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

Protein crystallography data

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

Zinc Binding Sites:

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 6z2q

Go back to Zinc Binding Sites List in 6z2q
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 6z2q

Go back to Zinc Binding Sites List in 6z2q
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

Reference:

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
Page generated: Wed Dec 16 13:21:10 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy