Atomistry » Magnesium » PDB 5avs-5b48 » 5aw7
Atomistry »
  Magnesium »
    PDB 5avs-5b48 »
      5aw7 »

Magnesium in PDB 5aw7: Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min

Protein crystallography data

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min, PDB code: 5aw7 was solved by H.Ogawa, F.Cornelius, A.Hirata, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.96 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 219.234, 50.521, 162.571, 90.00, 104.27, 90.00
R / Rfree (%) 29 / 29.3

Other elements in 5aw7:

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Rubidium (Rb) 3 atoms
Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min (pdb code 5aw7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min, PDB code: 5aw7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5aw7

Go back to Magnesium Binding Sites List in 5aw7
Magnesium binding site 1 out of 2 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:72.5
occ:1.00
MG A:MF42001 0.0 72.5 1.0
F3 A:MF42001 2.0 73.1 1.0
F1 A:MF42001 2.0 71.9 1.0
F4 A:MF42001 2.0 69.9 1.0
F2 A:MF42001 2.0 71.2 1.0
OD1 A:ASP376 2.5 65.4 1.0
OG1 A:THR617 3.3 64.7 1.0
O A:THR219 3.5 68.4 1.0
CG A:ASP376 3.6 66.5 1.0
N A:GLY618 3.8 64.9 1.0
N A:THR378 3.8 65.1 1.0
CB A:THR378 3.8 65.5 1.0
MG A:MG2002 3.9 66.6 1.0
OE1 A:GLU221 3.9 71.5 1.0
OD2 A:ASP376 3.9 65.8 1.0
OG1 A:THR378 4.0 65.8 1.0
CA A:GLY220 4.1 68.0 1.0
CB A:THR617 4.1 64.4 1.0
CA A:THR617 4.3 64.5 1.0
N A:LYS377 4.4 65.8 1.0
O A:GLY220 4.4 68.1 1.0
CA A:THR378 4.4 65.4 1.0
C A:GLY220 4.4 68.3 1.0
ND2 A:ASN720 4.5 68.4 1.0
NZ A:LYS698 4.5 68.2 1.0
C A:THR219 4.5 68.8 1.0
N A:ASP619 4.6 66.5 1.0
C A:THR617 4.6 64.5 1.0
CA A:GLY618 4.6 65.4 1.0
O A:THR378 4.6 65.3 1.0
N A:GLY220 4.8 68.2 1.0
C A:LYS377 4.8 65.3 1.0
CB A:ASP376 4.9 66.2 1.0
CD A:GLU221 4.9 70.8 1.0
CA A:LYS377 5.0 65.3 1.0
C A:GLY618 5.0 66.0 1.0

Magnesium binding site 2 out of 2 in 5aw7

Go back to Magnesium Binding Sites List in 5aw7
Magnesium binding site 2 out of 2 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:66.6
occ:1.00
F2 A:MF42001 1.9 71.2 1.0
O A:THR378 1.9 65.3 1.0
OD1 A:ASP717 1.9 69.9 1.0
OD2 A:ASP376 2.0 65.8 1.0
CG A:ASP717 3.0 69.0 1.0
CG A:ASP376 3.0 66.5 1.0
C A:THR378 3.1 65.6 1.0
OD2 A:ASP717 3.3 71.7 1.0
OD1 A:ASP376 3.4 65.4 1.0
CA A:THR378 3.8 65.4 1.0
MG A:MF42001 3.9 72.5 1.0
N A:THR378 4.0 65.1 1.0
CB A:THR378 4.0 65.5 1.0
OG1 A:THR380 4.2 67.1 1.0
N A:GLY379 4.2 66.0 1.0
OD2 A:ASP721 4.2 71.3 1.0
N A:GLY718 4.2 69.7 1.0
O A:GLY220 4.3 68.1 1.0
CB A:ASP717 4.3 69.0 1.0
CB A:ASP376 4.3 66.2 1.0
N A:ASP717 4.4 68.6 1.0
CA A:GLY379 4.5 66.7 1.0
F4 A:MF42001 4.6 69.9 1.0
F1 A:MF42001 4.6 71.9 1.0
CG2 A:THR378 4.6 63.5 1.0
C A:ASP717 4.7 69.4 1.0
CA A:ASP717 4.7 69.2 1.0
CA A:GLY220 4.7 68.0 1.0
N A:THR380 4.7 67.1 1.0
C A:LYS377 4.8 65.3 1.0
CA A:GLY718 4.8 70.3 1.0
C A:GLY379 4.8 67.3 1.0
C A:GLY220 5.0 68.3 1.0

Reference:

H.Ogawa, F.Cornelius, A.Hirata, C.Toyoshima. Sequential Substitution of K(+) Bound to Na(+),K(+)-Atpase Visualized By X-Ray Crystallography. Nat Commun V. 6 8004 2015.
ISSN: ESSN 2041-1723
PubMed: 26258479
DOI: 10.1038/NCOMMS9004
Page generated: Mon Dec 14 20:01:33 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy