Atomistry » Rubidium » PDB 5aw4-7w49 » 5ylv
Atomistry »
  Rubidium »
    PDB 5aw4-7w49 »
      5ylv »

Rubidium 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
Magnesium (Mg) 1 atom

Rubidium Binding Sites:

The binding sites of Rubidium 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 Rubidium atom.
In total 3 binding sites of Rubidium where determined in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080, PDB code: 5ylv:
Jump to Rubidium binding site number: 1; 2; 3;

Rubidium binding site 1 out of 3 in 5ylv

Go back to Rubidium Binding Sites List in 5ylv
Rubidium binding site 1 out of 3 in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb 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:Rb1104

b:98.1
occ:1.00
O A:VAL341 2.9 61.4 1.0
O A:ALA339 3.2 61.3 1.0
OE1 A:GLU343 3.4 60.5 1.0
OE2 A:GLU343 3.4 67.0 1.0
OE2 A:GLU820 3.6 66.9 1.0
CD A:GLU820 3.6 66.0 1.0
OE1 A:GLU820 3.7 68.3 1.0
CD A:GLU343 3.8 62.6 1.0
ND2 A:ASN792 3.9 60.9 1.0
C A:VAL341 3.9 57.7 1.0
OE1 A:GLU795 4.0 58.7 1.0
C A:ALA339 4.1 59.3 1.0
CA A:PRO342 4.3 52.8 1.0
CA A:ALA339 4.3 55.6 1.0
CG A:GLU820 4.4 57.2 1.0
CG A:ASN792 4.5 60.1 1.0
N A:PRO342 4.5 54.0 1.0
N A:GLU343 4.5 58.9 1.0
O A:VAL338 4.6 58.8 1.0
N A:VAL341 4.6 61.7 1.0
OD1 A:ASN792 4.7 52.2 1.0
CD1 A:ILE816 4.7 66.1 1.0
CD A:GLU795 4.7 60.5 1.0
CA A:VAL341 4.9 54.7 1.0
C A:PRO342 4.9 54.3 1.0

Rubidium binding site 2 out of 3 in 5ylv

Go back to Rubidium Binding Sites List in 5ylv
Rubidium binding site 2 out of 3 in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1105

b:93.2
occ:1.00
OD1 A:ASP756 2.7 47.1 1.0
O A:LYS735 2.7 55.2 1.0
O A:ALA737 2.9 47.3 1.0
O A:LEU734 3.2 56.8 1.0
O A:HOH1208 3.2 44.7 1.0
C A:LYS735 3.5 51.5 1.0
CA A:LYS735 3.7 52.2 1.0
CG A:ASP756 3.8 55.6 1.0
C A:ALA737 4.0 46.2 1.0
CB A:ASN288 4.1 62.7 1.0
N A:GLY740 4.1 49.6 1.0
O A:ALA754 4.2 49.2 1.0
C A:LEU734 4.2 43.8 1.0
OD2 A:ASP756 4.3 64.8 1.0
ND2 A:ASN288 4.4 59.2 1.0
N A:ALA737 4.4 54.8 1.0
N A:LYS735 4.5 50.6 1.0
C A:LYS736 4.6 51.9 1.0
CA A:ILE739 4.6 39.0 1.0
C A:ILE739 4.6 44.5 1.0
N A:LYS736 4.6 46.2 1.0
N A:ILE739 4.6 45.5 1.0
C A:ASP738 4.7 37.9 1.0
CA A:ALA737 4.7 49.9 1.0
CG A:ASN288 4.7 62.1 1.0
O A:LYS736 4.8 52.4 1.0
CA A:GLY740 4.8 39.7 1.0
O A:ASP738 4.8 45.9 1.0
CG A:LYS735 4.9 56.4 1.0
CB A:LYS735 4.9 49.3 1.0
CB A:ALA737 4.9 51.4 1.0

Rubidium binding site 3 out of 3 in 5ylv

Go back to Rubidium Binding Sites List in 5ylv
Rubidium binding site 3 out of 3 in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1106

b:60.0
occ:1.00
O A:SER408 2.9 42.7 1.0
OG A:SER408 2.9 54.1 1.0
O A:THR419 3.1 54.5 1.0
O A:GLN418 3.2 54.9 1.0
C A:THR419 3.6 54.9 1.0
C A:SER408 4.0 44.6 1.0
C A:GLN418 4.0 56.7 1.0
N A:PHE420 4.1 45.5 1.0
CA A:PHE420 4.1 42.1 1.0
CB A:SER408 4.2 50.3 1.0
CG A:GLN418 4.3 62.7 1.0
CA A:THR419 4.4 49.1 1.0
CA A:SER408 4.5 48.2 1.0
N A:SER408 4.5 48.3 1.0
N A:THR419 4.5 52.7 1.0
CB A:PHE420 4.5 43.0 1.0
CB A:GLN418 4.7 55.7 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: Wed Dec 16 02:07:05 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