Iron in PDB 8qdr: Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in A Detergent Bound Open Conformation

The structure of Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in A Detergent Bound Open Conformation, PDB code: 8qdr 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)	40.80 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.905, 105.818, 88.533, 90, 92.84, 90
R / Rfree (%)	17.4 / 21.8

The binding sites of Iron atom in the Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in A Detergent Bound Open Conformation (pdb code 8qdr). 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 A Detergent Bound Open Conformation, PDB code: 8qdr:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in A Detergent Bound Open 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 A Detergent Bound Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:44.3 occ:1.00 NE2 A:HIS559 2.1 37.7 1.0 NE2 A:HIS564 2.2 36.5 1.0 OXT A:ILE901 2.3 47.0 1.0 NE2 A:HIS751 2.3 44.7 1.0 O1 A:EDO1005 2.7 51.8 1.0 CE1 A:HIS559 2.9 46.6 1.0 CE1 A:HIS564 3.1 40.1 1.0 C A:ILE901 3.2 58.3 1.0 CE1 A:HIS751 3.2 40.1 1.0 CD2 A:HIS559 3.3 33.3 1.0 CD2 A:HIS564 3.3 35.7 1.0 CD2 A:HIS751 3.3 37.0 1.0 C1 A:EDO1005 3.4 54.2 1.0 O A:ILE901 3.4 59.3 1.0 ND2 A:ASN755 3.6 88.4 1.0 CG A:ASN755 3.7 89.7 1.0 OD1 A:ASN755 3.9 92.1 1.0 ND1 A:HIS559 4.1 49.1 1.0 ND1 A:HIS564 4.3 43.0 1.0 CG A:HIS559 4.3 38.2 1.0 CG A:HIS564 4.4 38.9 1.0 CG2 A:ILE899 4.4 47.9 1.0 ND1 A:HIS751 4.4 44.9 1.0 CB A:ASN755 4.5 83.4 1.0 CG A:HIS751 4.5 41.4 1.0 O2 A:EDO1005 4.6 61.7 1.0 C2 A:EDO1005 4.6 59.3 1.0 CA A:ILE901 4.6 60.9 1.0 N A:ILE901 4.8 62.1 1.0 CG2 A:ILE901 4.9 59.6 1.0 OG1 A:THR563 5.0 28.8 1.0

Iron binding site 2 out of 2 in the Vitis Vinifera Dimeric 13S-Lipoxygenase Loxa in A Detergent Bound Open 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 A Detergent Bound Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1001 b:40.9 occ:1.00 OXT B:ILE901 2.1 61.2 1.0 NE2 B:HIS559 2.2 29.9 1.0 NE2 B:HIS564 2.3 32.4 1.0 NE2 B:HIS751 2.4 32.1 1.0 O2 B:EDO1005 2.6 45.5 1.0 CE1 B:HIS559 3.0 34.3 1.0 C B:ILE901 3.1 63.7 1.0 CE1 B:HIS564 3.2 33.5 1.0 C2 B:EDO1005 3.2 49.3 1.0 CD2 B:HIS564 3.3 31.7 1.0 CE1 B:HIS751 3.3 31.6 1.0 CD2 B:HIS751 3.4 23.8 1.0 CD2 B:HIS559 3.4 26.5 1.0 O B:ILE901 3.4 64.7 1.0 ND2 B:ASN755 3.7 78.2 1.0 OD1 B:ASN755 3.9 80.1 1.0 ND1 B:HIS559 4.2 36.6 1.0 CG B:ASN755 4.2 77.5 1.0 ND1 B:HIS564 4.4 34.5 1.0 CG B:HIS564 4.4 28.8 1.0 CG B:HIS559 4.4 33.0 1.0 CG2 B:ILE899 4.4 46.0 1.0 ND1 B:HIS751 4.4 30.9 1.0 CA B:ILE901 4.5 65.7 1.0 CG B:HIS751 4.5 25.7 1.0 CG2 B:ILE901 4.5 63.7 1.0 C1 B:EDO1005 4.6 50.7 1.0 N B:ILE901 4.7 60.3 1.0 O1 B:EDO1005 4.7 56.3 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