Atomistry » Magnesium » PDB 5kfu-5ktd » 5ksz
Atomistry »
  Magnesium »
    PDB 5kfu-5ktd »
      5ksz »

Magnesium in PDB 5ksz: Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State

Protein crystallography data

The structure of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State, PDB code: 5ksz was solved by J.L.Klosowiak, P.J.Focia, S.E.Rice, D.M.Freymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.68 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.180, 74.180, 218.859, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 26.6

Other elements in 5ksz:

The structure of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State (pdb code 5ksz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State, PDB code: 5ksz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5ksz

Go back to Magnesium Binding Sites List in 5ksz
Magnesium binding site 1 out of 2 in the Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:52.6
occ:1.00
OD1 A:ASP199 2.0 77.7 1.0
O A:HOH804 2.0 67.5 1.0
OE1 A:GLU208 2.1 57.8 1.0
OD1 A:ASP201 2.1 56.4 1.0
O A:THR203 2.1 49.1 1.0
OD1 A:ASP197 2.1 69.2 1.0
CD A:GLU208 3.0 64.7 1.0
CG A:ASP199 3.0 78.0 1.0
CG A:ASP201 3.2 73.4 1.0
OE2 A:GLU208 3.2 78.9 1.0
CG A:ASP197 3.3 44.2 1.0
C A:THR203 3.4 67.7 1.0
OD2 A:ASP199 3.4 80.4 1.0
OD2 A:ASP201 3.6 79.8 1.0
OD2 A:ASP197 4.1 56.5 1.0
N A:ASN205 4.1 71.4 1.0
CA A:LEU204 4.2 62.6 1.0
N A:LEU204 4.2 67.6 1.0
CB A:ASP197 4.2 28.6 1.0
CA A:ASP197 4.2 43.6 1.0
N A:ASP201 4.3 68.4 1.0
N A:THR203 4.3 53.7 1.0
CB A:ASP199 4.3 80.0 1.0
N A:ASP199 4.4 58.9 1.0
CA A:THR203 4.4 64.5 1.0
CB A:ASP201 4.4 70.1 1.0
CG A:GLU208 4.4 61.3 1.0
OG1 A:THR203 4.4 76.5 1.0
ND2 A:ASN205 4.5 76.1 1.0
N A:ASN200 4.5 65.3 1.0
CG A:ASN205 4.5 67.9 1.0
C A:ASP197 4.5 64.7 1.0
OD1 A:ASN205 4.7 59.0 1.0
N A:GLN198 4.7 65.9 1.0
C A:LEU204 4.7 70.3 1.0
CA A:ASP199 4.7 66.7 1.0
CB A:GLU208 4.8 67.5 1.0
CA A:ASP201 4.8 68.2 1.0
C A:ASP199 4.8 69.7 1.0
N A:GLY202 4.9 49.9 1.0

Magnesium binding site 2 out of 2 in 5ksz

Go back to Magnesium Binding Sites List in 5ksz
Magnesium binding site 2 out of 2 in the Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:65.0
occ:1.00
OD1 A:ASP319 2.0 67.6 1.0
O A:ALA323 2.1 63.0 1.0
OE1 A:GLU328 2.1 61.7 1.0
OD1 A:ASP317 2.1 61.8 1.0
OD1 A:ASP321 2.1 58.4 1.0
O A:HOH801 2.1 55.1 1.0
CG A:ASP319 2.8 66.9 1.0
CD A:GLU328 2.9 64.1 1.0
OD2 A:ASP319 2.9 74.4 1.0
OE2 A:GLU328 3.0 63.7 1.0
CG A:ASP321 3.1 58.8 1.0
C A:ALA323 3.3 53.4 1.0
CG A:ASP317 3.3 56.5 1.0
OD2 A:ASP321 3.5 66.9 1.0
CA A:ASP317 4.0 56.9 1.0
N A:ALA323 4.1 69.7 1.0
N A:LEU324 4.1 54.2 1.0
CA A:LEU324 4.1 51.3 1.0
CB A:ASP317 4.2 50.6 1.0
CA A:ALA323 4.2 53.5 1.0
OD2 A:ASP317 4.2 63.0 1.0
CB A:ASP319 4.3 56.8 1.0
N A:SER325 4.3 53.8 1.0
CG A:GLU328 4.3 45.0 1.0
N A:ASP321 4.3 67.1 1.0
C A:ASP317 4.4 60.1 1.0
CB A:ASP321 4.4 58.1 1.0
N A:ASP319 4.5 57.3 1.0
N A:ARG320 4.7 60.6 1.0
C A:LEU324 4.7 57.9 1.0
CB A:ALA323 4.7 40.8 1.0
CA A:ASP319 4.8 55.3 1.0
N A:LEU318 4.8 65.0 1.0
CD2 A:LEU324 4.8 60.5 1.0
CA A:ASP321 4.8 67.3 1.0
O A:ASP317 4.9 60.2 1.0
C A:ASP319 4.9 58.9 1.0
CB A:GLU328 4.9 52.4 1.0
N A:CYS322 4.9 63.6 1.0

Reference:

J.L.Klosowiak, S.Park, K.P.Smith, M.E.French, P.J.Focia, D.M.Freymann, S.E.Rice. Structural Insights Into Parkin Substrate Lysine Targeting From Minimal Miro Substrates. Sci Rep V. 6 33019 2016.
ISSN: ESSN 2045-2322
PubMed: 27605430
DOI: 10.1038/SREP33019
Page generated: Sun Sep 29 19:11:55 2024

Last articles

Mg in 8FCV
Mg in 8FL8
Mg in 8FI8
Mg in 8FI7
Mg in 8FI2
Mg in 8FKL
Mg in 8FIY
Mg in 8FIX
Mg in 8FI1
Mg in 8FHZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy