Zinc in PDB 5nie: Crystal Structure of Human LTA4H Mutant R563A in Open Conformation

All present enzymatic activity of Crystal Structure of Human LTA4H Mutant R563A in Open Conformation:
3.3.2.6;

The structure of Crystal Structure of Human LTA4H Mutant R563A in Open Conformation, PDB code: 5nie was solved by A.Stsiapanava, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.47 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.970, 132.150, 320.120, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 29.1

The binding sites of Zinc atom in the Crystal Structure of Human LTA4H Mutant R563A in Open Conformation (pdb code 5nie). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human LTA4H Mutant R563A in Open Conformation, PDB code: 5nie:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human LTA4H Mutant R563A in Open Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human LTA4H Mutant R563A in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn900 b:47.6 occ:1.00 OE2 A:GLU318 2.0 57.6 1.0 NE2 A:HIS299 2.0 48.5 1.0 OE1 A:GLU318 2.0 53.7 1.0 NE2 A:HIS295 2.1 29.7 1.0 CD A:GLU318 2.3 55.7 1.0 CE1 A:HIS299 2.9 45.3 1.0 CE1 A:HIS295 2.9 26.9 1.0 HE1 A:TYR383 2.9 69.5 1.0 HE1 A:HIS299 3.0 54.4 1.0 HE1 A:HIS295 3.0 32.3 1.0 CD2 A:HIS299 3.1 49.5 1.0 CD2 A:HIS295 3.2 29.9 1.0 HD2 A:HIS299 3.4 59.4 1.0 HD2 A:HIS295 3.5 35.8 1.0 OE1 A:GLU271 3.6 59.4 1.0 CE1 A:TYR383 3.7 57.9 1.0 HG21 A:THR321 3.8 51.8 1.0 CG A:GLU318 3.8 52.7 1.0 OH A:TYR383 4.0 57.7 1.0 ND1 A:HIS299 4.0 43.8 1.0 ND1 A:HIS295 4.1 26.5 1.0 HG3 A:GLU318 4.1 63.2 1.0 CG A:HIS299 4.2 47.3 1.0 HA A:GLU318 4.2 60.5 1.0 CG A:HIS295 4.2 29.1 1.0 HG2 A:GLU318 4.3 63.2 1.0 CZ A:TYR383 4.3 57.8 1.0 CD A:GLU271 4.4 57.0 1.0 HB3 A:GLU318 4.5 58.9 1.0 CB A:GLU318 4.7 49.1 1.0 CG2 A:THR321 4.7 43.2 1.0 HB3 A:GLU271 4.7 66.5 1.0 OE2 A:GLU271 4.7 56.4 1.0 CD1 A:TYR383 4.7 56.4 1.0 HD1 A:TYR383 4.7 67.7 1.0 HB A:THR321 4.7 50.4 1.0 HH A:TYR383 4.8 69.2 1.0 HD1 A:HIS299 4.8 52.5 1.0 HG22 A:THR321 4.8 51.8 1.0 HD1 A:HIS295 4.8 31.8 1.0 CA A:GLU318 4.9 50.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human LTA4H Mutant R563A in Open Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human LTA4H Mutant R563A in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn900 b:46.8 occ:1.00 OE2 B:GLU318 2.0 41.2 1.0 OE1 B:GLU318 2.0 40.0 1.0 NE2 B:HIS295 2.1 47.6 1.0 NE2 B:HIS299 2.1 52.4 1.0 CD B:GLU318 2.3 41.8 1.0 CE1 B:HIS299 2.8 50.0 1.0 HE1 B:HIS299 2.9 60.0 1.0 CD2 B:HIS295 3.0 45.9 1.0 CE1 B:HIS295 3.0 48.5 1.0 CD2 B:HIS299 3.2 52.1 1.0 HD2 B:HIS295 3.2 55.1 1.0 HE1 B:HIS295 3.2 58.2 1.0 HE2 B:TYR383 3.3 48.8 1.0 HD2 B:HIS299 3.5 62.6 1.0 OE1 B:GLU271 3.7 73.5 1.0 HH B:TYR383 3.8 55.3 1.0 CG B:GLU318 3.8 44.6 1.0 ND1 B:HIS299 4.0 49.6 1.0 CE2 B:TYR383 4.1 40.6 1.0 ND1 B:HIS295 4.1 46.9 1.0 CG B:HIS299 4.2 49.3 1.0 CG B:HIS295 4.2 46.8 1.0 HG3 B:GLU318 4.2 53.5 1.0 HG2 B:GLU318 4.2 53.5 1.0 CD B:GLU271 4.3 70.7 1.0 OG1 B:THR321 4.4 60.0 1.0 HA B:GLU318 4.4 56.4 1.0 OE2 B:GLU271 4.5 71.3 1.0 OH B:TYR383 4.5 46.1 1.0 HG21 B:THR321 4.5 58.0 1.0 HB3 B:GLU318 4.5 55.2 1.0 O B:HOH1014 4.6 27.2 0.8 HD1 B:HIS299 4.7 59.6 1.0 CB B:GLU318 4.7 46.0 1.0 CZ B:TYR383 4.7 44.3 1.0 HG1 B:THR321 4.8 72.0 1.0 HB3 B:GLU271 4.8 72.4 1.0 HD1 B:HIS295 4.9 56.3 1.0 HD2 B:TYR383 4.9 47.8 1.0 HB B:THR321 5.0 63.4 1.0 CD2 B:TYR383 5.0 39.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human LTA4H Mutant R563A in Open Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human LTA4H Mutant R563A in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn900 b:53.9 occ:1.00 OE2 C:GLU318 2.0 49.8 1.0 OE1 C:GLU318 2.0 47.6 1.0 NE2 C:HIS299 2.0 52.9 1.0 NE2 C:HIS295 2.1 40.0 1.0 CD C:GLU318 2.3 47.3 1.0 CE1 C:HIS299 2.9 50.5 1.0 CE1 C:HIS295 3.0 36.1 1.0 O C:HOH1002 3.0 24.7 1.0 HE1 C:HIS299 3.0 60.6 1.0 HE1 C:HIS295 3.1 43.3 1.0 CD2 C:HIS299 3.1 53.1 1.0 CD2 C:HIS295 3.2 39.2 1.0 HE1 C:TYR383 3.3 47.2 1.0 HD2 C:HIS299 3.4 63.7 1.0 HD2 C:HIS295 3.4 47.0 1.0 CG C:GLU318 3.8 44.6 1.0 OE1 C:GLU271 3.9 66.7 1.0 ND1 C:HIS299 4.0 50.2 1.0 ND1 C:HIS295 4.1 34.4 1.0 CE1 C:TYR383 4.1 39.4 1.0 CG C:HIS299 4.2 50.9 1.0 HG2 C:GLU318 4.2 53.5 1.0 CG C:HIS295 4.2 36.5 1.0 HG3 C:GLU318 4.2 53.5 1.0 OE2 C:GLU271 4.3 62.3 1.0 OG1 C:THR321 4.3 66.2 1.0 HA C:GLU318 4.3 51.8 1.0 CD C:GLU271 4.3 61.1 1.0 HG21 C:THR321 4.3 64.3 1.0 HB3 C:GLU318 4.5 53.1 1.0 HG1 C:THR321 4.6 79.5 1.0 HB3 C:GLU271 4.7 61.3 1.0 CB C:GLU318 4.7 44.3 1.0 HD1 C:TYR383 4.7 44.9 1.0 HD1 C:HIS299 4.8 60.2 1.0 OH C:TYR383 4.8 46.8 1.0 HD1 C:HIS295 4.8 41.3 1.0 CD1 C:TYR383 4.9 37.4 1.0 CZ C:TYR383 4.9 41.5 1.0 CA C:GLU318 5.0 43.1 1.0 HB C:THR321 5.0 70.0 1.0

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