Manganese 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:

Magnesium

(Mg)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Tetrameric Dgtp-Bound Wild Type SAMHD1 Catalytic Core, PDB code: 4bzc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn750 b:25.2 occ:1.00 NE2 A:HIS167 2.0 30.4 1.0 OD1 A:ASP311 2.0 36.7 1.0 OD2 A:ASP207 2.1 32.9 1.0 NE2 A:HIS206 2.1 30.4 1.0 OD2 A:ASP311 2.7 38.1 1.0 CG A:ASP311 2.7 37.4 1.0 CG A:ASP207 3.0 32.9 1.0 CE1 A:HIS167 3.0 30.4 1.0 CD2 A:HIS206 3.0 31.1 1.0 CD2 A:HIS167 3.1 30.5 1.0 CE1 A:HIS206 3.1 30.6 1.0 OD1 A:ASP207 3.2 33.0 1.0 S1A A:T8T700 3.6 73.5 1.0 NH1 A:ARG164 3.8 34.0 1.0 ND1 A:HIS167 4.1 30.3 1.0 ND1 A:HIS206 4.2 30.9 1.0 CG A:HIS167 4.2 30.3 1.0 CG A:HIS206 4.2 31.1 1.0 CB A:ASP311 4.2 36.9 1.0 O5' A:T8T700 4.3 55.8 1.0 CB A:ASP207 4.3 32.5 1.0 CG2 A:VAL171 4.6 30.7 1.0 O3A A:T8T700 4.7 61.4 1.0 PA A:T8T700 4.7 63.9 1.0 CA A:ASP311 5.0 36.5 1.0 NE2 A:GLN149 5.0 35.7 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn750 b:51.1 occ:1.00 OD1 B:ASP311 2.0 50.6 1.0 NE2 B:HIS167 2.1 49.2 1.0 NE2 B:HIS206 2.3 53.4 1.0 OD2 B:ASP207 2.3 60.7 1.0 OD2 B:ASP311 2.6 55.6 1.0 CG B:ASP311 2.6 52.9 1.0 CE1 B:HIS167 2.9 48.1 1.0 CG B:ASP207 3.1 63.6 1.0 CD2 B:HIS167 3.2 48.2 1.0 CD2 B:HIS206 3.2 53.3 1.0 CE1 B:HIS206 3.3 53.8 1.0 OD1 B:ASP207 3.4 64.4 1.0 S1A B:T8T700 3.8 85.4 1.0 NH1 B:ARG164 3.8 43.6 1.0 ND1 B:HIS167 4.1 46.4 1.0 CB B:ASP311 4.1 52.8 1.0 CG B:HIS167 4.2 46.9 1.0 ND1 B:HIS206 4.4 53.7 1.0 CG B:HIS206 4.4 55.1 1.0 O2B B:T8T700 4.4 71.0 1.0 CB B:ASP207 4.5 63.4 1.0 CG2 B:VAL171 4.6 47.0 1.0 CD2 B:TYR315 4.8 53.1 1.0 O B:ASP311 4.9 54.2 1.0 O3A B:T8T700 4.9 75.0 1.0 CA B:ASP311 4.9 53.9 1.0 NE2 B:GLN149 4.9 54.8 1.0 C5' B:T8T700 5.0 69.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn750 b:25.2 occ:1.00 OD1 C:ASP311 2.0 41.8 1.0 NE2 C:HIS206 2.1 34.2 1.0 OD2 C:ASP207 2.1 37.6 1.0 NE2 C:HIS167 2.2 31.7 1.0 OD2 C:ASP311 2.6 43.5 1.0 CG C:ASP311 2.7 39.3 1.0 CG C:ASP207 3.0 38.3 1.0 CD2 C:HIS206 3.0 35.4 1.0 CE1 C:HIS167 3.1 31.6 1.0 CE1 C:HIS206 3.1 34.8 1.0 CD2 C:HIS167 3.2 32.6 1.0 OD1 C:ASP207 3.2 37.4 1.0 S1A C:T8T700 3.2 49.7 1.0 NH1 C:ARG164 3.8 39.2 1.0 CB C:ASP311 4.1 37.0 1.0 CG C:HIS206 4.2 36.1 1.0 ND1 C:HIS206 4.2 35.4 1.0 ND1 C:HIS167 4.2 32.1 1.0 CG C:HIS167 4.3 32.6 1.0 O2B C:T8T700 4.3 47.7 1.0 CB C:ASP207 4.3 38.8 1.0 O5' C:T8T700 4.4 51.9 1.0 CG2 C:VAL171 4.7 31.5 1.0 PA C:T8T700 4.8 50.0 1.0 CA C:ASP311 4.9 35.7 1.0 O C:ASP311 5.0 35.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn750 b:43.4 occ:1.00 OD1 D:ASP311 1.9 49.9 1.0 NE2 D:HIS167 1.9 46.0 1.0 NE2 D:HIS206 2.1 48.3 1.0 OD2 D:ASP207 2.2 53.7 1.0 CG D:ASP311 2.6 51.8 1.0 OD2 D:ASP311 2.7 52.1 1.0 CE1 D:HIS167 2.8 45.9 1.0 CE1 D:HIS206 3.0 48.4 1.0 CD2 D:HIS167 3.0 46.0 1.0 S1A D:T8T700 3.0 76.8 1.0 CD2 D:HIS206 3.1 49.4 1.0 CG D:ASP207 3.1 53.2 1.0 OD1 D:ASP207 3.4 55.0 1.0 NH1 D:ARG164 3.9 49.5 1.0 ND1 D:HIS167 4.0 44.8 1.0 CG D:HIS167 4.1 44.1 1.0 CB D:ASP311 4.1 52.0 1.0 ND1 D:HIS206 4.1 47.6 1.0 O5' D:T8T700 4.2 73.8 1.0 PA D:T8T700 4.2 79.3 1.0 CG D:HIS206 4.2 48.9 1.0 CB D:ASP207 4.4 51.9 1.0 CG2 D:VAL171 4.4 41.4 1.0 O3A D:T8T700 4.4 73.8 1.0 CA D:ASP311 4.8 53.1 1.0 O D:ASP311 4.9 54.8 1.0 NE2 D:GLN149 5.0 60.3 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