Iron in PDB 5th5: Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound

All present enzymatic activity of Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound:
4.3.99.3;

The structure of Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound, PDB code: 5th5 was solved by T.A.J.Grell, D.P.Dowling, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.879, 136.835, 141.187, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.3

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound (pdb code 5th5). 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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound, PDB code: 5th5:
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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:18.2 occ:1.00 FE1 A:SF4301 0.0 18.2 1.0 SG A:CYS38 2.3 21.1 1.0 S4 A:SF4301 2.3 18.3 1.0 S3 A:SF4301 2.3 22.4 1.0 S2 A:SF4301 2.3 35.1 1.0 FE3 A:SF4301 2.7 19.6 1.0 FE2 A:SF4301 2.7 37.2 1.0 FE4 A:SF4301 2.7 22.2 1.0 CB A:CYS38 3.1 25.6 1.0 CE A:LYS129 3.6 23.1 1.0 S1 A:SF4301 3.9 26.3 1.0 N A:CYS38 4.0 26.7 1.0 CB A:TYR36 4.1 26.6 1.0 CA A:CYS38 4.2 27.0 1.0 O A:MET303 4.3 22.7 1.0 CD A:LYS129 4.4 23.5 1.0 NZ A:LYS129 4.6 25.6 1.0 CD2 A:TYR36 4.6 24.4 1.0 CG A:LYS129 4.6 24.8 1.0 CB A:CYS41 4.6 27.2 1.0 SG A:CYS41 4.7 26.0 1.0 SG A:CYS34 4.7 29.1 1.0 N A:MET303 4.9 23.8 1.0 CG A:TYR36 4.9 25.5 1.0

Iron binding site 2 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:37.2 occ:1.00 FE2 A:SF4301 0.0 37.2 1.0 S3 A:SF4301 2.3 22.4 1.0 S1 A:SF4301 2.3 26.3 1.0 S4 A:SF4301 2.3 18.3 1.0 O A:MET303 2.4 22.7 1.0 N A:MET303 2.5 23.8 1.0 SD A:MET303 2.7 21.1 1.0 FE3 A:SF4301 2.7 19.6 1.0 FE1 A:SF4301 2.7 18.2 1.0 FE4 A:SF4301 2.7 22.2 1.0 C A:MET303 3.2 23.0 1.0 CA A:MET303 3.3 31.8 1.0 CE A:MET303 3.6 25.8 1.0 CG A:MET303 3.7 24.6 1.0 S2 A:SF4301 3.9 35.1 1.0 CB A:MET303 4.0 24.5 1.0 CE A:LYS129 4.1 23.1 1.0 OXT A:MET303 4.3 22.1 1.0 NZ A:LYS129 4.3 25.6 1.0 O A:GLY83 4.6 23.8 1.0 OE1 A:GLN110 4.7 21.8 1.0 C9 A:7C5302 4.7 25.0 1.0 SG A:CYS34 4.8 29.1 1.0 SG A:CYS38 4.9 21.1 1.0 SG A:CYS41 4.9 26.0 1.0 C10 A:7C5302 5.0 26.9 1.0

Iron binding site 3 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:19.6 occ:1.00 FE3 A:SF4301 0.0 19.6 1.0 SG A:CYS41 2.3 26.0 1.0 S4 A:SF4301 2.3 18.3 1.0 S2 A:SF4301 2.3 35.1 1.0 S1 A:SF4301 2.3 26.3 1.0 FE1 A:SF4301 2.7 18.2 1.0 FE2 A:SF4301 2.7 37.2 1.0 FE4 A:SF4301 2.7 22.2 1.0 CB A:CYS41 3.1 27.2 1.0 CE A:MET303 3.7 25.8 1.0 CA A:CYS41 3.8 36.2 1.0 NE1 A:TRP47 3.8 26.5 1.0 S3 A:SF4301 3.9 22.4 1.0 SD A:MET303 4.1 21.1 1.0 CD1 A:TRP47 4.5 26.5 1.0 CB A:CYS38 4.7 25.6 1.0 SG A:CYS38 4.7 21.1 1.0 C A:CYS41 4.7 27.4 1.0 N A:MET303 4.8 23.8 1.0 CE2 A:TRP47 4.8 27.7 1.0 SG A:CYS34 4.9 29.1 1.0 N A:CYS41 4.9 27.3 1.0

Iron binding site 4 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:22.2 occ:1.00 FE4 A:SF4301 0.0 22.2 1.0 S2 A:SF4301 2.3 35.1 1.0 S3 A:SF4301 2.3 22.4 1.0 S1 A:SF4301 2.3 26.3 1.0 SG A:CYS34 2.3 29.1 1.0 FE2 A:SF4301 2.7 37.2 1.0 FE1 A:SF4301 2.7 18.2 1.0 FE3 A:SF4301 2.7 19.6 1.0 N A:MET303 3.6 23.8 1.0 CB A:CYS34 3.6 33.7 1.0 S4 A:SF4301 3.9 18.3 1.0 CB A:TYR36 4.0 26.6 1.0 O A:TYR36 4.3 25.7 1.0 NE1 A:TRP47 4.4 26.5 1.0 CD1 A:TRP47 4.5 26.5 1.0 NE2 A:GLN110 4.6 24.2 1.0 C A:TYR36 4.6 25.4 1.0 SG A:CYS41 4.6 26.0 1.0 SG A:CYS38 4.6 21.1 1.0 CA A:TYR36 4.7 26.2 1.0 O A:MET303 4.7 22.7 1.0 O A:GLY83 4.7 23.8 1.0 OE1 A:GLN110 4.8 21.8 1.0 C A:GLY83 4.8 24.6 1.0 N A:TYR36 4.9 26.1 1.0 CD A:GLN110 4.9 22.9 1.0 CA A:CYS34 4.9 25.7 1.0 SD A:MET303 4.9 21.1 1.0 CA A:GLY83 5.0 27.2 1.0 N A:GLY83 5.0 41.7 1.0 CA A:MET303 5.0 31.8 1.0

Iron binding site 5 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:34.5 occ:1.00 FE1 B:SF4301 0.0 34.5 1.0 S4 B:SF4301 2.3 34.3 1.0 SG B:CYS38 2.3 38.3 1.0 S3 B:SF4301 2.3 33.7 1.0 S2 B:SF4301 2.3 39.5 1.0 FE3 B:SF4301 2.7 43.8 1.0 FE2 B:SF4301 2.7 38.6 1.0 FE4 B:SF4301 2.7 35.5 1.0 CB B:CYS38 3.1 45.1 1.0 CE B:LYS129 3.6 36.8 1.0 S1 B:SF4301 3.9 46.3 1.0 N B:CYS38 4.0 60.0 1.0 OXT B:MET303 4.1 44.4 1.0 CB B:TYR36 4.1 42.8 1.0 CA B:CYS38 4.2 52.7 1.0 CD B:LYS129 4.4 35.6 1.0 NZ B:LYS129 4.6 51.7 1.0 CD2 B:TYR36 4.6 42.6 1.0 CG B:LYS129 4.6 36.7 1.0 CB B:CYS41 4.6 43.5 1.0 SG B:CYS41 4.7 37.5 1.0 SG B:CYS34 4.7 38.7 1.0 N B:MET303 4.9 37.6 1.0 CG B:TYR36 4.9 41.1 1.0 SD B:MET303 5.0 33.6 1.0

Iron binding site 6 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:38.6 occ:1.00 FE2 B:SF4301 0.0 38.6 1.0 OXT B:MET303 2.0 44.4 1.0 S3 B:SF4301 2.3 33.7 1.0 S1 B:SF4301 2.3 46.3 1.0 S4 B:SF4301 2.3 34.3 1.0 SD B:MET303 2.5 33.6 1.0 N B:MET303 2.6 37.6 1.0 FE1 B:SF4301 2.7 34.5 1.0 FE3 B:SF4301 2.7 43.8 1.0 FE4 B:SF4301 2.7 35.5 1.0 C B:MET303 2.9 38.6 1.0 CA B:MET303 3.2 33.6 1.0 CG B:MET303 3.5 35.4 1.0 CE B:MET303 3.6 37.2 1.0 S2 B:SF4301 3.9 39.5 1.0 CB B:MET303 3.9 34.7 1.0 O B:MET303 4.0 32.9 1.0 CE B:LYS129 4.1 36.8 1.0 NZ B:LYS129 4.3 51.7 1.0 O B:GLY83 4.6 31.2 1.0 C9 B:7C5302 4.7 37.1 1.0 OE1 B:GLN110 4.7 35.0 1.0 SG B:CYS34 4.8 38.7 1.0 SG B:CYS38 4.9 38.3 1.0 SG B:CYS41 4.9 37.5 1.0 C10 B:7C5302 5.0 36.5 1.0

Iron binding site 7 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:43.8 occ:1.00 FE3 B:SF4301 0.0 43.8 1.0 SG B:CYS41 2.3 37.5 1.0 S2 B:SF4301 2.3 39.5 1.0 S4 B:SF4301 2.3 34.3 1.0 S1 B:SF4301 2.3 46.3 1.0 FE1 B:SF4301 2.7 34.5 1.0 FE2 B:SF4301 2.7 38.6 1.0 FE4 B:SF4301 2.7 35.5 1.0 CB B:CYS41 3.0 43.5 1.0 CE B:MET303 3.7 37.2 1.0 CA B:CYS41 3.8 44.1 1.0 NE1 B:TRP47 3.8 45.1 1.0 S3 B:SF4301 3.9 33.7 1.0 SD B:MET303 3.9 33.6 1.0 CD1 B:TRP47 4.5 48.1 1.0 OXT B:MET303 4.6 44.4 1.0 SG B:CYS38 4.7 38.3 1.0 CB B:CYS38 4.7 45.1 1.0 C B:CYS41 4.7 41.0 1.0 N B:MET303 4.8 37.6 1.0 CE2 B:TRP47 4.8 58.0 1.0 SG B:CYS34 4.9 38.7 1.0 N B:CYS41 4.9 47.9 1.0

Iron binding site 8 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:35.5 occ:1.00 FE4 B:SF4301 0.0 35.5 1.0 S1 B:SF4301 2.3 46.3 1.0 S2 B:SF4301 2.3 39.5 1.0 S3 B:SF4301 2.3 33.7 1.0 SG B:CYS34 2.3 38.7 1.0 FE3 B:SF4301 2.7 43.8 1.0 FE2 B:SF4301 2.7 38.6 1.0 FE1 B:SF4301 2.7 34.5 1.0 N B:MET303 3.6 37.6 1.0 CB B:CYS34 3.6 41.9 1.0 S4 B:SF4301 3.9 34.3 1.0 CB B:TYR36 4.0 42.8 1.0 O B:TYR36 4.4 45.0 1.0 NE1 B:TRP47 4.4 45.1 1.0 CD1 B:TRP47 4.4 48.1 1.0 OXT B:MET303 4.5 44.4 1.0 NE2 B:GLN110 4.6 49.0 1.0 C B:TYR36 4.6 45.1 1.0 SG B:CYS41 4.6 37.5 1.0 SG B:CYS38 4.7 38.3 1.0 O B:GLY83 4.7 31.2 1.0 CA B:TYR36 4.7 45.6 1.0 OE1 B:GLN110 4.8 35.0 1.0 C B:GLY83 4.8 33.7 1.0 SD B:MET303 4.8 33.6 1.0 CA B:MET303 4.9 33.6 1.0 N B:TYR36 4.9 44.7 1.0 CD B:GLN110 4.9 34.8 1.0 CA B:CYS34 4.9 45.1 1.0 CA B:GLY83 5.0 34.3 1.0 N B:GLY83 5.0 32.7 1.0

Iron binding site 9 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:29.9 occ:1.00 FE1 C:SF4301 0.0 29.9 1.0 SG C:CYS38 2.3 29.6 1.0 S4 C:SF4301 2.3 23.9 1.0 S3 C:SF4301 2.3 28.0 1.0 S2 C:SF4301 2.3 24.4 1.0 FE3 C:SF4301 2.7 21.7 1.0 FE2 C:SF4301 2.7 30.6 1.0 FE4 C:SF4301 2.7 25.4 1.0 CB C:CYS38 3.1 31.6 1.0 CE C:LYS129 3.6 28.6 1.0 S1 C:SF4301 3.9 28.1 1.0 N C:CYS38 4.0 32.0 1.0 CB C:TYR36 4.1 34.4 1.0 CA C:CYS38 4.2 32.4 1.0 OXT C:MET303 4.3 26.7 1.0 CD C:LYS129 4.4 27.5 1.0 NZ C:LYS129 4.6 26.9 1.0 CD2 C:TYR36 4.6 31.2 1.0 CG C:LYS129 4.6 29.1 1.0 CB C:CYS41 4.6 31.5 1.0 N C:MET303 4.7 28.9 1.0 SG C:CYS34 4.7 29.5 1.0 SG C:CYS41 4.7 33.2 1.0 CG C:TYR36 4.9 31.6 1.0

Iron binding site 10 out of 16 in the Crystal Structure of Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound


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 Quee From Bacillus Subtilis with 6-Carboxypterin- 5'-Deoxyadenosyl Ester Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:30.6 occ:1.00 FE2 C:SF4301 0.0 30.6 1.0 S3 C:SF4301 2.3 28.0 1.0 S1 C:SF4301 2.3 28.1 1.0 S4 C:SF4301 2.3 23.9 1.0 N C:MET303 2.3 28.9 1.0 OXT C:MET303 2.4 26.7 1.0 SD C:MET303 2.6 27.7 1.0 FE3 C:SF4301 2.7 21.7 1.0 FE1 C:SF4301 2.7 29.9 1.0 FE4 C:SF4301 2.7 25.4 1.0 C C:MET303 3.1 26.8 1.0 CA C:MET303 3.2 34.9 1.0 CG C:MET303 3.6 28.1 1.0 CE C:MET303 3.7 35.8 1.0 S2 C:SF4301 3.9 24.4 1.0 CB C:MET303 3.9 28.1 1.0 CE C:LYS129 4.1 28.6 1.0 O C:MET303 4.3 27.1 1.0 NZ C:LYS129 4.3 26.9 1.0 O C:GLY83 4.6 25.5 1.0 OE1 C:GLN110 4.7 25.6 1.0 C9 C:7C5302 4.7 28.8 1.0 SG C:CYS34 4.8 29.5 1.0 SG C:CYS38 4.9 29.6 1.0 SG C:CYS41 4.9 33.2 1.0 C10 C:7C5302 5.0 34.3 1.0

N.A.Bruender, T.A.Grell, D.P.Dowling, R.M.Mccarty, C.L.Drennan, V.Bandarian. 7-Carboxy-7-Deazaguanine Synthase: A Radical S-Adenosyl-L-Methionine Enzyme with Polar Tendencies. J. Am. Chem. Soc. V. 139 1912 2017.
ISSN: ESSN 1520-5126
PubMed: 28045519
DOI: 10.1021/JACS.6B11381