Iron in PDB 6vzy: Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor

The structure of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor, PDB code: 6vzy was solved by M.J.Mcbride, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.42 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.953, 105.848, 150.591, 90, 90, 90
R / Rfree (%)	19 / 22.2

The binding sites of Iron atom in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor (pdb code 6vzy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor, PDB code: 6vzy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:12.2 occ:0.93 OE2 A:GLU215 2.1 19.0 1.0 ND1 A:HIS225 2.1 10.0 1.0 NE2 A:HIS311 2.1 10.4 1.0 O A:HOH743 2.2 19.8 1.0 OE2 A:GLU189 2.2 21.3 1.0 OE1 A:GLU189 2.2 14.4 1.0 CD A:GLU189 2.5 19.6 1.0 CE1 A:HIS225 2.9 17.2 1.0 CE1 A:HIS311 3.0 16.8 1.0 CD2 A:HIS311 3.1 18.4 1.0 CD A:GLU215 3.2 19.9 1.0 CG A:HIS225 3.2 11.7 1.0 CB A:HIS225 3.7 15.2 1.0 CG A:GLU189 4.0 19.1 1.0 O A:HOH667 4.0 20.1 1.0 OE1 A:GLU215 4.0 19.5 1.0 CG A:GLU215 4.0 13.3 1.0 CB A:GLU215 4.0 12.3 1.0 O A:HOH760 4.0 26.2 1.0 NE2 A:HIS225 4.1 14.8 1.0 ND1 A:HIS311 4.2 12.4 1.0 CA A:GLU215 4.2 10.8 1.0 CG A:HIS311 4.2 15.7 1.0 CD2 A:HIS225 4.3 16.2 1.0 OH A:TYR307 4.5 13.1 1.0 O A:GLU215 4.8 12.8 1.0 CB A:GLU189 5.0 12.9 1.0 CE2 A:TYR307 5.0 10.2 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:11.4 occ:0.67 OE1 A:GLU281 2.0 22.9 1.0 OD1 A:ASP315 2.0 26.4 1.0 OE1 A:GLU215 2.0 19.5 1.0 ND1 A:HIS318 2.1 13.9 1.0 O A:HOH667 2.1 20.1 1.0 CE1 A:HIS318 2.9 18.8 1.0 CD A:GLU281 3.1 25.9 1.0 CG A:ASP315 3.1 33.2 1.0 CD A:GLU215 3.2 19.9 1.0 CG A:HIS318 3.2 18.2 1.0 OE2 A:GLU281 3.4 22.8 1.0 OD2 A:ASP315 3.5 22.5 1.0 OE2 A:GLU215 3.6 19.0 1.0 CB A:HIS318 3.7 19.8 1.0 NE2 A:HIS318 4.1 20.6 1.0 CD2 A:HIS318 4.3 23.2 1.0 CG1 A:VAL211 4.3 15.4 1.0 CG A:GLU281 4.4 18.7 1.0 CB A:ASP315 4.4 17.9 1.0 CG A:GLU215 4.5 13.3 1.0 O A:HOH743 4.5 19.8 1.0 CA A:ASP315 4.7 22.3 1.0 CD2 A:HIS311 4.7 18.4 1.0 CG2 A:ILE314 4.9 34.0 1.0 CB A:GLU281 5.0 19.6 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:16.0 occ:1.00 NE2 A:HIS409 2.2 13.2 1.0 NE2 A:HIS407 2.2 11.3 1.0 NE2 A:HIS448 2.2 10.7 1.0 O A:HOH780 2.3 20.1 1.0 CE1 A:HIS409 3.1 11.1 1.0 CD2 A:HIS407 3.1 16.3 1.0 CE1 A:HIS407 3.2 15.4 1.0 CE1 A:HIS448 3.2 14.6 1.0 CD2 A:HIS448 3.2 10.1 1.0 CD2 A:HIS409 3.2 11.1 1.0 O A:HOH771 4.0 27.4 1.0 OE2 A:GLU413 4.2 26.7 1.0 ND1 A:HIS409 4.3 16.6 1.0 ND1 A:HIS407 4.3 9.8 1.0 CG A:HIS407 4.3 10.2 1.0 ND1 A:HIS448 4.3 10.8 1.0 CG A:HIS409 4.3 12.4 1.0 CG A:HIS448 4.3 8.3 1.0 O A:HOH782 4.6 29.4 1.0 CD1 A:ILE442 4.9 16.9 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:13.2 occ:1.00 O B:HOH719 2.1 16.3 1.0 OE2 B:GLU189 2.1 16.6 1.0 NE2 B:HIS311 2.1 11.9 1.0 ND1 B:HIS225 2.1 10.7 1.0 OE2 B:GLU215 2.2 14.4 1.0 OE1 B:GLU189 2.3 15.9 1.0 CD B:GLU189 2.5 16.7 1.0 CE1 B:HIS225 2.9 12.0 1.0 CE1 B:HIS311 3.0 14.1 1.0 CD2 B:HIS311 3.1 17.3 1.0 CG B:HIS225 3.2 9.0 1.0 CD B:GLU215 3.3 18.7 1.0 CB B:HIS225 3.7 10.0 1.0 CG B:GLU189 3.9 13.4 1.0 CB B:GLU215 4.0 13.4 1.0 O B:HOH677 4.0 17.8 1.0 CG B:GLU215 4.1 12.5 1.0 NE2 B:HIS225 4.1 15.7 1.0 OE1 B:GLU215 4.1 17.6 1.0 ND1 B:HIS311 4.1 14.1 1.0 CG B:HIS311 4.2 12.1 1.0 O B:HOH777 4.2 21.8 1.0 CD2 B:HIS225 4.3 13.3 1.0 CA B:GLU215 4.3 12.7 1.0 O B:HOH793 4.3 24.4 1.0 OH B:TYR307 4.5 12.1 1.0 O B:GLU215 4.8 12.2 1.0 CE1 B:TYR307 4.9 12.5 1.0 CB B:GLU189 5.0 10.7 1.0 FE B:FE2502 5.0 14.6 0.8

Iron binding site 5 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:14.6 occ:0.84 OE1 B:GLU281 2.0 20.1 1.0 OD1 B:ASP315 2.0 22.2 1.0 OE1 B:GLU215 2.1 17.6 1.0 O B:HOH677 2.1 17.8 1.0 ND1 B:HIS318 2.2 17.2 1.0 CD B:GLU281 3.0 22.0 1.0 CE1 B:HIS318 3.1 21.9 1.0 CG B:ASP315 3.1 22.9 1.0 CD B:GLU215 3.2 18.7 1.0 CG B:HIS318 3.3 20.8 1.0 OE2 B:GLU281 3.4 21.2 1.0 OE2 B:GLU215 3.5 14.4 1.0 OD2 B:ASP315 3.6 23.4 1.0 CB B:HIS318 3.7 16.3 1.0 NE2 B:HIS318 4.3 26.3 1.0 CG1 B:VAL211 4.3 15.7 1.0 CG B:GLU281 4.3 19.7 1.0 CD2 B:HIS318 4.4 22.5 1.0 O B:HOH719 4.4 16.3 1.0 CB B:ASP315 4.4 18.3 1.0 CG B:GLU215 4.5 12.5 1.0 CA B:ASP315 4.6 19.7 1.0 CD2 B:HIS311 4.7 17.3 1.0 CG2 B:ILE314 4.8 29.3 1.0 CB B:GLU281 4.9 15.9 1.0 FE B:FE2501 5.0 13.2 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor


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 Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe503 b:17.4 occ:0.97 NE2 B:HIS409 2.2 16.3 1.0 NE2 B:HIS407 2.2 11.2 1.0 NE2 B:HIS448 2.2 11.7 1.0 O B:HOH789 2.3 18.6 1.0 CD2 B:HIS409 3.1 16.1 1.0 CE1 B:HIS407 3.1 18.8 1.0 CD2 B:HIS448 3.2 12.6 1.0 CD2 B:HIS407 3.2 13.4 1.0 CE1 B:HIS448 3.2 9.0 1.0 CE1 B:HIS409 3.2 9.6 1.0 OE2 B:GLU413 4.2 23.6 1.0 ND1 B:HIS407 4.3 12.7 1.0 CG B:HIS409 4.3 14.4 1.0 ND1 B:HIS448 4.3 9.1 1.0 CG B:HIS448 4.3 11.0 1.0 ND1 B:HIS409 4.3 16.8 1.0 CG B:HIS407 4.3 9.4 1.0 O B:HOH796 4.4 24.5 1.0 CD1 B:ILE442 4.7 13.9 1.0

M.J.Mcbride, S.R.Pope, K.Hu, C.D.Okafor, E.P.Balskus, J.M.Bollinger Jr., A.K.Boal. Structure and Assembly of the Diiron Cofactor in the Heme-Oxygenase-Like Domain of the N-Nitrosourea-Producing Enzyme Sznf Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490