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Rubidium in PDB 3e8b: Crystal Structure of the the Open Nak Channel- Rb+ Complex

Protein crystallography data

The structure of Crystal Structure of the the Open Nak Channel- Rb+ Complex, PDB code: 3e8b was solved by Y.Jiang, A.Alam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.09 / 1.70
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 68.134, 68.134, 89.359, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 22.9

Rubidium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Rubidium atom in the Crystal Structure of the the Open Nak Channel- Rb+ Complex (pdb code 3e8b). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 11 binding sites of Rubidium where determined in the Crystal Structure of the the Open Nak Channel- Rb+ Complex, PDB code: 3e8b:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Rubidium binding site 1 out of 11 in 3e8b

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Rubidium binding site 1 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


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 the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb2

b:9.1
occ:0.25
RB A:RB3 2.9 48.9 0.2
O A:THR63 2.9 12.1 1.0
O A:VAL64 3.0 14.6 1.0
C A:VAL64 3.6 13.0 1.0
RB A:RB6 3.8 16.3 0.2
C A:THR63 4.0 12.7 1.0
CA A:VAL64 4.1 11.9 1.0
N A:GLY65 4.4 11.1 1.0
N A:VAL64 4.6 12.2 1.0
CA A:GLY65 4.8 14.0 1.0

Rubidium binding site 2 out of 11 in 3e8b

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Rubidium binding site 2 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


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 the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb3

b:48.9
occ:0.25
O A:HOH506 2.8 16.3 1.0
RB A:RB2 2.9 9.1 0.2
RB A:RB10 3.0 97.0 0.2
O A:VAL64 3.1 14.6 1.0
C A:VAL64 4.2 13.0 1.0
CA A:GLY65 4.2 14.0 1.0
C A:GLY65 4.6 17.3 1.0
N A:GLY65 4.7 11.1 1.0
O A:GLY65 4.8 19.8 1.0

Rubidium binding site 3 out of 11 in 3e8b

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Rubidium binding site 3 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


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 the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb4

b:24.8
occ:0.25
O A:GLY67 2.5 15.0 1.0
O A:HOH505 2.8 20.7 1.0
C A:GLY67 3.7 15.3 1.0
RB A:RB9 4.1 72.6 0.2
CA A:GLY67 4.5 14.2 1.0
CA A:ASN68 4.6 16.1 1.0
N A:ASN68 4.6 13.1 1.0
ND2 A:ASN68 4.8 14.4 1.0
O A:HOH534 4.8 41.0 1.0

Rubidium binding site 4 out of 11 in 3e8b

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Rubidium binding site 4 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Crystal Structure of the the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb6

b:16.3
occ:0.25
OG1 A:THR63 2.9 17.2 1.0
O A:THR63 3.0 12.1 1.0
CB A:THR63 3.5 18.6 1.0
RB A:RB2 3.8 9.1 0.2
C A:THR63 3.8 12.7 1.0
CA A:THR63 4.4 14.0 1.0
CG2 A:THR63 4.8 14.5 1.0
N A:VAL64 4.8 12.2 1.0

Rubidium binding site 5 out of 11 in 3e8b

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Rubidium binding site 5 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Crystal Structure of the the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb9

b:72.6
occ:0.25
O A:HOH505 3.3 20.7 1.0
O A:HOH534 3.7 41.0 1.0
RB A:RB4 4.1 24.8 0.2

Rubidium binding site 6 out of 11 in 3e8b

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Rubidium binding site 6 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Crystal Structure of the the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb10

b:97.0
occ:0.25
O A:HOH506 2.7 16.3 1.0
RB A:RB3 3.0 48.9 0.2
O A:ASP66 3.8 17.6 1.0
CA A:GLY67 3.8 14.2 1.0
C A:ASP66 4.2 17.3 1.0
N A:GLY67 4.2 17.1 1.0
C A:GLY67 5.0 15.3 1.0

Rubidium binding site 7 out of 11 in 3e8b

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Rubidium binding site 7 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 7 of Crystal Structure of the the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb1

b:20.3
occ:0.25
RB B:RB7 2.8 87.7 0.2
O B:THR63 2.9 22.9 1.0
O B:VAL64 3.0 26.1 1.0
C B:VAL64 3.6 24.6 1.0
RB B:RB5 3.9 23.9 0.2
C B:THR63 4.0 23.1 1.0
CA B:VAL64 4.2 23.2 1.0
N B:GLY65 4.4 25.5 1.0
N B:VAL64 4.6 21.5 1.0
CA B:GLY65 4.7 29.0 1.0
O B:HOH513 4.8 30.1 1.0

Rubidium binding site 8 out of 11 in 3e8b

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Rubidium binding site 8 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 8 of Crystal Structure of the the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb5

b:23.9
occ:0.25
OG1 B:THR63 2.9 24.6 1.0
O B:THR63 3.1 22.9 1.0
CB B:THR63 3.4 25.1 1.0
C B:THR63 3.9 23.1 1.0
RB B:RB1 3.9 20.3 0.2
CA B:THR63 4.3 22.4 1.0
CG2 B:THR63 4.6 21.7 1.0
N B:VAL64 4.9 21.5 1.0

Rubidium binding site 9 out of 11 in 3e8b

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Rubidium binding site 9 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 9 of Crystal Structure of the the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb7

b:87.7
occ:0.25
O B:HOH513 2.6 30.1 1.0
RB B:RB1 2.8 20.3 0.2
O B:VAL64 3.2 26.1 1.0
CA B:GLY65 4.2 29.0 1.0
C B:VAL64 4.3 24.6 1.0
C B:GLY65 4.6 31.5 1.0
N B:GLY65 4.7 25.5 1.0
O B:GLY65 4.9 30.1 1.0

Rubidium binding site 10 out of 11 in 3e8b

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Rubidium binding site 10 out of 11 in the Crystal Structure of the the Open Nak Channel- Rb+ Complex


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 10 of Crystal Structure of the the Open Nak Channel- Rb+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb8

b:65.1
occ:0.25
O B:GLY67 2.8 46.2 1.0
C B:GLY67 3.8 45.5 1.0
RB B:RB11 4.2 75.3 0.2
OD1 B:ASN68 4.4 51.6 1.0
CA B:ASN68 4.6 47.2 1.0
N B:ASN68 4.6 46.3 1.0
CA B:GLY67 4.6 44.0 1.0

Reference:

A.Alam, Y.Jiang. Structural Analysis of Ion Selectivity in the Nak Channel Nat.Struct.Mol.Biol. V. 16 35 2009.
ISSN: ISSN 1545-9993
PubMed: 19098915
DOI: 10.1038/NSMB.1537
Page generated: Wed Dec 16 02:06:46 2020

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