Zinc in PDB 6z2q: Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product

The structure of Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product, PDB code: 6z2q was solved by B.Trastoy, A.Naegali, I.Anso, J.Sjogren, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.23 / 2.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.366, 65.366, 187.654, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.1

The binding sites of Zinc atom in the Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product (pdb code 6z2q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product, PDB code: 6z2q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product


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 Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:41.5 occ:1.00 OXT A:ACY402 2.0 48.7 1.0 NE2 A:HIS215 2.1 40.7 1.0 NE2 A:HIS205 2.1 35.7 1.0 NE2 A:HIS209 2.2 35.9 1.0 CE1 A:HIS215 3.0 41.6 1.0 CD2 A:HIS209 3.0 33.7 1.0 CD2 A:HIS205 3.0 36.2 1.0 CD2 A:HIS215 3.1 39.1 1.0 CE1 A:HIS205 3.2 36.0 1.0 C A:ACY402 3.2 50.3 1.0 CE1 A:HIS209 3.3 34.5 1.0 OH A:TYR318 3.7 47.9 1.0 O A:ACY402 3.9 49.2 1.0 ND1 A:HIS215 4.1 41.9 1.0 H1 A:ACY402 4.1 52.3 1.0 CG A:HIS209 4.2 34.1 1.0 CG A:HIS205 4.2 35.8 1.0 CG A:HIS215 4.2 39.4 1.0 ND1 A:HIS205 4.3 36.0 1.0 CH3 A:ACY402 4.3 43.6 1.0 ND1 A:HIS209 4.3 32.8 1.0 CE1 A:TYR318 4.4 39.7 1.0 CZ A:TYR318 4.4 45.3 1.0 N D:THR2 4.5 43.9 1.0 CA D:THR2 4.5 45.9 1.0 OE1 A:GLU206 4.7 39.1 1.0 H3 A:ACY402 4.8 52.3 1.0 CE A:MET231 4.8 32.8 1.0 H2 A:ACY402 5.0 52.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product


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 Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:74.0 occ:1.00 O A:ASP309 2.5 40.3 1.0 O A:GLN316 2.5 50.1 1.0 OD1 A:ASP319 2.6 41.3 1.0 OE1 A:GLN308 2.6 40.3 1.0 O A:PRO311 2.6 43.7 1.0 CG A:ASP319 3.3 40.2 1.0 OD2 A:ASP319 3.4 39.8 1.0 C A:ASP309 3.6 38.1 1.0 CD A:GLN308 3.6 38.9 1.0 C A:GLN316 3.7 51.9 1.0 O A:HOH587 3.7 51.7 1.0 C A:PRO311 3.8 43.1 1.0 CA A:ASP317 4.0 46.0 1.0 C A:PRO310 4.0 39.5 1.0 O A:PRO310 4.1 38.7 1.0 CG A:GLN308 4.1 34.6 1.0 CB A:GLN308 4.1 35.4 1.0 N A:PRO311 4.3 40.4 1.0 N A:ASP317 4.3 49.3 1.0 N A:ASP309 4.3 35.6 1.0 CA A:PRO310 4.4 39.4 1.0 N A:PRO310 4.4 38.4 1.0 CA A:ASP309 4.5 35.5 1.0 CA A:TYR312 4.6 45.3 1.0 N A:TYR312 4.7 44.4 1.0 CA A:PRO311 4.7 42.5 1.0 CD1 A:TYR312 4.7 39.1 1.0 CB A:ASP317 4.7 46.1 1.0 CB A:GLN316 4.7 50.3 1.0 CB A:ASP319 4.8 40.1 1.0 CA A:GLN316 4.8 52.5 1.0 NE2 A:GLN308 4.8 40.1 1.0 CB A:ASP309 4.9 34.2 1.0 C A:GLN308 4.9 36.0 1.0 C A:ASP317 5.0 42.3 1.0 CD A:PRO311 5.0 39.3 1.0

B.Trastoy, A.Naegali, I.Anso, J.Sjogren, M.E.Guerin. Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in Complex with An O-Glycopeptide (Galgalnac-Ts) Product Nat Commun 2020.
ISSN: ESSN 2041-1723