Magnesium in PDB 6kpu: Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride

Protein crystallography data

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 6kpu was solved by H.Ogawa, K.Motoyama, F.Cornelius, B.Vilsen, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.99 / 4.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.481, 118.371, 495.388, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.4

Other elements in 6kpu:

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride (pdb code 6kpu). 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 Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 6kpu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6kpu

Go back to Magnesium Binding Sites List in 6kpu
Magnesium binding site 1 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:89.5
occ:1.00
OD1 A:ASP710 2.0 98.4 1.0
O A:THR371 2.1 97.1 1.0
O A:HOH1202 2.1 99.3 1.0
O A:HOH1205 2.2 0.9 1.0
OD2 A:ASP369 2.3 93.7 1.0
F2 A:BEF1104 2.3 0.8 1.0
CG A:ASP710 2.9 0.1 1.0
OD2 A:ASP710 3.2 92.2 1.0
BE A:BEF1104 3.2 0.3 1.0
C A:THR371 3.3 0.3 1.0
CG A:ASP369 3.4 96.9 1.0
N A:GLY711 3.7 0.8 1.0
OD1 A:ASP369 3.8 0.2 1.0
OD2 A:ASP714 3.8 0.2 1.0
F3 A:BEF1104 4.1 0.6 1.0
CA A:THR371 4.2 1.0 1.0
N A:GLY372 4.2 0.7 1.0
CB A:THR371 4.3 0.2 1.0
F1 A:BEF1104 4.3 0.7 1.0
CA A:GLY711 4.3 1.0 1.0
CB A:ASP710 4.3 1.0 1.0
CA A:GLY372 4.3 0.0 1.0
N A:THR371 4.4 0.6 1.0
N A:ASP710 4.5 0.2 1.0
OD1 A:ASN713 4.5 0.6 1.0
CB A:ASP369 4.6 98.3 1.0
O A:SER209 4.6 0.8 1.0
C A:ASP710 4.6 0.1 1.0
CA A:ASP710 4.7 0.7 1.0
OG1 A:THR373 4.7 0.0 1.0
CG2 A:THR371 4.8 0.8 1.0
N A:THR373 4.8 0.9 1.0
ND2 A:ASN713 4.9 1.0 1.0
CG A:ASP714 4.9 0.1 1.0
C A:GLY372 4.9 0.4 1.0

Magnesium binding site 2 out of 4 in 6kpu

Go back to Magnesium Binding Sites List in 6kpu
Magnesium binding site 2 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:0.2
occ:1.00
OE2 A:GLU779 2.1 0.1 1.0
OD2 A:ASP804 2.1 0.3 1.0
O A:HOH1201 2.2 0.1 1.0
OD1 A:ASP804 2.2 0.7 1.0
CG A:ASP804 2.4 0.7 1.0
O A:HOH1203 2.5 90.2 1.0
O A:HOH1204 2.6 0.1 1.0
CD A:GLU779 2.9 0.7 1.0
OE2 A:GLU327 3.0 0.6 1.0
OE1 A:GLU779 3.1 0.8 1.0
CB A:ASP804 3.8 0.3 1.0
CD A:GLU327 3.8 0.4 1.0
OD1 A:ASN776 4.0 0.3 1.0
OE1 A:GLU327 4.1 0.9 1.0
CG A:GLU779 4.2 97.4 1.0
CG A:ASN776 4.4 0.4 1.0
CG2 A:ILE800 4.6 98.0 1.0
ND2 A:ASN776 4.7 0.3 1.0
OG A:SER775 4.7 84.6 1.0
CB A:GLU779 4.7 97.4 1.0
O A:VAL325 4.8 0.0 1.0
O A:ALA323 4.8 0.9 1.0
CA A:ASP804 4.9 0.4 1.0
CA A:ASN776 5.0 90.4 1.0
N A:GLU327 5.0 0.9 1.0

Magnesium binding site 3 out of 4 in 6kpu

Go back to Magnesium Binding Sites List in 6kpu
Magnesium binding site 3 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:0.3
occ:1.00
OD1 C:ASP710 2.0 0.2 1.0
O C:THR371 2.0 0.8 1.0
O C:HOH1201 2.1 0.4 1.0
OD2 C:ASP369 2.2 0.8 1.0
O C:HOH1203 2.2 0.8 1.0
F2 C:BEF1104 2.2 0.1 1.0
CG C:ASP710 3.0 0.8 1.0
BE C:BEF1104 3.2 0.7 1.0
CG C:ASP369 3.2 0.3 1.0
C C:THR371 3.3 0.9 1.0
OD2 C:ASP710 3.3 0.2 1.0
OD1 C:ASP369 3.7 0.1 1.0
N C:GLY711 3.7 0.8 1.0
OD2 C:ASP714 3.9 0.3 1.0
F3 C:BEF1104 4.1 0.1 1.0
CA C:THR371 4.1 0.9 1.0
CB C:THR371 4.2 1.0 1.0
F1 C:BEF1104 4.2 0.7 1.0
N C:GLY372 4.3 0.4 1.0
N C:THR371 4.3 0.7 1.0
O C:SER209 4.3 0.2 1.0
CA C:GLY711 4.3 0.4 1.0
CB C:ASP710 4.4 0.7 1.0
OD1 C:ASN713 4.4 0.4 1.0
CB C:ASP369 4.4 0.8 1.0
CA C:GLY372 4.4 0.5 1.0
N C:ASP710 4.5 0.9 1.0
OG1 C:THR373 4.6 0.8 1.0
C C:ASP710 4.7 0.1 1.0
CA C:ASP710 4.8 0.5 1.0
N C:THR373 4.8 0.2 1.0
ND2 C:ASN713 4.8 0.8 1.0
CG2 C:THR371 4.8 0.1 1.0
C C:GLY372 5.0 0.9 1.0
C C:LYS370 5.0 0.2 1.0

Magnesium binding site 4 out of 4 in 6kpu

Go back to Magnesium Binding Sites List in 6kpu
Magnesium binding site 4 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:0.2
occ:1.00
OE2 C:GLU779 2.1 0.6 1.0
OD2 C:ASP804 2.1 0.0 1.0
O C:HOH1202 2.3 0.3 1.0
OD1 C:ASP804 2.4 0.6 1.0
CG C:ASP804 2.5 0.9 1.0
O C:HOH1204 2.5 0.1 1.0
O C:HOH1205 2.7 98.9 1.0
CD C:GLU779 2.8 0.4 1.0
OE2 C:GLU327 2.9 0.4 1.0
OE1 C:GLU779 3.1 98.8 1.0
CD C:GLU327 3.9 0.1 1.0
CB C:ASP804 3.9 96.4 1.0
OD1 C:ASN776 4.1 0.6 1.0
CG C:GLU779 4.2 0.3 1.0
OE1 C:GLU327 4.3 95.8 1.0
CG C:ASN776 4.6 97.5 1.0
CG2 C:ILE800 4.6 97.1 1.0
CB C:GLU779 4.7 0.4 1.0
OG C:SER775 4.8 0.9 1.0
CA C:PRO326 4.8 0.5 1.0
O C:VAL325 4.8 0.0 1.0
O C:ALA323 4.8 0.9 1.0
ND2 C:ASN776 4.9 95.3 1.0
N C:GLU327 4.9 0.8 1.0
CA C:ASP804 5.0 89.1 1.0

Reference:

H.Ogawa, K.Motoyama, F.Cornelius, B.Vilsen, C.Toyoshima. X-Ray Crystal Structures of Na+,K+-Atpase in Complex with Cardiotonic Steroids To Be Published.
Page generated: Mon Jan 25 08:48:45 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy