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Rubidium in PDB 3b8e: Crystal Structure of the Sodium-Potassium Pump

Enzymatic activity of Crystal Structure of the Sodium-Potassium Pump

All present enzymatic activity of Crystal Structure of the Sodium-Potassium Pump:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of the Sodium-Potassium Pump, PDB code: 3b8e was solved by J.P.Morth, P.B.Pedersen, M.S.Toustrup-Jensen, T.L.M.Soerensen, J.Petersen, J.P.Andersen, B.Vilsen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.930, 261.500, 334.780, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.3

Other elements in 3b8e:

The structure of Crystal Structure of the Sodium-Potassium Pump also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 4 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of the Sodium-Potassium Pump (pdb code 3b8e). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 6 binding sites of Rubidium where determined in the Crystal Structure of the Sodium-Potassium Pump, PDB code: 3b8e:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6;

Rubidium binding site 1 out of 6 in 3b8e

Go back to Rubidium Binding Sites List in 3b8e
Rubidium binding site 1 out of 6 in the Crystal Structure of the Sodium-Potassium Pump


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 Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb2003

b:0.5
occ:1.00
 OG A:SER775 3.2 77.3 1.0
OD1 A:ASP804 3.4 0.5 1.0
O A:THR772 3.5 79.8 1.0
OE1 A:GLU779 3.5 0.6 1.0
N A:ASN776 3.6 95.9 1.0
C A:SER775 3.7 66.7 1.0
CA A:ASN776 3.7 95.9 1.0
CG A:ASP804 3.7 0.5 1.0
ND2 A:ASN776 3.8 0.2 1.0
CB A:ASP804 3.8 0.5 1.0
O A:SER775 3.9 66.7 1.0
CA A:LEU773 4.0 93.2 1.0
CG A:ASN776 4.1 0.2 1.0
RB A:RB2004 4.1 0.8 1.0
CD A:GLU779 4.1 0.6 1.0
CB A:ASN776 4.1 0.2 1.0
CB A:SER775 4.2 77.3 1.0
O A:LEU773 4.2 93.2 1.0
C A:THR772 4.3 79.8 1.0
CA A:SER775 4.4 66.7 1.0
C A:LEU773 4.4 93.2 1.0
OE2 A:GLU779 4.5 0.6 1.0
OD2 A:ASP804 4.6 0.5 1.0
N A:LEU773 4.6 93.2 1.0
N A:SER775 4.6 66.7 1.0
CA A:ASP804 4.7 0.7 1.0
OD2 A:ASP808 4.8 93.4 1.0
OD1 A:ASN776 4.8 0.2 1.0
CG A:GLU779 4.9 0.6 1.0
CB A:PRO326 4.9 75.7 1.0
CB A:LEU773 5.0 69.1 1.0

Rubidium binding site 2 out of 6 in 3b8e

Go back to Rubidium Binding Sites List in 3b8e
Rubidium binding site 2 out of 6 in the Crystal Structure of the Sodium-Potassium Pump


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 Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb2004

b:0.8
occ:1.00
 O A:VAL322 3.1 46.7 1.0
OE1 A:GLU327 3.4 97.5 1.0
N A:ASN324 3.4 88.4 1.0
OD1 A:ASN776 3.5 0.2 1.0
OD2 A:ASP804 3.5 0.5 1.0
OE2 A:GLU779 3.5 0.6 1.0
O A:VAL325 3.6 75.4 1.0
ND2 A:ASN776 3.9 0.2 1.0
CG A:ASN776 3.9 0.2 1.0
CG A:ASP804 3.9 0.5 1.0
C A:ALA323 4.0 69.3 1.0
C A:VAL325 4.0 75.4 1.0
OD1 A:ASP804 4.0 0.5 1.0
CA A:ALA323 4.0 69.3 1.0
C A:ASN324 4.0 88.4 1.0
CG2 A:ILE800 4.1 0.7 1.0
RB A:RB2003 4.1 0.5 1.0
CA A:ASN324 4.1 88.4 1.0
CA A:PRO326 4.2 69.1 1.0
C A:VAL322 4.2 46.7 1.0
CD A:GLU779 4.2 0.6 1.0
N A:VAL325 4.3 75.4 1.0
N A:PRO326 4.3 69.1 1.0
CD A:GLU327 4.4 97.5 1.0
O A:ASN324 4.4 88.4 1.0
OE2 A:GLU327 4.5 97.5 1.0
N A:ALA323 4.6 69.3 1.0
OE1 A:GLU779 4.7 0.6 1.0
N A:GLU327 4.8 81.4 1.0
CA A:VAL325 4.8 75.4 1.0
CB A:ASP804 4.9 0.5 1.0
O A:ALA323 4.9 69.3 1.0
CA A:ASN776 4.9 95.9 1.0
CB A:GLU779 4.9 0.6 1.0
CB A:ASN776 5.0 0.2 1.0

Rubidium binding site 3 out of 6 in 3b8e

Go back to Rubidium Binding Sites List in 3b8e
Rubidium binding site 3 out of 6 in the Crystal Structure of the Sodium-Potassium Pump


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 Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb2005

b:0.9
occ:1.00
 OD2 A:ASP740 3.5 0.6 1.0
OD1 A:ASP740 3.7 0.6 1.0
O A:LYS719 3.7 74.1 1.0
O A:ASP722 3.7 97.7 1.0
O A:ALA721 3.8 99.7 1.0
CG A:ASP740 4.0 0.6 1.0
C A:LYS719 4.6 74.1 1.0
CA A:LYS719 4.6 74.1 1.0
C A:ASP722 4.7 97.7 1.0
O A:SER718 4.9 91.9 1.0
CD A:LYS719 4.9 67.9 1.0
CA A:GLY272 5.0 0.5 1.0

Rubidium binding site 4 out of 6 in 3b8e

Go back to Rubidium Binding Sites List in 3b8e
Rubidium binding site 4 out of 6 in the Crystal Structure of the Sodium-Potassium Pump


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 Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb2003

b:0.7
occ:1.00
 OG C:SER775 3.2 0.8 1.0
O C:THR772 3.2 68.5 1.0
OE1 C:GLU779 3.4 0.5 1.0
OD1 C:ASN776 3.4 90.3 1.0
OD2 C:ASP804 3.5 0.7 1.0
OD1 C:ASP804 3.6 0.7 1.0
OE2 C:GLU779 3.8 0.5 1.0
CG C:ASP804 3.8 0.7 1.0
CD C:GLU779 3.9 0.5 1.0
N C:ASN776 4.0 92.5 1.0
CG C:ASN776 4.0 90.3 1.0
CG2 C:ILE803 4.2 0.6 1.0
CA C:ASN776 4.2 92.5 1.0
OG1 C:THR772 4.2 58.0 1.0
C C:THR772 4.2 68.5 1.0
C C:SER775 4.3 92.4 1.0
RB C:RB2004 4.4 0.6 1.0
CB C:SER775 4.4 0.8 1.0
ND2 C:ASN776 4.5 90.3 1.0
O C:SER775 4.6 92.4 1.0
OD2 C:ASP808 4.7 0.1 1.0
CB C:ASN776 4.7 90.3 1.0
CB C:ILE803 4.8 0.6 1.0
CA C:SER775 4.8 92.4 1.0
CB C:PRO326 4.9 90.9 1.0
CA C:THR772 4.9 68.5 1.0
N C:SER775 5.0 92.4 1.0
CB C:ASP804 5.0 0.7 1.0

Rubidium binding site 5 out of 6 in 3b8e

Go back to Rubidium Binding Sites List in 3b8e
Rubidium binding site 5 out of 6 in the Crystal Structure of the Sodium-Potassium Pump


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 Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb2004

b:0.6
occ:1.00
 OD1 C:ASN776 3.2 90.3 1.0
OD2 C:ASP804 3.5 0.7 1.0
O C:VAL325 3.5 80.5 1.0
OE1 C:GLU327 3.5 0.1 1.0
O C:VAL322 3.6 64.2 1.0
OD1 C:ASP804 3.6 0.7 1.0
OE2 C:GLU779 3.7 0.5 1.0
N C:ASN324 3.8 0.3 1.0
CA C:ALA323 3.8 80.3 1.0
CG C:ASP804 3.9 0.7 1.0
C C:ALA323 3.9 80.3 1.0
C C:VAL325 4.0 80.5 1.0
C C:VAL322 4.0 64.2 1.0
CG2 C:ILE800 4.1 94.7 1.0
N C:ALA323 4.1 80.3 1.0
OE2 C:GLU327 4.2 0.1 1.0
CD C:GLU327 4.2 0.1 1.0
N C:VAL325 4.3 80.5 1.0
CD C:GLU779 4.3 0.5 1.0
C C:ASN324 4.3 0.3 1.0
RB C:RB2003 4.4 0.7 1.0
N C:PRO326 4.4 68.7 1.0
CA C:PRO326 4.4 68.7 1.0
CG C:ASN776 4.5 90.3 1.0
CA C:ASN324 4.6 0.3 1.0
O C:ALA323 4.7 80.3 1.0
O C:ASN324 4.7 0.3 1.0
CA C:VAL325 4.7 80.5 1.0
CG C:GLU779 4.8 0.5 1.0
CG2 C:VAL325 4.9 0.1 1.0

Rubidium binding site 6 out of 6 in 3b8e

Go back to Rubidium Binding Sites List in 3b8e
Rubidium binding site 6 out of 6 in the Crystal Structure of the Sodium-Potassium Pump


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 Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb2005

b:0.3
occ:1.00
 OD2 C:ASP740 3.3 0.4 1.0
OD1 C:ASP740 3.5 0.4 1.0
O C:ASP722 3.8 98.2 1.0
CG C:ASP740 3.8 0.4 1.0
O C:LYS719 3.8 61.1 1.0
O C:ALA721 3.8 68.1 1.0
CA C:LYS719 4.6 61.1 1.0
C C:LYS719 4.7 61.1 1.0
C C:ASP722 4.7 98.2 1.0
O C:SER718 4.8 72.2 1.0
O C:ALA738 4.9 72.0 1.0
CD C:LYS719 4.9 52.7 1.0

Reference:

J.P.Morth, B.P.Pedersen, M.S.Toustrup-Jensen, T.L.Sorensen, J.Petersen, J.P.Andersen, B.Vilsen, P.Nissen. Crystal Structure of the Sodium-Potassium Pump. Nature V. 450 1043 2007.
ISSN: ISSN 0028-0836
PubMed: 18075585
DOI: 10.1038/NATURE06419
Page generated: Thu Oct 10 11:59:42 2024

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