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Yttrium in PDB 2bec: Crystal Structure of CHP2 in Complex with Its Binding Region in NHE1 and Insights Into the Mechanism of pH Regulation

Protein crystallography data

The structure of Crystal Structure of CHP2 in Complex with Its Binding Region in NHE1 and Insights Into the Mechanism of pH Regulation, PDB code: 2bec was solved by Y.Ben Ammar, S.Takeda, T.Hisamitsu, H.Mori, S.Wakabayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 49.262, 49.262, 102.587, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 28.7

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of CHP2 in Complex with Its Binding Region in NHE1 and Insights Into the Mechanism of pH Regulation (pdb code 2bec). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 2 binding sites of Yttrium where determined in the Crystal Structure of CHP2 in Complex with Its Binding Region in NHE1 and Insights Into the Mechanism of pH Regulation, PDB code: 2bec:
Jump to Yttrium binding site number: 1; 2;

Yttrium binding site 1 out of 2 in 2bec

Go back to Yttrium Binding Sites List in 2bec
Yttrium binding site 1 out of 2 in the Crystal Structure of CHP2 in Complex with Its Binding Region in NHE1 and Insights Into the Mechanism of pH Regulation


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of CHP2 in Complex with Its Binding Region in NHE1 and Insights Into the Mechanism of pH Regulation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y1201

b:93.3
occ:1.00
OD1 A:ASP167 2.2 98.8 1.0
OD2 A:ASP169 2.3 78.5 1.0
O A:ALA171 2.3 73.6 1.0
OE1 A:GLU176 2.5 95.5 1.0
OD1 A:ASP165 2.7 59.3 1.0
OE2 A:GLU176 2.8 85.2 1.0
CG A:ASP169 2.9 80.5 1.0
CD A:GLU176 2.9 83.8 1.0
OD1 A:ASP169 3.1 75.4 1.0
CG A:ASP167 3.3 89.1 1.0
C A:ALA171 3.4 68.8 1.0
CG A:ASP165 3.9 70.0 1.0
OD2 A:ASP167 3.9 87.3 1.0
N A:SER173 4.0 38.2 1.0
CB A:ASP169 4.1 77.1 1.0
CA A:VAL172 4.1 48.7 1.0
N A:VAL172 4.1 62.9 1.0
N A:ASP169 4.2 81.4 1.0
N A:ALA171 4.2 69.7 1.0
CG A:GLU176 4.2 76.5 1.0
CA A:ALA171 4.3 70.1 1.0
N A:ASP167 4.4 92.0 1.0
CB A:ASP167 4.4 85.2 1.0
C A:VAL172 4.5 48.5 1.0
CA A:ASP169 4.6 78.5 1.0
CA A:ASP165 4.7 75.7 1.0
OG A:SER173 4.7 78.3 1.0
N A:GLU166 4.7 91.7 1.0
OD2 A:ASP165 4.7 64.0 1.0
CB A:ASP165 4.7 71.7 1.0
C A:ASP167 4.8 88.0 1.0
CA A:ASP167 4.8 87.0 1.0
N A:GLY168 4.8 89.5 1.0
N A:GLY170 4.8 74.1 1.0
CB A:SER173 4.8 51.5 1.0
CB A:ALA171 4.9 58.1 1.0
C A:ASP169 4.9 79.8 1.0

Yttrium binding site 2 out of 2 in 2bec

Go back to Yttrium Binding Sites List in 2bec
Yttrium binding site 2 out of 2 in the Crystal Structure of CHP2 in Complex with Its Binding Region in NHE1 and Insights Into the Mechanism of pH Regulation


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of CHP2 in Complex with Its Binding Region in NHE1 and Insights Into the Mechanism of pH Regulation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y1202

b:47.7
occ:1.00
OE1 A:GLU135 2.1 48.8 1.0
OD2 A:ASP124 2.2 58.3 1.0
O A:LYS130 2.3 52.5 1.0
OD2 A:ASP128 2.3 56.5 1.0
OD1 A:ASP126 2.4 58.6 1.0
OE2 A:GLU135 2.4 33.1 1.0
CD A:GLU135 2.6 45.8 1.0
CG A:ASP128 2.7 65.1 1.0
OD1 A:ASP128 2.8 72.2 1.0
CG A:ASP124 3.2 55.9 1.0
CG A:ASP126 3.2 55.3 1.0
OD2 A:ASP126 3.5 55.0 1.0
C A:LYS130 3.5 46.4 1.0
OD1 A:ASP124 3.9 54.9 1.0
CB A:ASP128 4.0 56.9 1.0
CG A:GLU135 4.0 18.0 1.0
CB A:ASP124 4.1 44.6 1.0
N A:ASP128 4.2 55.1 1.0
CA A:ASP124 4.2 44.2 1.0
N A:LYS130 4.3 39.0 1.0
N A:SER132 4.3 53.6 1.0
CG A:LYS130 4.4 69.9 1.0
CA A:LYS130 4.4 48.0 1.0
N A:ILE131 4.4 42.1 1.0
CA A:ILE131 4.5 43.6 1.0
CB A:ASP126 4.5 39.8 1.0
CA A:ASP128 4.6 55.2 1.0
N A:ASP126 4.7 47.0 1.0
C A:ASP124 4.7 50.5 1.0
OG A:SER132 4.9 39.0 1.0
N A:ARG127 4.9 50.4 1.0
N A:GLY129 4.9 58.3 1.0
C A:ILE131 4.9 51.3 1.0
CB A:GLU135 4.9 34.0 1.0
CA A:ASP126 5.0 49.8 1.0
N A:LEU125 5.0 55.7 1.0

Reference:

Y.Ben Ammar, S.Takeda, T.Hisamitsu, H.Mori, S.Wakabayashi. Crystal Structure of CHP2 Complexed with NHE1-Cytosolic Region and An Implication For pH Regulation Embo J. V. 25 2315 2006.
ISSN: ISSN 0261-4189
PubMed: 16710297
DOI: 10.1038/SJ.EMBOJ.7601145
Page generated: Mon Jan 25 16:07:15 2021

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