Iron in PDB 8qdq: Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in the Closed Conformation

The structure of Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in the Closed Conformation, PDB code: 8qdq was solved by K.Wild, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.49 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.767, 110.647, 91.173, 90, 90.24, 90
R / Rfree (%)	19.9 / 23.5

The binding sites of Iron atom in the Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in the Closed Conformation (pdb code 8qdq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in the Closed Conformation, PDB code: 8qdq:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in the Closed Conformation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in the Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:21.8 occ:1.00 O A:HOH1116 1.9 29.7 1.0 NE2 A:HIS751 2.1 21.2 1.0 NE2 A:HIS564 2.2 25.6 1.0 NE2 A:HIS559 2.2 24.2 1.0 OXT A:ILE901 2.3 24.2 1.0 OD1 A:ASN755 3.0 29.5 1.0 CE1 A:HIS751 3.0 21.2 1.0 CD2 A:HIS751 3.1 18.6 1.0 CE1 A:HIS559 3.1 29.2 1.0 CD2 A:HIS564 3.1 25.7 1.0 CE1 A:HIS564 3.2 24.0 1.0 C A:ILE901 3.2 26.1 1.0 CD2 A:HIS559 3.3 23.0 1.0 O A:ILE901 3.4 27.1 1.0 CG A:ASN755 3.8 24.6 1.0 ND1 A:HIS751 4.2 19.4 1.0 CG A:HIS751 4.2 19.9 1.0 CB A:ASN755 4.2 19.9 1.0 ND1 A:HIS564 4.3 25.0 1.0 ND1 A:HIS559 4.3 29.8 1.0 CG A:HIS564 4.3 25.1 1.0 CG2 A:ILE899 4.3 22.4 1.0 CG A:HIS559 4.4 24.1 1.0 CA A:ILE901 4.6 24.0 1.0 ND2 A:ASN755 4.7 22.6 1.0 N A:ILE901 4.8 22.9 1.0 CG2 A:ILE901 4.9 24.5 1.0

Iron binding site 2 out of 2 in the Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in the Closed Conformation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in the Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1001 b:29.4 occ:1.00 O B:HOH1149 2.0 31.5 1.0 NE2 B:HIS559 2.1 31.5 1.0 NE2 B:HIS564 2.1 28.0 1.0 NE2 B:HIS751 2.2 25.8 1.0 OXT B:ILE901 2.2 32.0 1.0 CE1 B:HIS559 2.8 30.6 1.0 OD1 B:ASN755 2.8 31.9 1.0 CE1 B:HIS564 3.0 29.4 1.0 CE1 B:HIS751 3.1 21.2 1.0 CD2 B:HIS751 3.1 23.3 1.0 CD2 B:HIS564 3.2 27.9 1.0 CD2 B:HIS559 3.3 27.2 1.0 C B:ILE901 3.3 32.7 1.0 O B:ILE901 3.6 36.1 1.0 CG B:ASN755 3.6 23.7 1.0 ND1 B:HIS559 4.0 29.6 1.0 ND1 B:HIS564 4.1 28.6 1.0 CG B:HIS564 4.2 30.7 1.0 ND1 B:HIS751 4.3 24.2 1.0 CG B:HIS559 4.3 26.6 1.0 CB B:ASN755 4.3 22.4 1.0 CG2 B:ILE899 4.3 26.8 1.0 CG B:HIS751 4.3 23.5 1.0 ND2 B:ASN755 4.5 24.1 1.0 CA B:ILE901 4.6 30.8 1.0 N B:ILE901 4.8 29.5 1.0 CG2 B:ILE901 4.9 29.9 1.0

S.Pilati, K.Wild, A.Gumiero, I.Holdermann, Y.Hackmann, M.Dalla Serra, G.Guella, C.Moser, I.Sinning. Vitis Vinifera Lipoxygenase Loxa Is An Allosteric Dimer Activated By Lipidic Surfaces. J.Mol.Biol. 68821 2024.
ISSN: ESSN 1089-8638
PubMed: 39424098
DOI: 10.1016/J.JMB.2024.168821