Iron in PDB 2akj: Structure of Spinach Nitrite Reductase

All present enzymatic activity of Structure of Spinach Nitrite Reductase:
1.7.7.1;

The structure of Structure of Spinach Nitrite Reductase, PDB code: 2akj was solved by U.Swamy, M.Wang, J.N.Tripathy, S.-K.Kim, M.Hirasawa, D.B.Knaff, J.P.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.970, 128.970, 120.950, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 30

The binding sites of Iron atom in the Structure of Spinach Nitrite Reductase (pdb code 2akj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Structure of Spinach Nitrite Reductase, PDB code: 2akj:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Structure of Spinach Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Spinach Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe563 b:32.8 occ:1.00 FE1 A:SF4563 0.0 32.8 1.0 S2 A:SF4563 2.3 31.2 1.0 S3 A:SF4563 2.3 32.3 1.0 S4 A:SF4563 2.3 34.3 1.0 SG A:CYS441 2.3 29.9 1.0 FE3 A:SF4563 2.6 32.0 1.0 FE4 A:SF4563 2.7 32.6 1.0 FE2 A:SF4563 2.8 32.0 1.0 CB A:CYS441 3.2 31.2 1.0 N A:GLY481 3.7 32.7 1.0 S1 A:SF4563 3.9 32.2 1.0 CB A:CYS486 4.1 31.8 1.0 N A:GLY443 4.1 33.5 1.0 CA A:GLY481 4.2 32.3 1.0 OG1 A:THR480 4.3 33.3 1.0 N A:THR442 4.3 31.9 1.0 CA A:CYS441 4.5 31.3 1.0 SG A:CYS486 4.5 33.3 1.0 C A:CYS441 4.6 31.7 1.0 CA A:GLY443 4.7 34.3 1.0 N A:CYS482 4.7 32.3 1.0 SG A:CYS447 4.7 33.6 1.0 C A:THR480 4.8 33.0 1.0 C A:GLY481 4.8 32.6 1.0 CA A:THR480 4.9 33.1 1.0

Iron binding site 2 out of 5 in the Structure of Spinach Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Spinach Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe563 b:32.0 occ:1.00 FE2 A:SF4563 0.0 32.0 1.0 S3 A:SF4563 2.3 32.3 1.0 S4 A:SF4563 2.3 34.3 1.0 SG A:CYS482 2.3 31.9 1.0 S1 A:SF4563 2.3 32.2 1.0 FE3 A:SF4563 2.7 32.0 1.0 FE4 A:SF4563 2.8 32.6 1.0 FE1 A:SF4563 2.8 32.8 1.0 CB A:CYS482 3.2 31.8 1.0 N A:CYS482 3.6 32.3 1.0 O A:CYS482 3.8 31.6 1.0 CA A:CYS482 3.8 31.8 1.0 S2 A:SF4563 4.0 31.2 1.0 CB A:ASN484 4.0 32.2 1.0 C A:CYS482 4.1 31.8 1.0 C A:GLY481 4.1 32.6 1.0 ND2 A:ASN484 4.2 31.6 1.0 N A:GLY481 4.4 32.7 1.0 CA A:GLY481 4.5 32.3 1.0 CG A:ASN484 4.6 32.2 1.0 SG A:CYS486 4.7 33.3 1.0 CB A:GLN449 4.7 33.4 1.0 SG A:CYS447 4.7 33.6 1.0 N A:ASN484 4.8 32.4 1.0 O A:GLY481 4.8 33.1 1.0 SG A:CYS441 4.8 29.9 1.0 CA A:ALA450 4.9 32.9 1.0 CA A:ASN484 4.9 32.5 1.0 OG1 A:THR480 5.0 33.3 1.0 N A:SER485 5.0 33.1 1.0

Iron binding site 3 out of 5 in the Structure of Spinach Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Spinach Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe563 b:32.0 occ:1.00 FE3 A:SF4563 0.0 32.0 1.0 S4 A:SF4563 2.3 34.3 1.0 S1 A:SF4563 2.3 32.2 1.0 SG A:CYS486 2.3 33.3 1.0 S2 A:SF4563 2.3 31.2 1.0 FE1 A:SF4563 2.6 32.8 1.0 FE2 A:SF4563 2.7 32.0 1.0 FE4 A:SF4563 2.7 32.6 1.0 CB A:CYS486 2.9 31.8 1.0 S3 A:SF4563 3.8 32.3 1.0 NA A:SRM564 3.9 36.0 1.0 N A:CYS486 4.1 32.3 1.0 CA A:CYS486 4.1 32.2 1.0 FE A:SRM564 4.2 35.8 1.0 C1A A:SRM564 4.2 35.8 1.0 CB A:ASN484 4.2 32.2 1.0 C4A A:SRM564 4.3 36.1 1.0 C3A A:SRM564 4.4 35.5 1.0 ND A:SRM564 4.5 36.0 1.0 CHA A:SRM564 4.5 35.6 1.0 SG A:CYS482 4.6 31.9 1.0 C4D A:SRM564 4.6 35.9 1.0 SG A:CYS441 4.7 29.9 1.0 NB A:SRM564 4.7 35.8 1.0 ND2 A:ASN484 4.7 31.6 1.0 CHB A:SRM564 4.7 36.2 1.0 CB A:CYS441 4.7 31.2 1.0 SG A:CYS447 4.8 33.6 1.0 C2A A:SRM564 4.9 35.5 1.0 C1B A:SRM564 4.9 35.9 1.0 OG1 A:THR480 5.0 33.3 1.0 CDA A:SRM564 5.0 36.1 1.0

Iron binding site 4 out of 5 in the Structure of Spinach Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Spinach Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe563 b:32.6 occ:1.00 FE4 A:SF4563 0.0 32.6 1.0 S2 A:SF4563 2.3 31.2 1.0 S1 A:SF4563 2.3 32.2 1.0 SG A:CYS447 2.3 33.6 1.0 S3 A:SF4563 2.3 32.3 1.0 FE3 A:SF4563 2.7 32.0 1.0 FE1 A:SF4563 2.7 32.8 1.0 FE2 A:SF4563 2.8 32.0 1.0 CB A:CYS447 3.5 33.8 1.0 S4 A:SF4563 3.9 34.3 1.0 CB A:GLN449 4.3 33.4 1.0 C3A A:SRM564 4.3 35.5 1.0 CDA A:SRM564 4.4 36.1 1.0 CBA A:SRM564 4.4 35.5 1.0 SG A:CYS482 4.5 31.9 1.0 N A:ALA450 4.7 32.9 1.0 CB A:ALA450 4.7 32.6 1.0 SG A:CYS441 4.8 29.9 1.0 SG A:CYS486 4.8 33.3 1.0 C2A A:SRM564 4.9 35.5 1.0 O A:GLY443 4.9 35.0 1.0 CA A:ALA450 4.9 32.9 1.0 CA A:CYS447 4.9 33.8 1.0 C A:GLN449 5.0 33.3 1.0

Iron binding site 5 out of 5 in the Structure of Spinach Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Spinach Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe564 b:35.8 occ:1.00 FE A:SRM564 0.0 35.8 1.0 ND A:SRM564 2.0 36.0 1.0 NB A:SRM564 2.0 35.8 1.0 NA A:SRM564 2.0 36.0 1.0 NC A:SRM564 2.0 36.1 1.0 SG A:CYS486 2.3 33.3 1.0 C1D A:SRM564 3.0 35.9 1.0 C4A A:SRM564 3.0 36.1 1.0 C1B A:SRM564 3.0 35.9 1.0 C4D A:SRM564 3.0 35.9 1.0 C4B A:SRM564 3.0 36.0 1.0 C4C A:SRM564 3.0 36.1 1.0 C1A A:SRM564 3.0 35.8 1.0 C1C A:SRM564 3.0 35.8 1.0 CHB A:SRM564 3.3 36.2 1.0 CHD A:SRM564 3.3 36.2 1.0 CHA A:SRM564 3.4 35.6 1.0 CHC A:SRM564 3.4 36.0 1.0 CB A:CYS486 3.6 31.8 1.0 FE3 A:SF4563 4.2 32.0 1.0 C3A A:SRM564 4.2 35.5 1.0 C2B A:SRM564 4.2 35.5 1.0 C3D A:SRM564 4.2 36.0 1.0 C3B A:SRM564 4.2 36.0 1.0 C2D A:SRM564 4.3 35.8 1.0 CA A:CYS486 4.3 32.2 1.0 C2A A:SRM564 4.3 35.5 1.0 C2C A:SRM564 4.3 35.9 1.0 C3C A:SRM564 4.3 36.1 1.0 CAB A:SRM564 4.5 34.3 1.0 NZ A:LYS224 4.7 17.8 1.0 NH1 A:ARG109 4.8 31.1 1.0 CDB A:SRM564 4.8 36.1 1.0

U.Swamy, M.Wang, J.N.Tripathy, S.K.Kim, M.Hirasawa, D.B.Knaff, J.P.Allen. Structure of Spinach Nitrite Reductase: Implications For Multi-Electron Reactions By the Iron-Sulfur:Siroheme Cofactor Biochemistry V. 44 16054 2005.
ISSN: ISSN 0006-2960
PubMed: 16331965
DOI: 10.1021/BI050981Y