Atomistry » Zinc » PDB 6yzl-6z85 » 6z2d
Atomistry »
  Zinc »
    PDB 6yzl-6z85 »
      6z2d »

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: Tue Oct 29 15:22:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy