Magnesium in PDB 6mw7: Crystal Structure of Atpase Module of SMCHD1 Bound to Atp

The structure of Crystal Structure of Atpase Module of SMCHD1 Bound to Atp, PDB code: 6mw7 was solved by L.C.Pedersen, K.Inoue, S.Kim, L.Perera, N.D.Shaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.79 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.756, 148.012, 191.138, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23

The structure of Crystal Structure of Atpase Module of SMCHD1 Bound to Atp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Atpase Module of SMCHD1 Bound to Atp (pdb code 6mw7). 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 Atpase Module of SMCHD1 Bound to Atp, PDB code: 6mw7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Atpase Module of SMCHD1 Bound to 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 Atpase Module of SMCHD1 Bound to Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:29.4 occ:1.00 O3G A:ATP901 1.9 27.3 1.0 O A:HOH1071 1.9 35.6 1.0 O2B A:ATP901 2.0 25.1 1.0 O A:HOH1117 2.1 24.1 1.0 OD1 A:ASN151 2.2 29.9 1.0 O2A A:ATP901 2.3 27.2 1.0 CG A:ASN151 3.1 26.3 1.0 PB A:ATP901 3.2 21.9 1.0 PG A:ATP901 3.3 21.9 1.0 ND2 A:ASN151 3.5 26.3 1.0 PA A:ATP901 3.5 23.6 1.0 O3B A:ATP901 3.6 22.5 1.0 O3A A:ATP901 3.7 21.9 1.0 O A:HOH1058 3.7 24.3 1.0 O2G A:ATP901 4.1 24.6 1.0 O A:HOH1191 4.1 27.6 1.0 O A:HOH1237 4.1 28.5 1.0 O A:ALA147 4.2 25.8 1.0 N A:GLY239 4.2 28.0 1.0 O5' A:ATP901 4.2 25.4 1.0 O1G A:ATP901 4.3 28.7 1.0 O A:HOH1232 4.4 28.3 1.0 CA A:GLY238 4.4 26.8 1.0 CB A:ASN151 4.5 26.5 1.0 O1B A:ATP901 4.5 22.3 1.0 N A:GLY238 4.6 27.1 1.0 CB A:SER233 4.6 29.5 1.0 NZ A:LYS525 4.7 26.9 1.0 C A:GLY238 4.7 27.0 1.0 O1A A:ATP901 4.7 25.0 1.0 N A:ASN151 4.8 26.5 1.0 CA A:ASN151 4.8 27.8 1.0 CA A:SER233 4.8 30.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Atpase Module of SMCHD1 Bound to 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 Atpase Module of SMCHD1 Bound to Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:23.8 occ:1.00 O B:HOH727 1.9 25.8 1.0 O2B B:ATP601 2.0 25.8 1.0 O3G B:ATP601 2.0 27.3 1.0 O2A B:ATP601 2.0 22.6 1.0 O B:HOH759 2.0 34.2 1.0 OD1 B:ASN151 2.2 30.2 1.0 CG B:ASN151 3.1 29.6 1.0 PB B:ATP601 3.1 29.8 1.0 PA B:ATP601 3.2 25.7 1.0 PG B:ATP601 3.3 25.2 1.0 ND2 B:ASN151 3.4 28.8 1.0 O3A B:ATP601 3.5 24.6 1.0 O3B B:ATP601 3.6 25.8 1.0 O5' B:ATP601 4.0 28.1 1.0 N B:GLY239 4.0 33.3 1.0 O B:HOH791 4.2 33.6 1.0 O B:HOH882 4.2 42.6 1.0 O B:ALA147 4.3 29.1 1.0 O2G B:ATP601 4.3 25.3 1.0 O B:HOH850 4.3 31.2 1.0 O1G B:ATP601 4.3 28.5 1.0 O B:HOH901 4.3 31.7 1.0 CA B:GLY238 4.4 27.8 1.0 O1B B:ATP601 4.5 31.0 1.0 CB B:ASN151 4.5 30.1 1.0 O1A B:ATP601 4.5 24.9 1.0 N B:GLY238 4.5 26.4 1.0 C B:GLY238 4.6 31.0 1.0 CB B:SER233 4.7 34.1 1.0 CA B:GLY239 4.8 32.1 1.0 CA B:ASN151 4.8 31.0 1.0 N B:ASN151 4.8 30.4 1.0 NZ B:LYS525 4.9 32.2 1.0 CA B:SER233 5.0 33.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Atpase Module of SMCHD1 Bound to 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 Atpase Module of SMCHD1 Bound to Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:27.2 occ:1.00 O2B C:ATP601 1.9 26.3 1.0 O2G C:ATP601 1.9 30.1 1.0 O C:HOH782 2.0 35.0 1.0 O C:HOH753 2.0 28.2 1.0 O2A C:ATP601 2.0 29.7 1.0 OD1 C:ASN151 2.2 33.7 1.0 PB C:ATP601 3.1 24.5 1.0 CG C:ASN151 3.2 33.2 1.0 PA C:ATP601 3.3 25.3 1.0 PG C:ATP601 3.3 22.2 1.0 ND2 C:ASN151 3.6 33.7 1.0 O3A C:ATP601 3.6 24.8 1.0 O3B C:ATP601 3.6 24.2 1.0 O C:HOH743 4.0 25.4 1.0 O C:HOH874 4.0 33.8 1.0 O5' C:ATP601 4.0 27.6 1.0 O C:HOH864 4.1 36.8 1.0 O3G C:ATP601 4.1 23.4 1.0 N C:GLY239 4.2 30.8 1.0 O C:ALA147 4.3 30.1 1.0 O1G C:ATP601 4.4 26.0 1.0 CB C:SER233 4.4 39.6 1.0 O1B C:ATP601 4.5 24.6 1.0 CA C:GLY238 4.5 27.2 1.0 CB C:ASN151 4.5 32.5 1.0 O1A C:ATP601 4.6 26.8 1.0 NZ C:LYS525 4.6 29.3 1.0 N C:GLY238 4.6 27.5 1.0 O C:HOH906 4.7 49.1 1.0 C C:GLY238 4.8 30.4 1.0 N C:ASN151 4.8 30.4 1.0 CA C:ASN151 4.8 31.6 1.0 CA C:SER233 4.9 37.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Atpase Module of SMCHD1 Bound to 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 Atpase Module of SMCHD1 Bound to Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:25.8 occ:1.00 O2B D:ATP601 1.9 26.9 1.0 O D:HOH746 1.9 25.2 1.0 O2A D:ATP601 2.0 28.0 1.0 O3G D:ATP601 2.0 31.4 1.0 OD1 D:ASN151 2.1 32.6 1.0 O D:HOH797 2.1 34.7 1.0 CG D:ASN151 3.0 29.2 1.0 PB D:ATP601 3.1 27.3 1.0 PA D:ATP601 3.2 22.9 1.0 ND2 D:ASN151 3.3 29.1 1.0 PG D:ATP601 3.4 32.4 1.0 O3A D:ATP601 3.5 24.5 1.0 O3B D:ATP601 3.6 24.6 1.0 O D:HOH760 3.9 29.8 1.0 O5' D:ATP601 4.0 28.6 1.0 N D:GLY239 4.1 34.0 1.0 O D:HOH870 4.1 45.4 1.0 O D:HOH835 4.2 31.8 1.0 O D:ALA147 4.3 27.3 1.0 O2G D:ATP601 4.3 24.7 1.0 O D:HOH885 4.3 31.1 1.0 O1G D:ATP601 4.4 29.2 1.0 CB D:ASN151 4.4 28.5 1.0 O1B D:ATP601 4.4 30.2 1.0 CA D:GLY238 4.5 28.0 1.0 O1A D:ATP601 4.5 27.4 1.0 N D:GLY238 4.6 28.4 1.0 C D:GLY238 4.6 31.3 1.0 CB D:SER233 4.7 34.1 1.0 CA D:ASN151 4.8 28.7 1.0 N D:ASN151 4.8 31.5 1.0 CA D:GLY239 4.8 34.7 1.0 NZ D:LYS525 4.9 33.1 1.0

L.C.Pedersen, K.Inoue, S.Kim, L.Perera, N.D.Shaw. A Ubiquitin-Like Domain Is Required For Stabilizing the N-Terminal Atpase Module of Human SMCHD1. Commun Biol V. 2 255 2019.
ISSN: ESSN 2399-3642
PubMed: 31312724
DOI: 10.1038/S42003-019-0499-Y