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Magnesium in PDB 3wgu: Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin

Enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin

All present enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin, PDB code: 3wgu 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 (°) 106.383, 211.600, 257.124, 90.00, 90.00, 90.00
R / Rfree (%) 26.5 / 29.9

Other elements in 3wgu:

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin (pdb code 3wgu). 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 Without Oligomycin, PDB code: 3wgu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3wgu

Go back to Magnesium Binding Sites List in 3wgu
Magnesium binding site 1 out of 4 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:67.6
occ:1.00
 O1A A:ADP2004 2.8 50.1 1.0
O1B A:ADP2004 2.9 51.8 1.0
O A:HOH2106 2.9 3.0 1.0
O A:HOH2109 3.3 36.5 1.0
OG A:SER477 4.1 67.6 1.0
F2 A:ALF2002 4.1 42.8 1.0
PA A:ADP2004 4.1 38.2 1.0
PB A:ADP2004 4.2 41.0 1.0
MG A:MG2003 4.3 24.6 1.0
O A:HOH2108 4.3 55.3 1.0
O3A A:ADP2004 4.5 6.8 1.0
O5' A:ADP2004 4.7 16.9 1.0
CE2 A:PHE475 4.7 56.2 1.0
O A:HOH2107 4.8 12.7 1.0
OD1 A:ASN713 4.8 57.4 1.0
NH2 A:ARG544 4.8 52.2 1.0
CZ A:PHE475 4.9 58.1 1.0
ND2 A:ASN713 4.9 52.7 1.0
O2B A:ADP2004 4.9 24.7 1.0
CG A:ASN713 4.9 53.4 1.0

Magnesium binding site 2 out of 4 in 3wgu

Go back to Magnesium Binding Sites List in 3wgu
Magnesium binding site 2 out of 4 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:24.6
occ:1.00
 OD1 A:ASP710 2.3 42.9 1.0
F2 A:ALF2002 2.3 42.8 1.0
F4 A:ALF2002 2.4 0.9 1.0
O A:HOH2109 2.5 36.5 1.0
OD2 A:ASP369 2.7 38.9 1.0
O A:THR371 2.9 35.1 1.0
CG A:ASP710 3.1 45.3 1.0
AL A:ALF2002 3.2 9.4 1.0
OD2 A:ASP710 3.3 46.5 1.0
CG A:ASP369 3.4 44.7 1.0
N A:GLY711 3.5 38.8 1.0
OD1 A:ASP369 3.6 22.8 1.0
O A:HOH2108 3.6 55.3 1.0
OD2 A:ASP714 3.8 33.3 1.0
OD1 A:ASN713 3.9 57.4 1.0
CA A:GLY711 3.9 32.5 1.0
C A:THR371 4.1 37.5 1.0
O1B A:ADP2004 4.2 51.8 1.0
MG A:MG2001 4.3 67.6 1.0
OD1 A:ASP714 4.5 49.7 1.0
CG A:ASP714 4.5 38.2 1.0
CB A:ASP710 4.5 41.4 1.0
F3 A:ALF2002 4.6 22.8 1.0
F1 A:ALF2002 4.6 16.4 1.0
C A:ASP710 4.6 39.0 1.0
ND2 A:ASN713 4.6 52.7 1.0
CG A:ASN713 4.7 53.4 1.0
CB A:ASP369 4.7 42.1 1.0
OG1 A:THR373 4.7 39.8 1.0
N A:ASP710 4.7 42.7 1.0
CB A:THR371 4.8 51.8 1.0
CA A:THR371 4.8 48.8 1.0
N A:THR371 4.8 52.4 1.0
CA A:ASP710 4.8 40.9 1.0
O3B A:ADP2004 5.0 36.0 1.0

Magnesium binding site 3 out of 4 in 3wgu

Go back to Magnesium Binding Sites List in 3wgu
Magnesium binding site 3 out of 4 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2001

b:96.2
occ:1.00
 O C:HOH2105 1.9 48.9 1.0
O C:HOH2107 2.4 48.3 1.0
O1B C:ADP2004 3.1 66.0 1.0
O1A C:ADP2004 3.1 66.6 1.0
F2 C:ALF2002 3.2 56.6 1.0
MG C:MG2003 3.9 48.3 1.0
OG C:SER477 4.2 46.9 1.0
PB C:ADP2004 4.2 66.1 1.0
O3A C:ADP2004 4.2 8.3 1.0
PA C:ADP2004 4.3 60.8 1.0
OD1 C:ASN713 4.3 51.2 1.0
AL C:ALF2002 4.4 67.6 1.0
F4 C:ALF2002 4.5 48.1 1.0
O3B C:ADP2004 4.6 64.4 1.0
CA C:GLY711 4.7 63.5 1.0
CG C:ASN713 4.9 47.6 1.0
ND2 C:ASN713 4.9 45.5 1.0
O C:HOH2106 4.9 38.9 1.0
OD1 C:ASP710 5.0 84.7 1.0

Magnesium binding site 4 out of 4 in 3wgu

Go back to Magnesium Binding Sites List in 3wgu
Magnesium binding site 4 out of 4 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:48.3
occ:1.00
 OD1 C:ASP710 1.9 84.7 1.0
OD2 C:ASP369 2.0 64.3 1.0
O C:THR371 2.2 81.8 1.0
O C:HOH2105 2.3 48.9 1.0
F2 C:ALF2002 2.4 56.6 1.0
F4 C:ALF2002 2.5 48.1 1.0
CG C:ASP710 2.9 85.7 1.0
CG C:ASP369 3.2 64.3 1.0
OD2 C:ASP710 3.2 89.2 1.0
AL C:ALF2002 3.3 67.6 1.0
C C:THR371 3.3 79.8 1.0
OD1 C:ASP369 3.8 67.4 1.0
MG C:MG2001 3.9 96.2 1.0
N C:GLY711 4.0 71.2 1.0
CA C:THR371 4.0 77.8 1.0
CB C:THR371 4.1 80.1 1.0
N C:THR371 4.1 75.6 1.0
OD2 C:ASP714 4.1 80.3 1.0
CB C:ASP710 4.2 80.3 1.0
N C:GLY372 4.3 77.6 1.0
CB C:ASP369 4.4 59.9 1.0
O3B C:ADP2004 4.4 64.4 1.0
CA C:GLY372 4.5 76.6 1.0
CA C:GLY711 4.5 63.5 1.0
N C:ASP710 4.6 70.6 1.0
N C:THR373 4.6 76.1 1.0
F1 C:ALF2002 4.7 38.8 1.0
F3 C:ALF2002 4.7 56.9 1.0
OG1 C:THR373 4.7 69.7 1.0
C C:ASP710 4.8 72.1 1.0
OG1 C:THR371 4.8 85.4 1.0
CA C:ASP710 4.8 72.3 1.0
C C:LYS370 5.0 75.0 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 13:24:21 2024

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