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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5ni6:

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

Zinc (Zn) 1 atom

Ytterbium Binding Sites:

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 5ni6

Go back to Ytterbium Binding Sites List in 5ni6
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 5ni6

Go back to Ytterbium Binding Sites List in 5ni6
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

Reference:

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
Page generated: Wed Dec 16 02:42:18 2020

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