Atomistry » Rubidium » PDB 1dge-4z3p » 3kdp
Atomistry »
  Rubidium »
    PDB 1dge-4z3p »
      3kdp »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy