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Rubidium in PDB 3kdp: 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: 3kdp was solved by J.P.Morth, B.P.Pedersen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.86 / 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 (%) 24.2 / 28.6

Other elements in 3kdp:

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 3kdp). 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: 3kdp:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6;

Rubidium binding site 1 out of 6 in 3kdp

Go back to Rubidium Binding Sites List in 3kdp
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:0.0
occ:1.00
 OD2 A:ASP804 2.8 76.6 1.0
OG A:SER775 2.9 0.3 1.0
OD1 A:ASN776 2.9 91.2 1.0
OE2 A:GLU779 3.2 0.8 1.0
O A:THR772 3.4 77.8 1.0
CG2 A:ILE803 3.5 0.5 1.0
N A:ASN776 3.6 64.0 1.0
C A:SER775 3.7 87.6 1.0
CG A:ASP804 3.8 94.8 1.0
CA A:ASN776 3.9 63.3 1.0
CG A:ASN776 3.9 78.5 1.0
O A:SER775 4.0 91.5 1.0
CD A:GLU779 4.0 0.9 1.0
CB A:SER775 4.0 97.4 1.0
CB A:ASN776 4.2 63.7 1.0
RB A:RB2004 4.3 0.8 1.0
CB A:ASP804 4.3 0.7 1.0
C A:THR772 4.3 82.9 1.0
OD2 A:ASP808 4.3 0.1 1.0
CA A:SER775 4.3 85.5 1.0
OE1 A:GLU779 4.4 0.9 1.0
CG2 A:THR772 4.5 0.8 1.0
CB A:ILE803 4.7 0.7 1.0
N A:SER775 4.7 85.3 1.0
OD1 A:ASP804 4.8 0.1 1.0
N A:ASP804 5.0 1.0 1.0
CA A:THR772 5.0 95.4 1.0

Rubidium binding site 2 out of 6 in 3kdp

Go back to Rubidium Binding Sites List in 3kdp
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
 OD1 A:ASN776 2.9 91.2 1.0
OD2 A:ASP804 3.0 76.6 1.0
O A:VAL322 3.1 67.3 1.0
OE1 A:GLU327 3.1 0.2 1.0
O A:VAL325 3.1 82.5 1.0
OE2 A:GLU779 3.2 0.8 1.0
CG A:ASN776 3.8 78.5 1.0
CG A:ASP804 3.9 94.8 1.0
O A:ALA323 3.9 72.0 1.0
C A:VAL325 3.9 75.4 1.0
C A:ALA323 3.9 80.5 1.0
CG2 A:ILE800 3.9 0.8 1.0
CD A:GLU779 4.0 0.9 1.0
CA A:PRO326 4.0 0.6 1.0
ND2 A:ASN776 4.1 82.3 1.0
OD1 A:ASP804 4.1 0.1 1.0
CD A:GLU327 4.2 0.4 1.0
C A:VAL322 4.2 68.6 1.0
CA A:ALA323 4.2 90.7 1.0
OE1 A:GLU779 4.3 0.9 1.0
RB A:RB2003 4.3 0.0 1.0
N A:PRO326 4.4 0.8 1.0
N A:ASN324 4.4 0.8 1.0
C A:PRO326 4.4 0.1 1.0
OE2 A:GLU327 4.6 0.9 1.0
C A:ASN324 4.6 89.9 1.0
O A:PRO326 4.7 94.5 1.0
N A:ALA323 4.7 97.6 1.0
O A:ASN324 4.7 80.7 1.0
N A:VAL325 4.9 88.8 1.0
CA A:ASN324 4.9 95.2 1.0
N A:GLU327 4.9 0.6 1.0

Rubidium binding site 3 out of 6 in 3kdp

Go back to Rubidium Binding Sites List in 3kdp
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:0.0
occ:1.00
 O A:ALA721 3.4 0.1 1.0
OD1 A:ASP740 3.7 68.9 1.0
OD2 A:ASP740 3.7 97.1 1.0
CG A:ASP740 4.1 83.4 1.0
C A:LYS719 4.4 40.0 1.0
O A:LYS719 4.4 53.7 1.0
CA A:LYS719 4.5 45.7 1.0
C A:ALA721 4.5 1.0 1.0
N A:ALA721 4.7 0.1 1.0
O A:SER718 4.7 0.3 1.0
CA A:GLY272 4.8 0.2 1.0
CG A:LYS719 4.8 87.8 1.0
N A:LYS720 4.9 92.8 1.0
O A:GLY272 5.0 0.0 1.0

Rubidium binding site 4 out of 6 in 3kdp

Go back to Rubidium Binding Sites List in 3kdp
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:0.2
occ:1.00
 OD1 C:ASN776 2.9 0.0 1.0
OD2 C:ASP804 2.9 0.1 1.0
OG C:SER775 2.9 0.3 1.0
OE2 C:GLU779 3.2 0.9 1.0
O C:THR772 3.2 77.8 1.0
N C:ASN776 3.5 80.0 1.0
C C:SER775 3.6 93.0 1.0
CG2 C:ILE803 3.7 0.9 1.0
CA C:ASN776 3.7 82.8 1.0
CG C:ASN776 3.8 0.0 1.0
O C:SER775 3.9 98.9 1.0
CG C:ASP804 4.0 0.4 1.0
CB C:SER775 4.0 0.2 1.0
CB C:ASN776 4.0 86.8 1.0
CD C:GLU779 4.0 0.9 1.0
C C:THR772 4.2 78.4 1.0
CA C:SER775 4.2 88.6 1.0
OD2 C:ASP808 4.4 0.4 1.0
OE1 C:GLU779 4.4 0.0 1.0
CB C:ASP804 4.4 0.6 1.0
RB C:RB2004 4.5 0.2 1.0
CG2 C:THR772 4.5 96.7 1.0
N C:SER775 4.6 86.2 1.0
CB C:ILE803 4.9 0.4 1.0
CA C:THR772 4.9 79.6 1.0
OD1 C:ASP804 4.9 0.9 1.0
ND2 C:ASN776 5.0 0.6 1.0

Rubidium binding site 5 out of 6 in 3kdp

Go back to Rubidium Binding Sites List in 3kdp
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:0.2
occ:1.00
 OD1 C:ASN776 2.8 0.0 1.0
O C:VAL322 3.1 79.1 1.0
O C:VAL325 3.3 0.6 1.0
OD2 C:ASP804 3.3 0.1 1.0
OE2 C:GLU779 3.4 0.9 1.0
OE1 C:GLU327 3.4 0.3 1.0
CG C:ASN776 3.7 0.0 1.0
C C:VAL325 3.7 96.1 1.0
ND2 C:ASN776 3.9 0.6 1.0
OE2 C:GLU327 3.9 0.6 1.0
C C:ALA323 4.0 98.3 1.0
CD C:GLU327 4.1 0.3 1.0
CA C:PRO326 4.1 0.8 1.0
N C:PRO326 4.1 0.8 1.0
CG C:ASP804 4.1 0.4 1.0
N C:ASN324 4.1 0.0 1.0
N C:VAL325 4.2 96.6 1.0
CG2 C:ILE800 4.2 0.3 1.0
CD C:GLU779 4.2 0.9 1.0
CA C:ALA323 4.3 0.3 1.0
C C:VAL322 4.3 85.2 1.0
O C:ALA323 4.3 88.6 1.0
C C:ASN324 4.4 0.8 1.0
OD1 C:ASP804 4.4 0.9 1.0
RB C:RB2003 4.5 0.2 1.0
OE1 C:GLU779 4.5 0.0 1.0
CA C:VAL325 4.6 94.2 1.0
N C:GLU327 4.6 0.0 1.0
CA C:ASN324 4.7 0.2 1.0
N C:ALA323 4.8 0.5 1.0
O C:ASN324 4.9 99.5 1.0
C C:PRO326 4.9 0.6 1.0

Rubidium binding site 6 out of 6 in 3kdp

Go back to Rubidium Binding Sites List in 3kdp
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:0.4
occ:1.00
 OD2 C:ASP740 3.3 0.8 1.0
OD1 C:ASP740 3.4 79.6 1.0
O C:ALA721 3.6 0.1 1.0
CG C:ASP740 3.7 95.1 1.0
CA C:LYS719 4.6 43.1 1.0
O C:SER718 4.7 1.0 1.0
C C:LYS719 4.7 37.2 1.0
O C:LYS719 4.7 50.2 1.0
C C:ALA721 4.8 0.6 1.0
CG C:LYS719 4.8 86.2 1.0
N C:ALA721 5.0 0.3 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 12:01:41 2024

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