Atomistry » Rubidium » PDB 1dge-4z3p » 3b8e
Atomistry »
  Rubidium »
    PDB 1dge-4z3p »
      3b8e »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy