Iron in PDB 6m9s: Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697

The structure of Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697, PDB code: 6m9s was solved by R.Rohac, A.J.Mitchell, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.09 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.510, 109.460, 365.980, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 18.9

The binding sites of Iron atom in the Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 (pdb code 6m9s). 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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697, PDB code: 6m9s:
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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:42.6 occ:1.00 NE2 A:HIS448 2.1 31.4 1.0 NE2 A:HIS409 2.3 43.2 1.0 NE2 A:HIS407 2.3 34.9 1.0 CE1 A:HIS448 3.0 31.9 1.0 CD2 A:HIS409 3.1 40.7 1.0 CD2 A:HIS448 3.1 32.3 1.0 CD2 A:HIS407 3.1 33.6 1.0 CE1 A:HIS407 3.3 33.8 1.0 CE1 A:HIS409 3.3 42.8 1.0 ND1 A:HIS448 4.1 32.1 1.0 CG A:HIS448 4.2 31.9 1.0 OE1 A:GLU413 4.2 51.4 1.0 CG A:HIS407 4.2 33.5 1.0 CG A:HIS409 4.3 39.9 1.0 ND1 A:HIS407 4.3 34.0 1.0 ND1 A:HIS409 4.3 42.2 1.0 O A:HOH839 4.6 54.2 1.0 CD1 A:ILE442 4.8 36.3 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:51.3 occ:0.40 OE1 A:GLU215 1.2 0.7 1.0 OE1 A:GLU189 1.5 83.3 1.0 NE2 A:HIS311 2.1 98.6 1.0 CD A:GLU215 2.3 95.0 1.0 ND1 A:HIS225 2.5 86.2 1.0 CD A:GLU189 2.7 77.5 1.0 OE2 A:GLU215 2.9 99.1 1.0 CE1 A:HIS311 2.9 99.4 1.0 CE1 A:HIS225 3.2 86.5 1.0 CD2 A:HIS311 3.2 96.5 1.0 OE2 A:GLU189 3.6 81.6 1.0 CG A:GLU215 3.6 90.1 1.0 CG A:GLU189 3.6 71.8 1.0 CG A:HIS225 3.7 85.6 1.0 CB A:GLU215 4.0 86.0 1.0 ND1 A:HIS311 4.1 98.5 1.0 OH A:TYR307 4.1 57.6 1.0 CG A:HIS311 4.2 95.8 1.0 CB A:HIS225 4.2 82.9 1.0 CA A:GLU215 4.3 84.6 1.0 NE2 A:HIS225 4.4 86.9 1.0 O A:HOH866 4.5 67.6 1.0 CD2 A:HIS225 4.7 86.3 1.0 CZ A:TYR307 4.7 55.4 1.0 O A:GLU215 4.8 81.1 1.0 CE1 A:TYR307 4.9 55.7 1.0 CB A:GLU189 5.0 66.8 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:52.3 occ:1.00 NE2 B:HIS448 2.1 43.4 1.0 NE2 B:HIS409 2.2 48.4 1.0 NE2 B:HIS407 2.3 46.1 1.0 CD2 B:HIS409 3.0 47.4 1.0 CE1 B:HIS448 3.1 44.0 1.0 CD2 B:HIS448 3.1 43.4 1.0 CD2 B:HIS407 3.1 43.6 1.0 CE1 B:HIS409 3.3 48.7 1.0 CE1 B:HIS407 3.3 45.8 1.0 ND1 B:HIS448 4.2 44.0 1.0 OE1 B:GLU413 4.2 57.1 1.0 CG B:HIS448 4.2 43.6 1.0 CG B:HIS409 4.2 46.3 1.0 CG B:HIS407 4.3 43.7 1.0 ND1 B:HIS407 4.3 45.3 1.0 ND1 B:HIS409 4.3 47.9 1.0 CD1 B:ILE442 4.7 47.2 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:65.4 occ:0.50 NE2 B:HIS311 2.1 99.3 1.0 ND1 B:HIS225 2.6 79.1 1.0 OE1 B:GLU215 2.7 85.7 1.0 OE1 B:GLU189 2.9 74.8 1.0 OE2 B:GLU189 2.9 72.5 1.0 CD B:GLU189 2.9 72.7 1.0 CE1 B:HIS311 3.0 99.8 1.0 CD2 B:HIS311 3.2 98.4 1.0 CE1 B:HIS225 3.4 80.0 1.0 CD B:GLU215 3.5 84.0 1.0 CG B:HIS225 3.8 78.1 1.0 CG B:GLU189 3.9 69.9 1.0 OE2 B:GLU215 4.0 82.1 1.0 ND1 B:HIS311 4.1 0.1 1.0 CB B:HIS225 4.2 77.0 1.0 CG B:HIS311 4.2 97.4 1.0 OH B:TYR307 4.3 57.6 1.0 CB B:GLU215 4.3 84.7 1.0 CG B:GLU215 4.6 82.7 1.0 NE2 B:HIS225 4.6 79.4 1.0 O B:ASP214 4.7 86.9 1.0 CD2 B:HIS225 4.8 78.3 1.0 CZ B:TYR307 4.9 58.8 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:44.4 occ:1.00 NE2 C:HIS448 2.1 33.5 1.0 NE2 C:HIS407 2.2 37.2 1.0 NE2 C:HIS409 2.3 39.5 1.0 CD2 C:HIS448 3.1 34.3 1.0 CE1 C:HIS448 3.1 32.7 1.0 CD2 C:HIS407 3.1 33.6 1.0 CD2 C:HIS409 3.1 38.0 1.0 CE1 C:HIS407 3.2 37.0 1.0 CE1 C:HIS409 3.3 39.9 1.0 ND1 C:HIS448 4.2 33.2 1.0 CG C:HIS448 4.2 33.3 1.0 OE1 C:GLU413 4.2 54.5 1.0 CG C:HIS407 4.2 34.5 1.0 ND1 C:HIS407 4.3 35.8 1.0 CG C:HIS409 4.3 36.9 1.0 ND1 C:HIS409 4.3 38.4 1.0 CD1 C:ILE442 4.7 40.1 1.0 O C:HOH773 4.9 59.1 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:53.8 occ:0.50 OE1 C:GLU215 1.8 98.2 1.0 NE2 C:HIS311 2.1 92.4 1.0 ND1 C:HIS225 2.5 81.3 1.0 CE1 C:HIS311 2.8 92.0 1.0 OE2 C:GLU189 2.8 72.2 1.0 CD C:GLU215 2.9 92.8 1.0 CE1 C:HIS225 3.2 81.3 1.0 CD C:GLU189 3.3 71.8 1.0 CD2 C:HIS311 3.4 91.9 1.0 OE2 C:GLU215 3.5 98.8 1.0 CG C:GLU189 3.5 67.2 1.0 CG C:HIS225 3.7 79.8 1.0 ND1 C:HIS311 4.0 91.8 1.0 CG C:GLU215 4.0 85.4 1.0 CA C:GLU215 4.1 80.6 1.0 CB C:HIS225 4.1 79.7 1.0 CB C:GLU215 4.1 80.5 1.0 OH C:TYR307 4.2 48.3 1.0 CG C:HIS311 4.3 90.1 1.0 OE1 C:GLU189 4.3 75.5 1.0 O C:GLU215 4.4 80.3 1.0 NE2 C:HIS225 4.5 81.2 1.0 CD2 C:HIS225 4.7 80.1 1.0 C C:GLU215 4.8 79.0 1.0 CZ C:TYR307 4.8 48.3 1.0 CE1 C:TYR307 4.9 48.9 1.0 CB C:GLU189 5.0 62.1 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:41.2 occ:1.00 NE2 D:HIS448 2.1 30.4 1.0 NE2 D:HIS409 2.2 38.7 1.0 NE2 D:HIS407 2.3 35.2 1.0 CE1 D:HIS448 3.0 31.2 1.0 CD2 D:HIS409 3.0 37.2 1.0 CD2 D:HIS448 3.0 31.1 1.0 CD2 D:HIS407 3.1 32.9 1.0 CE1 D:HIS407 3.3 33.9 1.0 CE1 D:HIS409 3.3 38.9 1.0 ND1 D:HIS448 4.1 31.6 1.0 CG D:HIS448 4.2 30.6 1.0 O D:HOH658 4.2 52.9 1.0 CG D:HIS409 4.2 37.7 1.0 CG D:HIS407 4.2 33.0 1.0 OE1 D:GLU413 4.2 52.9 1.0 ND1 D:HIS407 4.3 33.9 1.0 ND1 D:HIS409 4.3 38.2 1.0 O D:HOH884 4.7 70.2 1.0 CD1 D:ILE442 4.7 37.0 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Semet Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:53.9 occ:0.50 NE2 D:HIS311 1.9 93.2 1.0 OE1 D:GLU215 2.3 80.8 1.0 ND1 D:HIS225 2.5 73.5 1.0 CE1 D:HIS311 2.6 92.1 1.0 CD D:GLU215 2.8 78.2 1.0 OE1 D:GLU189 2.8 75.2 1.0 OE2 D:GLU215 2.9 79.3 1.0 OE2 D:GLU189 3.1 76.1 1.0 CD2 D:HIS311 3.1 93.4 1.0 CD D:GLU189 3.1 69.9 1.0 CE1 D:HIS225 3.3 73.9 1.0 CG D:HIS225 3.7 72.7 1.0 ND1 D:HIS311 3.9 92.7 1.0 O D:HOH847 3.9 68.2 1.0 CB D:HIS225 4.1 69.0 1.0 CG D:HIS311 4.1 92.1 1.0 CG D:GLU215 4.1 73.5 1.0 CG D:GLU189 4.3 63.7 1.0 OH D:TYR307 4.3 51.6 1.0 CB D:GLU215 4.3 73.3 1.0 CA D:GLU215 4.4 74.1 1.0 NE2 D:HIS225 4.5 74.5 1.0 CD2 D:HIS225 4.7 73.7 1.0 CZ D:TYR307 4.8 48.5 1.0 CE1 D:TYR307 4.9 48.2 1.0

T.L.Ng, R.Rohac, A.J.Mitchell, A.K.Boal, E.P.Balskus. An N-Nitrosating Metalloenzyme Constructs the Pharmacophore of Streptozotocin. Nature V. 566 94 2019.
ISSN: ESSN 1476-4687
PubMed: 30728519
DOI: 10.1038/S41586-019-0894-Z