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Potassium in PDB 6afs: Proton Pyrophosphatase - Two Phosphates-Bound

Enzymatic activity of Proton Pyrophosphatase - Two Phosphates-Bound

All present enzymatic activity of Proton Pyrophosphatase - Two Phosphates-Bound:
3.6.1.1;

Protein crystallography data

The structure of Proton Pyrophosphatase - Two Phosphates-Bound, PDB code: 6afs was solved by J.-Y.Tsai, K.-M.Li, Y.-J.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.49 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 217.641, 88.433, 159.050, 90.00, 125.47, 90.00
R / Rfree (%) 20.8 / 24

Other elements in 6afs:

The structure of Proton Pyrophosphatase - Two Phosphates-Bound also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Proton Pyrophosphatase - Two Phosphates-Bound (pdb code 6afs). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Proton Pyrophosphatase - Two Phosphates-Bound, PDB code: 6afs:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6afs

Go back to Potassium Binding Sites List in 6afs
Potassium binding site 1 out of 2 in the Proton Pyrophosphatase - Two Phosphates-Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Proton Pyrophosphatase - Two Phosphates-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1008

b:41.7
occ:1.00
O A:HOH1181 2.8 31.9 1.0
O A:HOH1264 2.8 34.2 1.0
O A:HOH1193 2.9 31.7 1.0
O A:HOH1215 3.1 35.7 1.0
O A:HOH1138 3.2 33.4 1.0
OD1 A:ASN534 3.3 34.9 1.0
O3 A:PO41001 3.4 36.1 1.0
O A:GLY533 3.5 35.5 1.0
C A:GLY533 3.8 34.6 1.0
N A:ASN534 4.0 33.5 1.0
CA A:ASN534 4.0 33.8 1.0
MG A:MG1007 4.0 37.1 1.0
O A:HOH1131 4.1 39.0 1.0
CB A:ALA537 4.1 30.3 1.0
CG A:ASN534 4.4 34.5 1.0
P A:PO41001 4.4 50.3 1.0
O A:HOH1152 4.4 26.2 1.0
C A:GLY503 4.5 34.2 1.0
O1 A:PO41001 4.5 36.0 1.0
OD2 A:ASP287 4.5 34.6 1.0
OD1 A:ASP530 4.6 37.8 1.0
O A:GLY503 4.6 31.1 1.0
O2 A:PO41001 4.6 32.0 1.0
CA A:GLY533 4.6 31.1 1.0
N A:PRO504 4.7 34.5 1.0
CA A:GLY503 4.7 30.0 1.0
CB A:ASN534 4.8 32.5 1.0
O A:ASP530 4.9 38.3 1.0
OD2 A:ASP507 4.9 34.8 1.0
CD A:PRO504 5.0 30.6 1.0

Potassium binding site 2 out of 2 in 6afs

Go back to Potassium Binding Sites List in 6afs
Potassium binding site 2 out of 2 in the Proton Pyrophosphatase - Two Phosphates-Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Proton Pyrophosphatase - Two Phosphates-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1008

b:57.6
occ:1.00
O B:HOH1205 2.7 44.0 1.0
O B:HOH1128 2.9 42.7 1.0
O B:HOH1202 2.9 42.2 1.0
O B:HOH1167 3.0 48.1 1.0
O3 B:PO41001 3.2 45.5 1.0
OD1 B:ASN534 3.2 44.2 1.0
MG B:MG1007 3.8 44.3 1.0
O B:GLY533 4.0 51.9 1.0
O1 B:PO41001 4.1 42.4 1.0
P B:PO41001 4.2 52.3 1.0
O B:HOH1158 4.2 49.7 1.0
CA B:ASN534 4.2 46.2 1.0
C B:GLY533 4.3 52.4 1.0
N B:ASN534 4.3 45.8 1.0
CG B:ASN534 4.4 48.8 1.0
CB B:ALA537 4.4 45.6 1.0
OD2 B:ASP287 4.4 49.4 1.0
O4 B:PO41001 4.6 41.5 1.0
C B:GLY503 4.7 45.8 1.0
OD1 B:ASP530 4.8 49.8 1.0
O B:GLY503 4.8 44.5 1.0
OD2 B:ASP507 4.9 44.6 1.0
N B:PRO504 4.9 48.2 1.0
CB B:ASN534 4.9 50.3 1.0
CA B:GLY503 5.0 43.5 1.0
O B:HOH1198 5.0 42.3 1.0

Reference:

J.Y.Tsai, K.Z.Tang, K.M.Li, B.L.Hsu, Y.W.Chiang, A.Goldman, Y.J.Sun. Roles of the Hydrophobic Gate and Exit Channel in Vigna Radiata Pyrophosphatase Ion Translocation. J. Mol. Biol. V. 431 1619 2019.
ISSN: ESSN 1089-8638
PubMed: 30878480
DOI: 10.1016/J.JMB.2019.03.009
Page generated: Mon Dec 14 00:16:59 2020

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