Zinc in PDB 6z2d: Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in P 41 21 2

Protein crystallography data

The structure of Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in P 41 21 2, PDB code: 6z2d 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) 29.02 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.861, 64.861, 187.426, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in P 41 21 2 (pdb code 6z2d). 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 P 41 21 2, PDB code: 6z2d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6z2d

Go back to Zinc Binding Sites List in 6z2d
Zinc binding site 1 out of 2 in the Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in P 41 21 2


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 P 41 21 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:22.7
occ:0.31
OE1 A:GLN308 2.2 32.5 1.0
OD1 A:ASP319 2.2 33.4 1.0
O A:GLN316 2.3 30.8 1.0
O A:ASP309 2.3 24.0 1.0
O A:HOH588 2.5 27.5 1.0
O A:PRO311 2.6 32.6 1.0
CG A:ASP319 3.1 30.3 1.0
OD2 A:ASP319 3.3 37.7 1.0
CD A:GLN308 3.3 27.3 1.0
C A:GLN316 3.4 38.0 1.0
C A:ASP309 3.5 25.9 1.0
C A:PRO311 3.8 29.6 1.0
CA A:ASP317 3.8 29.7 1.0
CG A:GLN308 4.0 23.1 1.0
C A:PRO310 4.0 22.2 1.0
N A:ASP317 4.1 31.8 1.0
O A:HOH599 4.1 35.1 1.0
CB A:GLN308 4.1 25.0 1.0
O A:PRO310 4.2 23.0 1.0
N A:PRO311 4.3 28.2 1.0
N A:ASP309 4.3 20.7 1.0
CA A:PRO310 4.4 23.9 1.0
CA A:ASP309 4.4 21.5 1.0
N A:PRO310 4.4 18.6 1.0
NE2 A:GLN308 4.4 29.0 1.0
O A:HOH649 4.5 43.9 1.0
CB A:ASP319 4.6 32.9 1.0
CA A:TYR312 4.6 37.4 1.0
CA A:GLN316 4.6 35.3 1.0
CB A:ASP317 4.6 32.9 1.0
N A:TYR312 4.7 31.0 1.0
CB A:GLN316 4.7 37.1 1.0
CA A:PRO311 4.7 28.4 1.0
CD1 A:TYR312 4.8 29.0 1.0
CB A:ASP309 4.8 21.3 1.0
C A:ASP317 4.8 29.3 1.0
C A:GLN308 4.9 24.2 1.0
CD A:PRO311 4.9 28.3 1.0

Zinc binding site 2 out of 2 in 6z2d

Go back to Zinc Binding Sites List in 6z2d
Zinc binding site 2 out of 2 in the Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in P 41 21 2


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 P 41 21 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:28.1
occ:1.00
NE2 A:HIS215 2.0 27.9 1.0
NE2 A:HIS205 2.1 21.6 1.0
NE2 A:HIS209 2.1 22.2 1.0
O A:HOH509 2.3 36.9 1.0
O A:HOH609 2.3 31.3 1.0
O A:HOH632 2.4 37.3 1.0
CD2 A:HIS205 3.0 18.4 1.0
CD2 A:HIS209 3.0 21.1 1.0
CE1 A:HIS215 3.0 27.9 1.0
CD2 A:HIS215 3.0 24.2 1.0
CE1 A:HIS209 3.1 23.9 1.0
CE1 A:HIS205 3.1 24.6 1.0
ND1 A:HIS215 4.1 28.1 1.0
CG A:HIS205 4.1 22.0 1.0
CG A:HIS215 4.2 27.6 1.0
ND1 A:HIS205 4.2 23.4 1.0
CG A:HIS209 4.2 21.8 1.0
ND1 A:HIS209 4.2 20.2 1.0
OH A:TYR318 4.2 45.1 1.0
CE1 A:TYR318 4.2 35.5 1.0
O A:HOH637 4.3 39.2 1.0
CZ A:TYR318 4.7 34.6 1.0
OD1 A:ASN315 4.8 53.8 0.9
CE A:MET231 4.8 20.0 1.0
OE1 A:GLU206 4.9 24.8 1.0
OE2 A:GLU206 5.0 36.4 1.0

Reference:

B.Trastoy, A.Naegali, I.Anso, J.Sjogren, M.E.Guerin. Crystal Structure of Wild Type Ogpa From Akkermansia Muciniphila in P 41 21 2 Nat Commun 2020.
ISSN: ESSN 2041-1723
Page generated: Wed Dec 16 13:20:41 2020

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