Atomistry » Magnesium » PDB 3wcw-3wow » 3wgv
Atomistry »
  Magnesium »
    PDB 3wcw-3wow »
      3wgv »

Magnesium in PDB 3wgv: Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin

Enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin

All present enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin, PDB code: 3wgv was solved by R.Kanai, H.Ogawa, B.Vilsen, F.Cornelius, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.99 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.285, 210.183, 256.086, 90.00, 90.00, 90.00
R / Rfree (%) 27 / 29.8

Other elements in 3wgv:

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Aluminium (Al) 2 atoms
Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin (pdb code 3wgv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin, PDB code: 3wgv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3wgv

Go back to Magnesium Binding Sites List in 3wgv
Magnesium binding site 1 out of 4 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:61.4
occ:1.00
 O A:HOH2102 2.2 24.5 1.0
O2B A:ADP2004 2.6 47.1 1.0
O A:HOH2103 3.4 21.1 1.0
O2A A:ADP2004 3.5 21.2 1.0
F2 A:ALF2002 4.0 28.4 1.0
PB A:ADP2004 4.1 35.5 1.0
NH2 A:ARG544 4.4 35.5 1.0
MG A:MG2003 4.5 15.1 1.0
F4 A:ALF2002 4.5 14.1 1.0
O3A A:ADP2004 4.6 11.4 1.0
PA A:ADP2004 4.7 22.7 1.0
OG A:SER477 4.8 54.1 1.0
O3B A:ADP2004 4.8 16.2 1.0
AL A:ALF2002 4.9 29.8 1.0
O1B A:ADP2004 5.0 10.0 1.0

Magnesium binding site 2 out of 4 in 3wgv

Go back to Magnesium Binding Sites List in 3wgv
Magnesium binding site 2 out of 4 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:15.1
occ:1.00
 OD2 A:ASP369 2.0 58.3 1.0
F4 A:ALF2002 2.1 14.1 1.0
OD1 A:ASP710 2.2 36.3 1.0
F2 A:ALF2002 2.3 28.4 1.0
O A:THR371 2.4 21.6 1.0
AL A:ALF2002 3.0 29.8 1.0
O A:HOH2103 3.1 21.1 1.0
CG A:ASP710 3.1 33.9 1.0
CG A:ASP369 3.2 53.4 1.0
OD2 A:ASP710 3.3 20.9 1.0
C A:THR371 3.6 39.5 1.0
N A:GLY711 3.8 28.8 1.0
OD1 A:ASP369 3.8 21.2 1.0
OD2 A:ASP714 3.9 51.9 1.0
CB A:ASP369 4.3 22.0 1.0
F1 A:ALF2002 4.3 19.1 1.0
CA A:GLY711 4.3 26.7 1.0
OG1 A:THR373 4.4 39.6 1.0
F3 A:ALF2002 4.4 14.4 1.0
CA A:THR371 4.4 36.6 1.0
N A:THR371 4.4 39.3 1.0
MG A:MG2001 4.5 61.4 1.0
CB A:ASP710 4.5 34.5 1.0
O2B A:ADP2004 4.6 47.1 1.0
CB A:THR371 4.6 40.7 1.0
O3B A:ADP2004 4.6 16.2 1.0
OD1 A:ASN713 4.6 50.3 1.0
N A:GLY372 4.6 23.1 1.0
CA A:GLY372 4.7 22.9 1.0
OG1 A:THR371 4.8 50.1 1.0
N A:ASP710 4.8 30.1 1.0
CG A:ASP714 4.8 18.7 1.0
C A:ASP710 4.9 31.4 1.0
CA A:ASP710 5.0 30.6 1.0
C A:GLY372 5.0 34.4 1.0

Magnesium binding site 3 out of 4 in 3wgv

Go back to Magnesium Binding Sites List in 3wgv
Magnesium binding site 3 out of 4 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2001

b:55.0
occ:1.00
 O C:HOH2102 2.6 15.3 1.0
F2 C:ALF2002 3.0 71.1 1.0
O C:HOH2103 3.1 36.4 1.0
O1A C:ADP2004 3.4 51.1 1.0
O1B C:ADP2004 3.5 57.5 1.0
MG C:MG2003 3.8 51.8 1.0
OG C:SER477 4.1 57.8 1.0
OD1 C:ASN713 4.2 46.4 1.0
CA C:GLY711 4.2 56.1 1.0
AL C:ALF2002 4.5 20.9 1.0
F4 C:ALF2002 4.6 51.7 1.0
O3A C:ADP2004 4.6 31.4 1.0
PB C:ADP2004 4.6 53.1 1.0
PA C:ADP2004 4.6 53.9 1.0
ND2 C:ASN713 4.7 58.7 1.0
CG C:ASN713 4.7 50.6 1.0
OD2 C:ASP710 4.9 54.4 1.0
N C:GLY711 5.0 55.5 1.0

Magnesium binding site 4 out of 4 in 3wgv

Go back to Magnesium Binding Sites List in 3wgv
Magnesium binding site 4 out of 4 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:51.8
occ:1.00
 OD1 C:ASP710 1.9 58.2 1.0
O C:HOH2102 2.1 15.3 1.0
OD2 C:ASP369 2.1 51.1 1.0
O C:THR371 2.4 73.4 1.0
F4 C:ALF2002 2.5 51.7 1.0
F2 C:ALF2002 2.6 71.1 1.0
CG C:ASP710 2.8 55.5 1.0
OD2 C:ASP710 3.0 54.4 1.0
CG C:ASP369 3.3 52.9 1.0
AL C:ALF2002 3.4 20.9 1.0
C C:THR371 3.5 68.8 1.0
N C:GLY711 3.8 55.5 1.0
MG C:MG2001 3.8 55.0 1.0
OD1 C:ASP369 3.9 51.9 1.0
OD2 C:ASP714 4.2 65.8 1.0
CA C:GLY711 4.2 56.1 1.0
CB C:ASP710 4.2 53.6 1.0
CB C:THR371 4.2 61.3 1.0
CA C:THR371 4.2 61.5 1.0
N C:THR371 4.4 58.6 1.0
CB C:ASP369 4.4 51.1 1.0
N C:GLY372 4.5 66.2 1.0
C C:ASP710 4.6 51.2 1.0
CA C:GLY372 4.6 60.4 1.0
O3B C:ADP2004 4.6 46.7 1.0
N C:ASP710 4.6 54.4 1.0
F1 C:ALF2002 4.7 24.5 1.0
CA C:ASP710 4.7 51.8 1.0
F3 C:ALF2002 4.8 0.8 1.0
OG1 C:THR371 4.8 69.2 1.0
N C:THR373 4.9 58.9 1.0
OG1 C:THR373 4.9 60.1 1.0
O1B C:ADP2004 4.9 57.5 1.0
OD1 C:ASN713 5.0 46.4 1.0

Reference:

R.Kanai, H.Ogawa, B.Vilsen, F.Cornelius, C.Toyoshima. Crystal Structure of A NA1-Bound NA1,K1-Atpase Preceding the E1P State Nature V. 502 201 2013.
ISSN: ISSN 0028-0836
Page generated: Thu Aug 15 13:24:26 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