND1 A:HIS117 4.3 78.9 1.0 CE1 A:HIS60 4.6 32.4 0.5 NE2 A:HIS60 4.7 35.5 0.5 SG A:CYS16 4.8 31.9 1.0 SG A:CYS23 4.9 34.0 1.0 SG A:CYS20 4.9 34.0 1.0

P.J.Goldman, T.L.Grove, S.J.Booker, C.L.Drennan. X-Ray Analysis of Butirosin Biosynthetic Enzyme Btrn Redefines Structural Motifs For Adomet Radical Chemistry. Proc.Natl.Acad.Sci.Usa V. 110 15949 2013.
ISSN: ISSN 0027-8424
PubMed: 24048029
DOI: 10.1073/PNAS.1312228110