Zinc in PDB 5h6b: Crystal Structure of A Thermostable Lipase From Marine Streptomyces

All present enzymatic activity of Crystal Structure of A Thermostable Lipase From Marine Streptomyces:
3.1.1.3;

The structure of Crystal Structure of A Thermostable Lipase From Marine Streptomyces, PDB code: 5h6b was solved by S.Hou, Z.Zhao, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.63 / 2.30
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	90.730, 90.730, 70.620, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 20.6

The binding sites of Zinc atom in the Crystal Structure of A Thermostable Lipase From Marine Streptomyces (pdb code 5h6b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Thermostable Lipase From Marine Streptomyces, PDB code: 5h6b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Thermostable Lipase From Marine Streptomyces


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 A Thermostable Lipase From Marine Streptomyces within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:76.4 occ:1.00 O A:HOH441 2.1 49.7 1.0 OD1 A:ASP44 2.2 44.2 1.0 OXT A:ACT306 2.4 63.1 1.0 O A:HOH440 2.6 53.4 1.0 CG A:ASP44 2.9 42.4 1.0 OD2 A:ASP44 2.9 47.6 1.0 O A:HOH438 3.4 53.2 1.0 C A:ACT306 3.7 66.1 1.0 CB A:ASP44 4.3 41.8 1.0 O A:ACT306 4.4 64.4 1.0 CH3 A:ACT306 4.7 59.9 1.0 CG2 A:ILE43 4.7 38.0 1.0 CA A:ASP44 4.9 41.0 1.0 CE1 A:PHE73 4.9 58.5 1.0 N A:ASP44 4.9 38.5 1.0 CB A:ILE43 5.0 38.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Thermostable Lipase From Marine Streptomyces


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 A Thermostable Lipase From Marine Streptomyces within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:40.4 occ:1.00 OD2 A:ASP64 1.8 36.2 1.0 N1 A:IMD308 2.1 45.9 1.0 NE2 A:HIS75 2.1 32.9 1.0 C2 A:IMD308 2.5 46.9 1.0 CG A:ASP64 2.8 38.0 1.0 CD2 A:HIS75 3.1 34.0 1.0 CE1 A:HIS75 3.1 36.6 1.0 OD1 A:ASP64 3.2 38.6 1.0 C5 A:IMD308 3.4 55.3 1.0 N3 A:IMD308 3.9 52.8 1.0 CB A:ASN41 4.0 35.0 1.0 CB A:ASP64 4.1 40.1 1.0 ND1 A:HIS75 4.2 34.2 1.0 CG A:HIS75 4.2 33.2 1.0 C4 A:IMD308 4.3 54.6 1.0 N A:PHE73 4.7 42.7 1.0 CG A:ASN41 4.9 33.8 1.0 CG A:GLN67 4.9 39.5 1.0 CA A:PHE73 5.0 41.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Thermostable Lipase From Marine Streptomyces


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 A Thermostable Lipase From Marine Streptomyces within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:43.0 occ:1.00 OD1 A:ASP185 2.0 32.8 1.0 N3 A:IMD307 2.1 47.0 1.0 NE2 A:HIS139 2.3 40.9 1.0 C2 A:IMD307 2.4 43.4 1.0 O A:ACT305 2.6 52.2 1.0 OXT A:ACT305 2.7 55.4 1.0 CG A:ASP185 2.7 37.4 1.0 OD2 A:ASP185 2.8 41.0 1.0 C A:ACT305 3.0 52.7 1.0 CD2 A:HIS139 3.0 38.9 1.0 CE1 A:HIS139 3.3 38.9 1.0 C4 A:IMD307 3.3 49.4 1.0 N1 A:IMD307 3.7 50.2 1.0 CB A:ASP185 4.1 40.5 1.0 C5 A:IMD307 4.2 45.8 1.0 CG A:HIS139 4.2 38.6 1.0 ND1 A:HIS139 4.3 38.6 1.0 O A:HOH434 4.4 36.7 1.0 CH3 A:ACT305 4.5 48.9 1.0 O A:HOH426 4.6 39.5 1.0 CA A:ASP185 4.7 42.6 1.0 N A:ASP185 4.7 48.7 1.0 CB A:THR181 5.0 48.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Thermostable Lipase From Marine Streptomyces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Thermostable Lipase From Marine Streptomyces within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:99.3 occ:1.00 OD1 A:ASP88 2.6 59.1 1.0 O A:HOH408 2.8 67.2 1.0 OD2 A:ASP92 2.9 68.1 1.0 NZ A:LYS127 3.0 75.3 1.0 OD2 A:ASP88 3.3 56.1 1.0 CG A:ASP88 3.3 56.5 1.0 CG A:ASP92 3.8 60.6 1.0 OD1 A:ASP92 4.0 64.7 1.0 CE A:LYS127 4.5 74.0 1.0 CB A:ASP88 4.7 54.9 1.0 O A:LEU122 4.8 52.6 1.0 O A:ASP88 4.9 52.4 1.0

Z.Zhao, S.Hou, D.Lan, X.Wang, J.Liu, F.I.Khan, Y.Wang. Crystal Structure of A Lipase From Streptomyces Sp. Strain W007 - Implications For Thermostability and Regiospecificity Febs J. V. 284 3506 2017.
ISSN: ISSN 1742-4658
PubMed: 28857479
DOI: 10.1111/FEBS.14211