Ytterbium in PDB 5ni6: Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4

All present enzymatic activity of Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4:
3.3.2.6;

The structure of Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4, PDB code: 5ni6 was solved by A.Stsiapanava, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.23 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.130, 87.450, 99.460, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.1

The structure of Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Ytterbium atom in the Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4 (pdb code 5ni6). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 2 binding sites of Ytterbium where determined in the Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4, PDB code: 5ni6:
Jump to Ytterbium binding site number: 1; 2;

Ytterbium binding site 1 out of 2 in the Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb702 b:20.2 occ:0.95 O A:HOH893 2.1 18.5 1.0 OXT A:ACY704 2.3 22.1 1.0 O A:HOH1255 2.3 28.1 1.0 OD1 A:ASP47 2.3 19.7 1.0 OD2 A:ASP47 2.4 20.4 1.0 O A:ACY704 2.6 27.0 1.0 CG A:ASP47 2.7 20.7 1.0 C A:ACY704 2.8 29.8 1.0 HG A:SER95 3.9 26.6 0.4 HB2 A:ASN48 3.9 29.3 1.0 H A:ASN48 4.1 27.1 1.0 CB A:ASP47 4.2 21.8 1.0 CH3 A:ACY704 4.3 27.6 1.0 O A:HOH1419 4.5 46.7 1.0 O A:HOH962 4.5 18.8 1.0 N A:ASN48 4.5 22.6 1.0 HB2 A:ASP47 4.6 26.2 1.0 HB3 A:ASP47 4.6 26.2 1.0 OG A:SER95 4.7 22.2 0.4 H3 A:ACY704 4.7 33.1 1.0 H2 A:ACY704 4.7 33.1 1.0 O A:HOH998 4.7 27.8 1.0 O A:HOH979 4.8 35.8 1.0 HA A:ASP47 4.8 24.7 1.0 H1 A:ACY704 4.8 33.1 1.0 HA A:SER95 4.8 26.4 0.4 CB A:ASN48 4.8 24.4 1.0 HA A:SER95 4.9 26.4 0.6 HA A:ASN48 4.9 28.4 1.0 HB3 A:SER95 5.0 25.7 0.6 O A:HOH1505 5.0 35.8 0.8 CA A:ASP47 5.0 20.6 1.0

Ytterbium binding site 2 out of 2 in the Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Crystal Structure of Human LTA4H Mutant D375N in Complex with LTA4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb703 b:78.4 occ:0.95 OD1 A:ASP175 2.2 39.3 1.0 O A:HOH1372 3.3 49.1 1.0 CG A:ASP175 3.3 39.2 1.0 OD2 A:ASP175 3.8 43.0 1.0 HA A:ASP175 4.0 26.5 1.0 HD13 A:ILE192 4.2 33.6 0.3 HD12 A:ILE192 4.4 39.0 0.7 CB A:ASP175 4.5 24.7 1.0 CA A:ASP175 4.7 22.1 1.0 O A:ASP175 4.7 30.6 1.0 HD11 A:ILE192 4.7 39.0 0.7 HD11 A:ILE192 4.8 33.6 0.3 HB2 A:ASP175 4.8 29.7 1.0 CD1 A:ILE192 5.0 28.0 0.3

A.Stsiapanava, B.Samuelsson, J.Z.Haeggstrom. Capturing LTA4 Hydrolase in Action: Insights to the Chemistry and Dynamics of Chemotactic LTB4 Synthesis. Proc. Natl. Acad. Sci. V. 114 9689 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28827365
DOI: 10.1073/PNAS.1710850114