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Rubidium in PDB 1x2w: Crystal Structure of Apo-Habu IX-Bp at pH 4.6

Protein crystallography data

The structure of Crystal Structure of Apo-Habu IX-Bp at pH 4.6, PDB code: 1x2w was solved by N.Suzuki, Z.Fujimoto, T.Morita, A.Fukamizu, H.Mizuno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.68 / 2.29
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.121, 37.831, 55.828, 90.00, 110.46, 90.00
R / Rfree (%) 21.4 / 28

Other elements in 1x2w:

The structure of Crystal Structure of Apo-Habu IX-Bp at pH 4.6 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of Apo-Habu IX-Bp at pH 4.6 (pdb code 1x2w). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 2 binding sites of Rubidium where determined in the Crystal Structure of Apo-Habu IX-Bp at pH 4.6, PDB code: 1x2w:
Jump to Rubidium binding site number: 1; 2;

Rubidium binding site 1 out of 2 in 1x2w

Go back to Rubidium Binding Sites List in 1x2w
Rubidium binding site 1 out of 2 in the Crystal Structure of Apo-Habu IX-Bp at pH 4.6


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 Apo-Habu IX-Bp at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb402

b:53.5
occ:0.50
O A:HOH564 3.1 50.4 1.0
O A:HOH455 3.7 27.8 1.0
N A:LYS77 3.8 26.5 1.0
CG A:LYS77 4.0 22.6 1.0
CB A:LYS77 4.3 24.1 1.0
CA A:GLU76 4.3 27.1 1.0
C A:GLU76 4.6 27.2 1.0
CA A:LYS77 4.7 25.8 1.0
OE1 A:GLU92 4.8 24.8 1.0
CB A:GLU76 4.9 27.7 1.0

Rubidium binding site 2 out of 2 in 1x2w

Go back to Rubidium Binding Sites List in 1x2w
Rubidium binding site 2 out of 2 in the Crystal Structure of Apo-Habu IX-Bp at pH 4.6


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 Apo-Habu IX-Bp at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb403

b:48.3
occ:0.70
O A:TRP6 3.0 27.7 1.0
O A:HOH437 3.1 20.3 1.0
O A:CYS2 3.2 30.7 1.0
O A:HOH540 3.4 35.0 1.0
O A:PRO3 3.4 34.0 1.0
O A:ASP1 3.8 46.5 1.0
O A:HOH428 3.9 25.5 1.0
C A:PRO3 3.9 33.7 1.0
C A:CYS2 4.0 33.8 1.0
C A:TRP6 4.2 26.4 1.0
CA A:SER4 4.2 32.4 1.0
N A:SER4 4.3 32.6 1.0
CB A:CYS2 4.4 32.5 1.0
O A:HOH480 4.5 35.0 1.0
N A:GLY5 4.5 28.7 1.0
N A:TRP6 4.6 24.3 1.0
N A:PRO3 4.7 33.5 1.0
CA A:CYS2 4.7 35.1 1.0
C A:SER4 4.8 30.3 1.0
C A:ASP1 4.8 45.6 1.0
CA A:PRO3 4.8 34.0 1.0
CA A:TRP6 4.9 25.8 1.0

Reference:

N.Suzuki, Z.Fujimoto, T.Morita, A.Fukamizu, H.Mizuno. pH-Dependent Structural Changes at Ca(2+)-Binding Sites of Coagulation Factor IX-Binding Protein J.Mol.Biol. V. 353 80 2005.
ISSN: ISSN 0022-2836
PubMed: 16165155
DOI: 10.1016/J.JMB.2005.08.018
Page generated: Mon Jan 25 16:02:00 2021

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