Atomistry » Magnesium » PDB 5x86-5xf5 » 5x9g
Atomistry »
  Magnesium »
    PDB 5x86-5xf5 »
      5x9g »

Magnesium in PDB 5x9g: Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp

Protein crystallography data

The structure of Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp, PDB code: 5x9g was solved by A.Tomita, M.Hattori, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.80 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 138.317, 106.672, 90.170, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 29.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp (pdb code 5x9g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp, PDB code: 5x9g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5x9g

Go back to Magnesium Binding Sites List in 5x9g
Magnesium binding site 1 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:59.9
occ:1.00
 OD2 A:ASP247 2.0 68.2 1.0
OD2 A:ASP91 2.2 53.1 1.0
CG A:ASP91 3.1 53.0 1.0
CG A:ASP247 3.1 66.2 1.0
OG1 A:THR244 3.3 70.7 1.0
OE2 A:GLU166 3.5 71.0 1.0
OD1 A:ASP91 3.5 52.8 1.0
OD1 A:ASP247 3.6 72.1 1.0
CD A:GLU166 3.8 72.5 1.0
OE1 A:GLU166 4.0 67.7 1.0
OD1 A:ASP246 4.3 77.2 1.0
CB A:ASP247 4.3 69.1 1.0
CB A:ASP91 4.3 50.8 1.0
CG A:GLU166 4.5 65.6 1.0
OD1 A:ASP92 4.6 61.6 1.0
CB A:THR244 4.6 59.4 1.0
OD2 A:ASP246 4.6 77.1 1.0
CG2 A:THR139 4.7 53.0 1.0
CG2 A:THR244 4.8 62.5 1.0
CG A:ASP246 4.9 80.1 1.0
O A:LEU137 4.9 52.1 1.0

Magnesium binding site 2 out of 8 in 5x9g

Go back to Magnesium Binding Sites List in 5x9g
Magnesium binding site 2 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:46.0
occ:1.00
 OD1 A:ASP95 1.8 55.1 1.0
O A:GLY136 2.0 60.9 1.0
CG A:ASP95 2.7 54.1 1.0
OD2 A:ASP95 3.0 59.1 1.0
C A:GLY136 3.2 58.2 1.0
O A:ASP91 3.9 48.1 1.0
CA A:GLY136 4.0 56.5 1.0
CB A:ASP95 4.1 42.4 1.0
N A:LEU137 4.2 53.1 1.0
CA A:LEU137 4.4 54.7 1.0
N A:ASP95 4.4 50.9 1.0
CA A:ASP95 4.5 48.8 1.0
CD2 A:LEU137 4.7 67.0 1.0
C A:ASP91 4.8 50.9 1.0
OE1 A:GLN98 4.8 52.8 1.0
O A:GLU131 4.9 68.5 1.0

Magnesium binding site 3 out of 8 in 5x9g

Go back to Magnesium Binding Sites List in 5x9g
Magnesium binding site 3 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:36.1
occ:1.00
 OD1 B:ASP95 1.8 53.0 1.0
O B:GLY136 2.1 60.2 1.0
CG B:ASP95 2.9 43.9 1.0
C B:GLY136 3.3 48.5 1.0
OD2 B:ASP95 3.3 49.0 1.0
CA B:GLY136 4.0 43.9 1.0
O B:ASP91 4.1 31.3 1.0
CB B:ASP95 4.2 30.2 1.0
OE1 B:GLN98 4.3 46.3 1.0
N B:LEU137 4.4 45.3 1.0
CA B:ASP95 4.5 30.6 1.0
N B:ASP95 4.5 32.6 1.0
CA B:LEU137 4.6 46.3 1.0
O B:GLU131 4.6 55.6 1.0
CB B:GLU131 4.8 59.0 1.0
CD2 B:LEU137 5.0 47.1 1.0
C B:ASP91 5.0 34.5 1.0

Magnesium binding site 4 out of 8 in 5x9g

Go back to Magnesium Binding Sites List in 5x9g
Magnesium binding site 4 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:49.9
occ:1.00
 OD2 B:ASP91 2.3 48.9 1.0
OD2 B:ASP247 2.4 56.2 1.0
CG B:ASP91 3.1 44.9 1.0
CG B:ASP247 3.2 57.6 1.0
OE2 B:GLU166 3.2 51.1 1.0
OD1 B:ASP247 3.3 59.6 1.0
OD1 B:ASP91 3.3 49.8 1.0
CD B:GLU166 3.8 53.1 1.0
OE1 B:GLU166 3.9 53.2 1.0
OD2 B:ASP92 4.2 49.9 1.0
OD1 B:ASP92 4.2 51.5 1.0
OD2 B:ASP246 4.2 55.9 1.0
OG1 B:THR244 4.3 54.2 1.0
CG B:ASP92 4.5 49.1 1.0
CB B:ASP91 4.5 34.5 1.0
CB B:ASP247 4.6 55.1 1.0
OD1 B:ASP246 4.7 63.8 1.0
CB B:SER89 4.9 47.0 1.0
CG B:ASP246 4.9 61.2 1.0
CG B:GLU166 5.0 48.7 1.0

Magnesium binding site 5 out of 8 in 5x9g

Go back to Magnesium Binding Sites List in 5x9g
Magnesium binding site 5 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:44.6
occ:1.00
 OD2 C:ASP247 2.2 50.0 1.0
OD2 C:ASP91 2.3 48.6 1.0
CG C:ASP91 3.2 45.8 1.0
OG1 C:THR244 3.2 46.8 1.0
OE2 C:GLU166 3.2 46.7 1.0
CG C:ASP247 3.4 51.7 1.0
CD C:GLU166 3.6 47.4 1.0
OD1 C:ASP91 3.6 47.2 1.0
OE1 C:GLU166 3.7 45.5 1.0
OD1 C:ASP247 4.0 56.7 1.0
OD2 C:ASP246 4.3 48.7 1.0
OD1 C:ASP246 4.4 54.7 1.0
CB C:ASP91 4.4 38.4 1.0
CG2 C:THR139 4.5 45.4 1.0
CB C:ASP247 4.5 48.4 1.0
CB C:THR244 4.5 49.8 1.0
CG C:GLU166 4.5 49.1 1.0
OD1 C:ASP92 4.7 47.1 1.0
CG2 C:THR244 4.7 47.1 1.0
CG C:ASP246 4.8 53.9 1.0
CB C:THR139 4.9 44.5 1.0

Magnesium binding site 6 out of 8 in 5x9g

Go back to Magnesium Binding Sites List in 5x9g
Magnesium binding site 6 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:47.0
occ:1.00
 O C:GLY136 2.1 54.0 1.0
OD1 C:ASP95 2.4 50.6 1.0
OD2 C:ASP95 3.1 45.7 1.0
CG C:ASP95 3.1 45.3 1.0
C C:GLY136 3.2 46.7 1.0
CD2 C:LEU137 3.7 45.6 1.0
O C:GLU131 3.9 60.2 1.0
N C:LEU137 4.0 41.6 1.0
CA C:LEU137 4.0 41.9 1.0
CA C:GLY136 4.1 44.8 1.0
CB C:ASP95 4.6 37.9 1.0
CA C:GLU131 4.6 58.0 1.0
CG C:LEU137 4.7 49.9 1.0
C C:GLU131 4.7 58.3 1.0
O C:ASP91 4.8 37.1 1.0
OE1 C:GLN98 4.9 47.7 1.0
CB C:LEU137 4.9 47.8 1.0
CB C:GLU131 5.0 55.7 1.0
C C:LEU137 5.0 38.9 1.0

Magnesium binding site 7 out of 8 in 5x9g

Go back to Magnesium Binding Sites List in 5x9g
Magnesium binding site 7 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:51.0
occ:1.00
 OD2 D:ASP247 2.1 48.2 1.0
OD2 D:ASP91 2.3 52.4 1.0
CG D:ASP247 3.2 58.0 1.0
CG D:ASP91 3.3 50.3 1.0
OD1 D:ASP91 3.5 52.8 1.0
OE2 D:GLU166 3.6 65.0 1.0
OG1 D:THR244 3.6 58.6 1.0
OD1 D:ASP247 3.7 60.5 1.0
CD D:GLU166 3.8 60.4 1.0
OE1 D:GLU166 3.8 65.6 1.0
OD1 D:ASP92 4.1 49.0 1.0
OD2 D:ASP246 4.2 62.0 1.0
OD1 D:ASP246 4.3 58.1 1.0
CB D:ASP247 4.4 53.2 1.0
OD2 D:ASP92 4.5 61.0 1.0
CB D:ASP91 4.6 43.2 1.0
CG D:ASP246 4.6 64.1 1.0
CG D:ASP92 4.7 48.9 1.0
CG D:GLU166 4.7 55.5 1.0
CB D:THR244 4.9 48.7 1.0

Magnesium binding site 8 out of 8 in 5x9g

Go back to Magnesium Binding Sites List in 5x9g
Magnesium binding site 8 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:51.7
occ:1.00
 OD1 D:ASP95 2.0 52.7 1.0
O D:GLY136 2.1 52.0 1.0
CG D:ASP95 2.9 43.0 1.0
OD2 D:ASP95 3.2 41.7 1.0
C D:GLY136 3.3 48.5 1.0
CD2 D:LEU137 4.2 51.2 1.0
CA D:GLY136 4.2 45.8 1.0
N D:LEU137 4.2 45.6 1.0
O D:GLU131 4.3 62.1 1.0
CB D:ASP95 4.3 40.8 1.0
CA D:LEU137 4.3 39.8 1.0
OE1 D:GLN98 4.4 60.2 1.0
O D:ASP91 4.5 38.8 1.0
CA D:GLU131 4.7 59.4 1.0
CA D:ASP95 4.8 48.7 1.0
CB D:GLU131 4.8 59.8 1.0
N D:ASP95 4.9 49.1 1.0
C D:GLU131 5.0 60.8 1.0

Reference:

A.Tomita, M.Zhang, F.Jin, W.Zhuang, H.Takeda, T.Maruyama, M.Osawa, K.I.Hashimoto, H.Kawasaki, K.Ito, N.Dohmae, R.Ishitani, I.Shimada, Z.Yan, M.Hattori, O.Nureki. Atp-Dependent Modulation of Mgte in Mg(2+) Homeostasis Nat Commun V. 8 148 2017.
ISSN: ESSN 2041-1723
PubMed: 28747715
DOI: 10.1038/S41467-017-00082-W
Page generated: Mon Sep 30 09:12:14 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