Magnesium in PDB 5ylv: Crystal Structure of the Gastric Proton Pump Complexed with SCH28080

Enzymatic activity of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080

All present enzymatic activity of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080:
3.6.3.10;

Protein crystallography data

The structure of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080, PDB code: 5ylv was solved by K.Abe, K.Irie, H.Nakanishi, Y.Fujiyoshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.30 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.050, 105.050, 368.540, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 29.2

Other elements in 5ylv:

The structure of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Rubidium (Rb) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 (pdb code 5ylv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080, PDB code: 5ylv:

Magnesium binding site 1 out of 1 in 5ylv

Go back to Magnesium Binding Sites List in 5ylv
Magnesium binding site 1 out of 1 in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:39.0
occ:1.00
 F1 A:BFD385 1.3 46.7 1.0
OD1 A:ASP726 2.2 48.4 1.0
OD2 A:BFD385 2.5 48.9 1.0
O A:THR387 2.6 47.4 1.0
CG A:ASP726 3.0 43.6 1.0
BE A:BFD385 3.0 44.3 1.0
OD2 A:ASP726 3.1 43.4 1.0
O A:SER225 3.4 46.4 1.0
CG A:BFD385 3.5 46.9 1.0
C A:THR387 3.8 43.8 1.0
OD1 A:BFD385 3.8 45.9 1.0
N A:GLY727 3.8 38.3 1.0
OD1 A:ASN729 4.0 44.9 1.0
F3 A:BFD385 4.0 49.4 1.0
CA A:GLY727 4.1 43.7 1.0
CB A:THR387 4.2 48.9 1.0
F2 A:BFD385 4.3 48.8 1.0
OD2 A:ASP730 4.3 47.5 1.0
CA A:THR387 4.4 41.2 1.0
CB A:ASP726 4.5 43.7 1.0
C A:SER225 4.6 46.3 1.0
ND2 A:ASN729 4.6 40.8 1.0
CG2 A:THR387 4.7 45.4 1.0
CG A:ASN729 4.7 39.1 1.0
N A:THR387 4.8 37.6 1.0
OG1 A:THR389 4.8 34.7 1.0
N A:GLY388 4.8 38.4 1.0
C A:ASP726 4.8 43.6 1.0
CB A:BFD385 4.9 45.9 1.0
N A:ASP726 4.9 42.5 1.0
CA A:ASP726 5.0 46.4 1.0

Reference:

K.Abe, K.Irie, H.Nakanishi, H.Suzuki, Y.Fujiyoshi. Crystal Structures of the Gastric Proton Pump Nature V. 556 214 2018.
ISSN: ESSN 1476-4687
PubMed: 29618813
DOI: 10.1038/S41586-018-0003-8
Page generated: Mon Dec 14 22:14:01 2020

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