Iron in PDB 5t5v: Lipoxygenase-1 (Soybean) at 293K

All present enzymatic activity of Lipoxygenase-1 (Soybean) at 293K:
1.13.11.12;

The structure of Lipoxygenase-1 (Soybean) at 293K, PDB code: 5t5v was solved by E.M.Poss, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.38 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.572, 92.754, 100.919, 90.00, 93.76, 90.00
R / Rfree (%)	13.4 / 17.1

The binding sites of Iron atom in the Lipoxygenase-1 (Soybean) at 293K (pdb code 5t5v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Lipoxygenase-1 (Soybean) at 293K, PDB code: 5t5v:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Lipoxygenase-1 (Soybean) at 293K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Lipoxygenase-1 (Soybean) at 293K within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:10.5 occ:0.88 HE2 A:HIS690 1.3 9.7 0.5 HE1 A:HIS499 1.6 14.1 0.4 O A:HOH1045 2.0 14.9 1.0 NE2 A:HIS504 2.1 10.6 0.2 OXT A:ILE839 2.1 11.6 0.4 NE2 A:HIS504 2.2 11.2 0.8 NE2 A:HIS690 2.2 8.1 0.5 NE2 A:HIS499 2.2 11.1 0.6 NE2 A:HIS690 2.2 8.0 0.6 OXT A:ILE839 2.3 11.6 0.6 CE1 A:HIS499 2.4 11.8 0.4 OD1 A:ASN694 2.6 12.9 0.3 CE1 A:HIS504 2.8 11.2 0.2 HE1 A:HIS504 2.8 13.4 0.2 NE2 A:HIS499 3.0 12.6 0.4 CE1 A:HIS504 3.1 10.7 0.8 CE1 A:HIS499 3.1 11.8 0.6 C A:ILE839 3.1 11.9 0.4 CD2 A:HIS690 3.1 8.0 0.6 CD2 A:HIS690 3.1 8.1 0.5 HE1 A:HIS499 3.2 14.2 0.6 HE1 A:HIS504 3.2 12.8 0.8 CE1 A:HIS690 3.2 9.6 0.5 HD2 A:HIS690 3.2 9.6 0.6 C A:ILE839 3.2 12.2 0.6 CD2 A:HIS504 3.2 10.5 0.8 CE1 A:HIS690 3.3 9.7 0.6 CD2 A:HIS504 3.3 10.3 0.2 HD2 A:HIS690 3.3 9.7 0.5 CD2 A:HIS499 3.3 13.0 0.6 O A:ILE839 3.3 12.1 0.4 HE1 A:HIS690 3.4 11.5 0.5 O A:ILE839 3.4 12.0 0.6 OD1 A:ASN694 3.4 13.3 0.7 HD2 A:HIS504 3.5 12.6 0.8 HE1 A:HIS690 3.5 11.6 0.6 ND1 A:HIS499 3.5 13.3 0.4 HD2 A:HIS499 3.5 15.6 0.6 HD2 A:HIS504 3.6 12.3 0.2 CG A:ASN694 3.6 11.2 0.3 HG23 A:ILE837 3.7 13.9 1.0 HB2 A:ASN694 3.7 12.9 0.7 CG A:ASN694 3.7 11.4 0.7 HB2 A:ASN694 3.8 12.7 0.3 HD1 A:HIS499 3.8 15.9 0.4 HG23 A:ILE839 3.9 17.6 0.4 ND1 A:HIS504 4.0 11.3 0.2 H A:ILE839 4.2 15.7 0.4 ND1 A:HIS504 4.2 12.8 0.8 CD2 A:HIS499 4.2 11.2 0.4 H A:ILE839 4.2 16.1 0.6 CB A:ASN694 4.2 10.8 0.7 ND1 A:HIS499 4.2 12.4 0.6 CG A:HIS504 4.3 10.7 0.2 ND1 A:HIS690 4.3 9.2 0.5 ND2 A:ASN694 4.3 12.0 0.7 CB A:ASN694 4.3 10.5 0.3 CG A:HIS690 4.3 9.2 0.5 CG A:HIS690 4.3 9.3 0.6 CG A:HIS504 4.3 10.4 0.8 ND1 A:HIS690 4.3 9.2 0.6 HD21 A:ASN694 4.4 14.4 0.7 CG A:HIS499 4.4 12.6 0.6 CG2 A:ILE837 4.4 11.6 1.0 HG22 A:ILE837 4.4 13.9 1.0 CA A:ILE839 4.5 12.0 0.4 HG23 A:ILE839 4.5 17.9 0.6 CG A:HIS499 4.5 12.2 0.4 CA A:ILE839 4.6 11.8 0.6 HG22 A:ILE839 4.6 17.6 0.4 ND2 A:ASN694 4.6 11.6 0.3 CG2 A:ILE839 4.6 14.7 0.4 HG21 A:ILE837 4.7 13.9 1.0 HD21 A:ASN694 4.7 13.9 0.3 HB3 A:ASN694 4.8 12.9 0.7 HD1 A:HIS504 4.8 13.6 0.2 N A:ILE839 4.8 13.1 0.4 N A:ILE839 4.8 13.5 0.6 HD22 A:ASN694 4.8 14.4 0.7 HD22 A:LEU754 4.8 19.9 0.4 HD13 A:LEU754 4.8 22.3 0.4 HB3 A:ASN694 4.9 12.7 0.3 HB3 A:LEU754 5.0 17.6 0.6 HD13 A:LEU754 5.0 23.2 0.6 HB3 A:LEU754 5.0 17.7 0.4 HD1 A:HIS504 5.0 15.4 0.8 HD2 A:HIS499 5.0 13.4 0.4 HD22 A:LEU754 5.0 20.2 0.6 HD1 A:HIS499 5.0 14.9 0.6

Iron binding site 2 out of 2 in the Lipoxygenase-1 (Soybean) at 293K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Lipoxygenase-1 (Soybean) at 293K within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe901 b:11.5 occ:0.91 HE2 B:HIS690 1.4 10.5 0.7 HE1 B:HIS499 1.5 11.4 0.4 O B:HOH1039 2.0 17.4 1.0 NE2 B:HIS504 2.2 12.6 0.5 NE2 B:HIS504 2.2 12.7 0.5 NE2 B:HIS499 2.2 9.5 0.6 OXT B:ILE839 2.2 10.3 0.5 NE2 B:HIS690 2.2 8.8 0.7 NE2 B:HIS690 2.3 9.1 0.3 OXT B:ILE839 2.3 9.2 0.5 CE1 B:HIS499 2.3 9.5 0.4 OD1 B:ASN694 2.9 13.7 0.7 NE2 B:HIS499 2.9 10.8 0.4 CE1 B:HIS499 3.1 9.7 0.6 CE1 B:HIS504 3.1 13.8 0.5 CE1 B:HIS504 3.1 13.8 0.5 CD2 B:HIS690 3.2 9.8 0.3 HE1 B:HIS499 3.2 11.7 0.6 CD2 B:HIS690 3.2 10.5 0.7 CD2 B:HIS504 3.2 11.5 0.5 CD2 B:HIS504 3.2 11.4 0.5 C B:ILE839 3.2 10.8 0.5 HD2 B:HIS690 3.2 11.7 0.3 C B:ILE839 3.2 10.8 0.5 HE1 B:HIS504 3.2 16.5 0.5 CE1 B:HIS690 3.3 9.8 0.7 CD2 B:HIS499 3.3 11.2 0.6 HD2 B:HIS690 3.3 12.6 0.7 HE1 B:HIS504 3.3 16.5 0.5 CE1 B:HIS690 3.3 9.6 0.3 HD2 B:HIS504 3.4 13.7 0.5 HD2 B:HIS504 3.4 13.8 0.5 O B:ILE839 3.4 11.2 0.5 O B:ILE839 3.4 11.9 0.5 HE1 B:HIS690 3.5 11.8 0.7 ND1 B:HIS499 3.5 11.9 0.4 HD2 B:HIS499 3.5 13.4 0.6 HE1 B:HIS690 3.6 11.5 0.3 CG B:ASN694 3.6 10.9 0.3 HB2 B:ASN694 3.7 13.6 0.3 CG B:ASN694 3.7 10.8 0.7 HG23 B:ILE837 3.7 12.3 1.0 HB2 B:ASN694 3.7 13.9 0.7 OD1 B:ASN694 3.7 10.3 0.3 HD1 B:HIS499 3.8 14.2 0.4 ND2 B:ASN694 3.8 12.0 0.3 HG23 B:ILE839 3.9 14.2 0.5 HD21 B:ASN694 3.9 14.4 0.3 HD22 B:ASN694 4.1 14.4 0.3 CB B:ASN694 4.2 11.3 0.3 H B:ILE839 4.2 16.1 0.5 H B:ILE839 4.2 15.9 0.5 CD2 B:HIS499 4.2 9.7 0.4 ND1 B:HIS504 4.2 12.9 0.5 ND1 B:HIS499 4.3 10.0 0.6 CB B:ASN694 4.3 11.6 0.7 ND1 B:HIS504 4.3 12.8 0.5 CG B:HIS504 4.3 12.0 0.5 CG B:HIS504 4.3 12.0 0.5 CG B:HIS690 4.4 9.1 0.3 CG B:HIS690 4.4 8.9 0.7 ND1 B:HIS690 4.4 9.2 0.7 CG B:HIS499 4.4 12.0 0.6 HD23 B:LEU754 4.4 22.1 0.1 ND1 B:HIS690 4.4 9.1 0.3 HG22 B:ILE837 4.5 12.3 1.0 CG2 B:ILE837 4.5 10.3 1.0 CG B:HIS499 4.5 11.9 0.4 CA B:ILE839 4.5 11.4 0.5 CA B:ILE839 4.6 11.4 0.5 ND2 B:ASN694 4.6 9.3 0.7 HG23 B:ILE839 4.6 16.3 0.5 HG B:LEU754 4.6 21.2 0.1 HB3 B:ASN694 4.7 13.6 0.3 CG2 B:ILE839 4.7 11.8 0.5 HD21 B:ASN694 4.7 11.2 0.7 HG21 B:ILE837 4.8 12.3 1.0 N B:ILE839 4.8 13.3 0.5 HB3 B:ASN694 4.8 13.9 0.7 N B:ILE839 4.8 13.4 0.5 HG22 B:ILE839 4.8 14.2 0.5 HD22 B:LEU754 4.9 21.6 0.9 HD13 B:LEU754 4.9 24.1 0.9 HG13 B:ILE839 4.9 16.1 0.5 HD2 B:HIS499 5.0 11.7 0.4

A.R.Offenbacher, S.Hu, E.M.Poss, C.A.M.Carr, A.D.Scouras, D.M.Prigozhin, A.T.Iavarone, A.Palla, T.Alber, J.S.Fraser, J.P.Klinman. Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers A Relationship Between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier For Catalytic Proton-Coupled Electron Tunneling. Acs Cent Sci V. 3 570 2017.
ISSN: ESSN 2374-7943
PubMed: 28691068
DOI: 10.1021/ACSCENTSCI.7B00142