Calcium in PDB 8viy: 15-Lipoxygenase-2 V427L

All present enzymatic activity of 15-Lipoxygenase-2 V427L:
1.13.11.33;

The structure of 15-Lipoxygenase-2 V427L, PDB code: 8viy was solved by N.C.Gilbert, A.R.Offenbacher, A.R.L.Ohler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.20 / 2.34
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	155.406, 155.406, 263.405, 90, 90, 120
R / Rfree (%)	18.4 / 22.4

The structure of 15-Lipoxygenase-2 V427L also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the 15-Lipoxygenase-2 V427L (pdb code 8viy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the 15-Lipoxygenase-2 V427L, PDB code: 8viy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the 15-Lipoxygenase-2 V427L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 15-Lipoxygenase-2 V427L within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca726 b:98.2 occ:1.00 O A:GLY15 2.4 78.7 1.0 OD1 A:ASP85 2.5 91.2 1.0 O A:HOH932 2.5 69.1 1.0 O A:ALA86 2.6 76.5 1.0 O A:GLY17 2.6 75.2 1.0 C A:GLY15 3.3 75.6 1.0 HA2 A:GLY15 3.3 93.2 1.0 CG A:ASP85 3.6 87.0 1.0 HB3 A:ALA86 3.6 93.6 1.0 C A:ALA86 3.7 76.5 1.0 CA A:GLY15 3.7 78.0 1.0 HA3 A:GLY15 3.8 93.2 1.0 H A:ALA86 3.8 100.6 1.0 N A:ALA86 3.8 83.8 1.0 C A:GLY17 3.8 75.2 1.0 HA A:THR18 4.0 94.7 1.0 OD2 A:ASP85 4.1 93.3 1.0 CA A:ALA86 4.1 76.6 1.0 C A:ASP85 4.2 82.5 1.0 HZ3 A:TRP109 4.2 88.2 1.0 CB A:ALA86 4.3 78.0 1.0 N A:GLY17 4.3 72.0 1.0 H A:GLY17 4.4 86.4 1.0 C A:ALA16 4.4 72.1 1.0 N A:ALA16 4.4 71.3 1.0 HA A:ASP85 4.5 101.1 1.0 HA A:TRP87 4.6 82.3 1.0 O A:ASP85 4.6 80.6 1.0 CA A:ASP85 4.7 84.2 1.0 O A:ALA16 4.7 74.7 1.0 CB A:ASP85 4.7 87.8 1.0 CA A:GLY17 4.7 75.7 1.0 CA A:THR18 4.8 78.9 1.0 N A:THR18 4.8 73.9 1.0 N A:TRP87 4.8 73.5 1.0 HG1 A:THR18 4.8 99.0 1.0 HB1 A:ALA86 4.9 93.6 1.0 CA A:ALA16 4.9 71.1 1.0 HA A:ALA16 4.9 85.4 1.0 HB A:THR18 5.0 96.2 1.0

Calcium binding site 2 out of 2 in the 15-Lipoxygenase-2 V427L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 15-Lipoxygenase-2 V427L within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca727 b:125.7 occ:1.00 O A:ASP39 2.8 137.0 1.0 O A:GLY42 2.8 134.7 1.0 H A:GLU44 2.9 165.1 1.0 HA A:ASP39 2.9 154.4 1.0 HB2 A:ASP39 3.1 153.3 1.0 HB2 A:GLU44 3.2 162.9 1.0 CA A:ASP39 3.5 128.6 1.0 HG2 A:GLU44 3.5 171.6 1.0 C A:ASP39 3.5 131.5 1.0 HG3 A:GLU44 3.7 171.6 1.0 HD2 A:PHE45 3.7 114.4 1.0 N A:GLU44 3.7 137.5 1.0 CB A:ASP39 3.8 127.7 1.0 HA A:LYS43 3.9 169.4 1.0 CG A:GLU44 3.9 142.9 1.0 CB A:GLU44 3.9 135.7 1.0 C A:GLY42 4.0 137.8 1.0 HE2 A:PHE45 4.3 116.4 1.0 HB3 A:ASP39 4.4 153.3 1.0 CA A:GLU44 4.4 136.3 1.0 CD2 A:PHE45 4.5 95.3 1.0 HE2 A:LYS21 4.5 120.6 1.0 CA A:LYS43 4.5 141.1 1.0 C A:LYS43 4.6 140.5 1.0 H A:PHE45 4.6 122.9 1.0 N A:LYS43 4.7 137.3 1.0 HB3 A:GLU44 4.8 162.9 1.0 CE2 A:PHE45 4.8 97.0 1.0 CG A:ASP39 4.8 121.5 1.0 N A:ASN40 4.8 125.8 1.0 N A:ASP39 4.9 108.7 1.0 O A:LEU38 4.9 96.5 1.0 H A:GLY42 4.9 193.7 1.0 N A:GLY42 5.0 161.3 1.0

A.Ohler, P.E.Taylor, J.A.Bledsoe, A.T.Iavarone, N.C.Gilbert, A.R.Offenbacher. Identification of the Thermal Activation Network in Human 15-Lipoxygenase-2: Divergence From Plant Orthologs and Its Relationship to Hydrogen Tunneling Activation Barriers. Acs Catalysis V. 14 5444 2024.
ISSN: ESSN 2155-5435
PubMed: 38601784
DOI: 10.1021/ACSCATAL.4C00439