Magnesium in PDB 4bzc: Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core

The structure of Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core, PDB code: 4bzc was solved by X.Ji, H.Yang, Y.Wu, J.Yan, J.Mehrens, M.Delucia, C.Hao, A.M.Gronenborn, J.Skowronski, J.Ahn, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.71 / 2.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.002, 138.727, 93.715, 90.00, 113.56, 90.00
R / Rfree (%)	19.032 / 24.48

The structure of Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core (pdb code 4bzc). 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 the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core, PDB code: 4bzc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core


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 Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg950 b:25.1 occ:1.00 O2B A:T8T800 1.6 25.6 1.0 O2B A:T8T900 1.7 29.0 1.0 O A:HOH2012 1.9 16.8 1.0 O3G A:T8T800 2.0 26.4 1.0 O1G A:T8T900 2.1 29.2 1.0 O2A A:T8T900 2.2 28.7 1.0 PB A:T8T800 2.9 25.2 1.0 PB A:T8T900 3.0 29.6 1.0 PG A:T8T800 3.1 25.8 1.0 PA A:T8T900 3.3 29.2 1.0 PG A:T8T900 3.4 30.0 1.0 O3B A:T8T800 3.4 25.2 1.0 O3A A:T8T900 3.6 29.7 1.0 O3B A:T8T900 3.6 30.2 1.0 NZ D:LYS116 3.7 43.2 1.0 O1G A:T8T800 3.7 25.4 1.0 O1B A:T8T800 3.8 25.5 1.0 NZ C:LYS523 3.8 45.1 1.0 O3' A:T8T900 3.8 27.6 1.0 O A:HOH2014 3.9 19.3 1.0 C5' A:T8T900 3.9 28.8 1.0 O3G A:T8T900 4.1 30.1 1.0 O3A A:T8T800 4.1 24.6 1.0 O5' A:T8T900 4.2 29.0 1.0 C3' A:T8T900 4.2 28.1 1.0 O1B A:T8T900 4.2 30.0 1.0 NZ A:LYS377 4.4 39.7 1.0 O2G A:T8T800 4.4 25.8 1.0 C4' A:T8T900 4.5 28.3 1.0 O2G A:T8T900 4.5 30.5 1.0 O A:HOH2013 4.6 29.9 1.0 S1A A:T8T900 4.8 30.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core


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 Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg950 b:36.2 occ:1.00 O1G B:T8T900 1.8 44.5 1.0 O2A B:T8T900 2.1 40.2 1.0 O2B B:T8T900 2.1 47.0 1.0 O2B B:T8T800 2.3 39.5 1.0 O3G B:T8T800 2.4 41.6 1.0 NZ C:LYS116 2.8 51.0 1.0 PG B:T8T900 3.1 45.4 1.0 PG B:T8T800 3.3 42.0 1.0 O1G B:T8T800 3.3 39.2 1.0 PB B:T8T900 3.3 46.7 1.0 PA B:T8T900 3.4 42.2 1.0 O B:HOH2009 3.5 38.7 1.0 O3B B:T8T900 3.5 45.3 1.0 PB B:T8T800 3.6 40.0 1.0 O3' B:T8T900 3.8 43.6 1.0 NZ D:LYS523 3.8 80.5 1.0 O3B B:T8T800 3.9 40.6 1.0 O3A B:T8T900 3.9 44.6 1.0 O2G B:T8T900 4.0 45.8 1.0 CE C:LYS116 4.2 50.6 1.0 C3' B:T8T900 4.2 42.0 1.0 O3G B:T8T900 4.2 46.7 1.0 O5' B:T8T900 4.4 43.0 1.0 C5' B:T8T900 4.5 43.4 1.0 CG C:LYS116 4.5 51.8 1.0 O3A B:T8T800 4.5 39.3 1.0 O1B B:T8T900 4.6 47.8 1.0 O2G B:T8T800 4.7 42.4 1.0 CD C:LYS116 4.7 49.9 1.0 S1A B:T8T900 4.7 40.3 1.0 O1B B:T8T800 4.8 42.6 1.0 C4' B:T8T900 4.8 42.4 1.0 O B:HOH2007 4.9 45.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core


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 Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg950 b:28.7 occ:1.00 O1G C:T8T900 2.0 42.1 1.0 O2B C:T8T900 2.0 36.6 1.0 O2B C:T8T800 2.3 35.3 1.0 O2A C:T8T900 2.3 37.6 1.0 O3G C:T8T800 2.3 37.5 1.0 NZ B:LYS116 3.1 46.0 1.0 NZ A:LYS523 3.1 66.0 1.0 PG C:T8T900 3.2 42.5 1.0 PG C:T8T800 3.2 36.3 1.0 PB C:T8T900 3.3 39.5 1.0 O1G C:T8T800 3.3 35.2 1.0 PB C:T8T800 3.4 34.3 1.0 O3' C:T8T900 3.6 41.6 1.0 PA C:T8T900 3.6 39.3 1.0 O3B C:T8T900 3.6 40.9 1.0 O3B C:T8T800 3.7 34.2 1.0 O2G C:T8T900 3.9 42.0 1.0 O3A C:T8T900 4.0 39.1 1.0 CE A:LYS523 4.0 66.5 1.0 O3G C:T8T900 4.3 41.7 1.0 O3A C:T8T800 4.4 33.5 1.0 O1B C:T8T800 4.4 34.2 1.0 CE B:LYS116 4.4 47.9 1.0 C3' C:T8T900 4.5 40.6 1.0 O1B C:T8T900 4.5 38.6 1.0 O2G C:T8T800 4.6 36.4 1.0 O5' C:T8T900 4.6 39.9 1.0 CG B:LYS116 4.6 49.9 1.0 C5' C:T8T900 4.8 40.5 1.0 CD B:LYS116 4.9 48.5 1.0 S1A C:T8T900 5.0 40.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core


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 Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg950 b:34.4 occ:1.00 O1G D:T8T900 1.8 42.8 1.0 O2A D:T8T900 2.1 38.8 1.0 O2B D:T8T900 2.1 40.6 1.0 O3G D:T8T800 2.2 44.2 1.0 O2B D:T8T800 2.3 42.8 1.0 NZ A:LYS116 3.1 53.7 1.0 PG D:T8T900 3.2 42.5 1.0 PB D:T8T900 3.3 40.9 1.0 PA D:T8T900 3.4 39.6 1.0 PG D:T8T800 3.4 46.3 1.0 PB D:T8T800 3.5 42.4 1.0 O3B D:T8T900 3.6 40.8 1.0 O3B D:T8T800 3.7 45.0 1.0 O3A D:T8T900 3.8 40.8 1.0 O3' D:T8T900 4.0 38.6 1.0 O1G D:T8T800 4.0 44.9 1.0 O2G D:T8T900 4.0 41.1 1.0 NZ B:LYS523 4.3 66.6 1.0 O3G D:T8T900 4.3 43.1 1.0 O3A D:T8T800 4.3 41.2 1.0 O5' D:T8T900 4.4 39.1 1.0 C5' D:T8T900 4.4 39.2 1.0 CE A:LYS116 4.5 52.9 1.0 C3' D:T8T900 4.5 38.3 1.0 CG A:LYS116 4.6 53.0 1.0 O1B D:T8T900 4.7 41.7 1.0 S1A D:T8T900 4.7 40.0 1.0 O2G D:T8T800 4.7 46.6 1.0 O1B D:T8T800 4.8 43.8 1.0 CD A:LYS116 4.8 52.8 1.0

X.Ji, Y.Wu, J.Yan, J.Mehrens, H.Yang, M.Delucia, C.Hao, A.M.Gronenborn, J.Skowronski, J.Ahn, Y.Xiong. Mechanism of Allosteric Activation of SAMHD1 By Dgtp Nat.Struct.Mol.Biol. V. 20 1304 2013.
ISSN: ISSN 1545-9993
PubMed: 24141705
DOI: 10.1038/NSMB.2692