Magnesium in PDB 6pwy: Structure of C. Elegans ZK177.8, SAMHD1 Ortholog

The structure of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog, PDB code: 6pwy was solved by C.S.Lim, T.Maehigashi, L.R.Wade, N.Bowen, K.Knecht, Y.Xiong, B.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.03 / 1.81
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	90.681, 90.557, 93.357, 65.58, 65.49, 86.22
R / Rfree (%)	18.2 / 20.9

The binding sites of Magnesium atom in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog (pdb code 6pwy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog, PDB code: 6pwy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:12.4 occ:1.00 O C:HOH915 2.0 12.1 1.0 O3G B:DTP603 2.1 12.7 1.0 O2A B:GTP602 2.1 11.4 1.0 O1G B:GTP602 2.1 16.0 1.0 O2B B:DTP603 2.1 10.6 1.0 O1B B:GTP602 2.2 13.4 1.0 PB B:GTP602 3.2 13.5 1.0 PG B:GTP602 3.3 17.9 1.0 PB B:DTP603 3.3 11.6 1.0 PG B:DTP603 3.3 12.7 1.0 PA B:GTP602 3.4 11.8 1.0 O3B B:GTP602 3.4 13.8 1.0 O3B B:DTP603 3.5 12.0 1.0 O3A B:GTP602 3.7 12.6 1.0 O B:HOH787 3.9 20.4 1.0 O3' B:GTP602 3.9 11.0 1.0 NZ A:LYS493 3.9 21.2 1.0 O B:HOH813 4.0 13.9 1.0 O2G B:DTP603 4.0 12.5 1.0 O3G B:GTP602 4.1 18.0 1.0 O B:HOH864 4.1 29.5 1.0 O1B B:DTP603 4.1 11.0 1.0 ND1 C:HIS44 4.2 14.3 1.0 NZ B:LYS409 4.3 43.6 1.0 C5' B:GTP602 4.3 11.0 1.0 O2G B:GTP602 4.3 18.0 1.0 O5' B:GTP602 4.3 11.1 1.0 CE1 C:HIS44 4.3 16.3 1.0 O1G B:DTP603 4.4 12.3 1.0 O3A B:DTP603 4.4 9.8 1.0 C3' B:GTP602 4.4 11.4 1.0 O1A B:GTP602 4.6 11.8 1.0 O2B B:GTP602 4.6 14.5 1.0 C4' B:GTP602 4.9 11.0 1.0 CE A:LYS493 4.9 22.2 1.0

Magnesium binding site 2 out of 4 in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:18.6 occ:1.00 O2A D:GTP603 2.0 15.3 1.0 O D:HOH922 2.1 15.7 1.0 O2G D:GTP603 2.1 21.8 1.0 O1B D:GTP603 2.1 15.9 1.0 O1B D:DTP604 2.1 14.4 1.0 O1G D:DTP604 2.2 14.6 1.0 PB D:GTP603 3.1 18.0 1.0 PG D:GTP603 3.2 22.7 1.0 PA D:GTP603 3.3 16.6 1.0 PB D:DTP604 3.3 13.2 1.0 O3B D:GTP603 3.4 20.8 1.0 PG D:DTP604 3.4 14.8 1.0 O3A D:GTP603 3.5 17.8 1.0 O3B D:DTP604 3.6 13.7 1.0 O3' D:GTP603 3.8 14.2 1.0 O D:HOH821 4.0 21.9 1.0 NZ C:LYS493 4.0 25.2 1.0 O1G D:GTP603 4.0 22.0 1.0 O D:HOH887 4.1 33.9 1.0 O2B D:DTP604 4.1 14.0 1.0 O3G D:DTP604 4.1 13.8 1.0 C5' D:GTP603 4.2 14.5 1.0 O D:HOH772 4.2 16.1 1.0 O5' D:GTP603 4.2 15.2 1.0 O3G D:GTP603 4.3 22.6 1.0 ND1 A:HIS44 4.3 16.0 1.0 C3' D:GTP603 4.3 14.9 1.0 CE1 A:HIS44 4.4 17.6 1.0 O1A D:GTP603 4.4 16.8 1.0 O3A D:DTP604 4.5 13.2 1.0 O2G D:DTP604 4.5 16.0 1.0 O2B D:GTP603 4.5 18.1 1.0 NZ D:LYS409 4.6 37.9 1.0 C4' D:GTP603 4.8 14.5 1.0

Magnesium binding site 3 out of 4 in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:13.4 occ:1.00 O B:HOH888 2.0 12.8 1.0 O1G C:GTP602 2.1 14.6 1.0 O3G C:DTP603 2.1 12.9 1.0 O2A C:GTP602 2.1 10.5 1.0 O2B C:DTP603 2.1 11.2 1.0 O1B C:GTP602 2.1 12.9 1.0 PB C:GTP602 3.2 13.7 1.0 PG C:GTP602 3.3 16.4 1.0 PB C:DTP603 3.3 11.9 1.0 PG C:DTP603 3.3 13.0 1.0 PA C:GTP602 3.4 11.9 1.0 O3B C:GTP602 3.4 13.6 1.0 O3B C:DTP603 3.5 12.3 1.0 O3A C:GTP602 3.6 12.7 1.0 O C:HOH756 3.8 19.3 1.0 O3' C:GTP602 3.9 11.9 1.0 NZ D:LYS493 3.9 22.6 1.0 O C:HOH828 4.0 13.3 1.0 O3G C:GTP602 4.0 17.3 1.0 O2G C:DTP603 4.0 13.6 1.0 O C:HOH836 4.1 28.3 1.0 O1B C:DTP603 4.2 11.3 1.0 NZ C:LYS409 4.2 44.9 1.0 ND1 B:HIS44 4.2 16.2 1.0 C5' C:GTP602 4.2 10.9 1.0 O5' C:GTP602 4.3 10.8 1.0 CE1 B:HIS44 4.3 17.7 1.0 O2G C:GTP602 4.4 17.6 1.0 C3' C:GTP602 4.4 11.9 1.0 O1G C:DTP603 4.4 12.8 1.0 O3A C:DTP603 4.4 11.0 1.0 O1A C:GTP602 4.5 11.3 1.0 O2B C:GTP602 4.6 14.5 1.0 C4' C:GTP602 4.8 11.4 1.0 CE D:LYS493 5.0 22.8 1.0

Magnesium binding site 4 out of 4 in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:15.0 occ:1.00 O2A A:GTP602 2.0 14.1 1.0 O1G A:DTP603 2.1 14.5 1.0 O1B A:DTP603 2.1 12.5 1.0 O D:HOH901 2.1 16.8 1.0 O2G A:GTP602 2.1 20.2 1.0 O1B A:GTP602 2.2 14.8 1.0 PB A:GTP602 3.2 17.8 1.0 PB A:DTP603 3.2 13.7 1.0 PG A:GTP602 3.3 23.6 1.0 PG A:DTP603 3.3 15.8 1.0 PA A:GTP602 3.3 14.8 1.0 O3B A:GTP602 3.4 18.7 1.0 O3B A:DTP603 3.5 14.8 1.0 O3A A:GTP602 3.6 16.3 1.0 O3' A:GTP602 3.8 14.7 1.0 O A:HOH805 3.9 24.2 1.0 NZ B:LYS493 4.0 25.6 1.0 O A:HOH929 4.0 32.8 1.0 O2B A:DTP603 4.1 12.7 1.0 O1G A:GTP602 4.1 21.9 1.0 O3G A:DTP603 4.1 14.0 1.0 O A:HOH802 4.2 19.8 1.0 C5' A:GTP602 4.2 14.4 1.0 O5' A:GTP602 4.3 14.5 1.0 ND1 D:HIS44 4.3 15.9 1.0 O3G A:GTP602 4.4 22.9 1.0 C3' A:GTP602 4.4 15.0 1.0 CE1 D:HIS44 4.4 18.4 1.0 O3A A:DTP603 4.4 13.1 1.0 O2G A:DTP603 4.4 16.8 1.0 O1A A:GTP602 4.5 15.4 1.0 O2B A:GTP602 4.6 18.0 1.0 NZ A:LYS409 4.6 34.3 1.0 C4' A:GTP602 4.8 14.4 1.0

T.Maehigashi, C.Lim, L.R.Wade, N.Bowen, K.Knecht, R.F.Schinazi, Y.Xiong, B.Kim. ZK177.8 of Caenorhabditis Elegans: Aicardi-Goutieres Syndrome SAMHD1 Ortholog To Be Published.