Magnesium in PDB 5yhw: Crystal Structure of Pig SAMHD1

The structure of Crystal Structure of Pig SAMHD1, PDB code: 5yhw was solved by X.H.Qin, J.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	86.540, 95.909, 130.749, 78.66, 88.12, 82.68
R / Rfree (%)	26.3 / 29

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Pig SAMHD1 (pdb code 5yhw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of Pig SAMHD1, PDB code: 5yhw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Crystal Structure of Pig SAMHD1


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 Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:57.5 occ:1.00 O2B A:DGT701 2.2 61.1 1.0 O1G A:DGT701 3.0 58.3 1.0 O3G A:DGT701 3.3 60.3 1.0 PB A:DGT701 3.4 61.0 1.0 NH2 A:ARG206 3.5 37.3 1.0 PG A:DGT701 3.6 59.3 1.0 NZ A:LYS312 3.7 37.8 1.0 O3B A:DGT701 3.9 59.9 1.0 O1B A:DGT701 3.9 60.6 1.0 OD2 A:ASP309 4.2 41.4 1.0 O3A A:DGT701 4.8 62.5 1.0 CZ A:ARG206 4.8 38.7 1.0

Magnesium binding site 2 out of 16 in the Crystal Structure of Pig SAMHD1


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 Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:60.5 occ:1.00 O2B H:DGT705 1.9 67.8 1.0 O1G B:DGT705 2.1 68.8 1.0 O2G H:DGT705 2.1 69.9 1.0 O1B B:DGT705 2.2 69.7 1.0 O2A B:DGT705 2.4 67.0 1.0 PG H:DGT705 3.2 70.0 1.0 PB H:DGT705 3.2 68.2 1.0 PB B:DGT705 3.4 69.9 1.0 PG B:DGT705 3.4 69.2 1.0 O3B H:DGT705 3.5 69.7 1.0 O1G H:DGT705 3.6 69.1 1.0 NZ H:LYS524 3.6 54.4 1.0 PA B:DGT705 3.7 66.9 1.0 O3B B:DGT705 3.7 70.0 1.0 O3A B:DGT705 3.9 68.6 1.0 O1B H:DGT705 4.0 68.3 1.0 O3' B:DGT705 4.1 64.8 1.0 C5' B:DGT705 4.2 66.0 1.0 O2G B:DGT705 4.2 68.2 1.0 O3A H:DGT705 4.3 67.1 1.0 O3G B:DGT705 4.4 70.0 1.0 O3G H:DGT705 4.5 71.1 1.0 O5' B:DGT705 4.5 66.0 1.0 C3' B:DGT705 4.6 64.3 1.0 O2B B:DGT705 4.6 71.1 1.0 NZ A:LYS116 4.7 51.0 1.0 O1A B:DGT705 4.8 66.2 1.0 CE A:LYS116 4.8 49.8 1.0 C4' B:DGT705 4.9 64.7 1.0 CE H:LYS524 4.9 54.7 1.0

Magnesium binding site 3 out of 16 in the Crystal Structure of Pig SAMHD1


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 Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:50.6 occ:1.00 O3G D:DGT701 1.8 37.1 1.0 O1G A:DGT703 1.9 89.0 1.0 O D:HOH802 2.1 36.5 1.0 O1B A:DGT703 2.1 88.5 1.0 O2B D:DGT701 2.2 38.3 1.0 O1A A:DGT703 2.3 90.4 1.0 PG A:DGT703 3.1 89.6 1.0 PG D:DGT701 3.1 36.1 1.0 PB A:DGT703 3.1 89.7 1.0 PB D:DGT701 3.3 37.3 1.0 O3B A:DGT703 3.4 90.2 1.0 O3B D:DGT701 3.4 36.3 1.0 PA A:DGT703 3.5 91.2 1.0 O3A A:DGT703 3.6 90.6 1.0 O2G A:DGT703 4.0 88.8 1.0 O1G D:DGT701 4.0 35.4 1.0 O2G D:DGT701 4.1 35.9 1.0 O3' A:DGT703 4.1 90.0 1.0 NZ B:LYS116 4.2 37.4 1.0 O3G A:DGT703 4.2 90.4 1.0 O1B D:DGT701 4.3 37.4 1.0 C5' A:DGT703 4.3 90.5 1.0 O2B A:DGT703 4.5 89.6 1.0 O5' A:DGT703 4.5 91.5 1.0 O3A D:DGT701 4.5 37.3 1.0 CE B:LYS116 4.5 37.4 1.0 O2A A:DGT703 4.6 92.4 1.0 C3' A:DGT703 4.7 91.1 1.0 C4' A:DGT703 5.0 90.8 1.0

Magnesium binding site 4 out of 16 in the Crystal Structure of Pig SAMHD1


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 Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:53.9 occ:1.00 O1G B:DGT703 2.3 61.3 1.0 O1B B:DGT703 2.5 61.2 1.0 NH2 B:ARG206 3.2 48.7 1.0 NZ B:LYS312 3.4 50.4 1.0 PG B:DGT703 3.6 62.5 1.0 OD1 B:ASP309 3.7 50.1 1.0 PB B:DGT703 3.9 61.9 1.0 O3G B:DGT703 4.1 63.9 1.0 O3B B:DGT703 4.1 62.2 1.0 CZ B:ARG206 4.4 48.0 1.0 CG B:ASP309 4.6 49.5 1.0 OD2 B:ASP309 4.7 48.9 1.0 CE B:LYS312 4.7 50.3 1.0 NH1 B:ARG206 4.8 47.8 1.0 O2G B:DGT703 4.8 62.4 1.0 O2B B:DGT703 4.8 63.3 1.0 O3A B:DGT703 4.8 60.7 1.0

Magnesium binding site 5 out of 16 in the Crystal Structure of Pig SAMHD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:56.5 occ:1.00 O C:HOH801 2.0 57.1 1.0 O1B C:DGT701 2.4 56.4 1.0 O1G C:DGT701 2.5 53.8 1.0 NH2 C:ARG206 3.5 35.1 1.0 PG C:DGT701 3.7 53.6 1.0 NZ C:LYS312 3.7 36.1 1.0 PB C:DGT701 3.8 56.8 1.0 OD2 C:ASP309 4.1 42.0 1.0 O3G C:DGT701 4.1 52.6 1.0 O3B C:DGT701 4.2 55.3 1.0 O2B C:DGT701 4.6 57.2 1.0 CZ C:ARG206 4.6 36.1 1.0 O3A C:DGT701 4.9 58.3 1.0 NH1 C:ARG206 4.9 36.7 1.0 O2G C:DGT701 4.9 52.8 1.0 CE C:LYS312 5.0 35.3 1.0

Magnesium binding site 6 out of 16 in the Crystal Structure of Pig SAMHD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:55.3 occ:1.00 O2G C:DGT705 1.9 69.4 1.0 O3G E:DGT704 2.0 69.4 1.0 O E:HOH805 2.1 75.5 1.0 O2B E:DGT704 2.2 67.1 1.0 O1A C:DGT705 2.3 67.1 1.0 O1B C:DGT705 2.8 69.6 1.0 PG E:DGT704 3.2 69.3 1.0 PG C:DGT705 3.3 70.0 1.0 PB E:DGT704 3.5 67.1 1.0 O1G E:DGT704 3.7 68.6 1.0 NZ C:LYS116 3.7 47.6 1.0 PA C:DGT705 3.7 67.1 1.0 PB C:DGT705 3.7 69.8 1.0 O3B E:DGT704 3.8 68.4 1.0 O3B C:DGT705 3.9 70.2 1.0 O3G C:DGT705 3.9 69.0 1.0 O3' C:DGT705 4.0 64.4 1.0 CE C:LYS116 4.0 46.7 1.0 O3A C:DGT705 4.2 68.5 1.0 O1G C:DGT705 4.4 71.2 1.0 O2G E:DGT704 4.4 70.4 1.0 O3A E:DGT704 4.4 65.9 1.0 C5' C:DGT705 4.5 65.8 1.0 O1B E:DGT704 4.5 67.1 1.0 O5' C:DGT705 4.6 66.0 1.0 O2A C:DGT705 4.7 66.9 1.0 C3' C:DGT705 4.7 64.1 1.0 CG C:LYS116 4.9 46.2 1.0

Magnesium binding site 7 out of 16 in the Crystal Structure of Pig SAMHD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:59.1 occ:1.00 O3G H:DGT703 1.9 62.3 1.0 O1B B:DGT702 2.0 67.8 1.0 O2G B:DGT702 2.1 69.0 1.0 O2A H:DGT703 2.5 61.4 1.0 O1B H:DGT703 2.8 63.1 1.0 PG B:DGT702 3.2 68.8 1.0 PB B:DGT702 3.3 68.0 1.0 PG H:DGT703 3.4 63.1 1.0 NZ D:LYS116 3.5 59.1 1.0 O1G B:DGT702 3.6 68.0 1.0 O3' H:DGT703 3.6 59.6 1.0 O3B B:DGT702 3.7 68.6 1.0 PB H:DGT703 3.9 63.6 1.0 PA H:DGT703 3.9 61.7 1.0 O3B H:DGT703 4.0 63.7 1.0 O1G H:DGT703 4.1 62.5 1.0 O2G H:DGT703 4.3 63.8 1.0 O3A B:DGT702 4.3 66.9 1.0 O2B B:DGT702 4.3 68.6 1.0 O3A H:DGT703 4.4 62.9 1.0 C5' H:DGT703 4.4 61.2 1.0 C3' H:DGT703 4.4 59.6 1.0 O3G B:DGT702 4.5 69.7 1.0 O5' H:DGT703 4.7 61.3 1.0 CE D:LYS116 4.7 58.4 1.0 CD D:LYS116 4.8 57.1 1.0 O1A H:DGT703 4.8 61.4 1.0 CG D:LYS116 4.8 56.6 1.0 C4' H:DGT703 4.9 60.2 1.0

Magnesium binding site 8 out of 16 in the Crystal Structure of Pig SAMHD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:61.2 occ:1.00 NH2 D:ARG206 2.6 46.3 1.0 O2G D:DGT703 2.7 65.0 1.0 O2B D:DGT703 2.9 66.2 1.0 OD2 D:ASP309 3.3 63.2 1.0 OD1 D:ASP309 3.8 64.5 1.0 CZ D:ARG206 3.8 47.1 1.0 NZ D:LYS312 3.9 46.9 1.0 CG D:ASP309 3.9 63.7 1.0 PG D:DGT703 4.0 65.9 1.0 PB D:DGT703 4.2 67.0 1.0 O3B D:DGT703 4.3 66.9 1.0 NH1 D:ARG206 4.5 47.9 1.0 OD2 D:ASP311 4.6 49.5 1.0 NE D:ARG206 4.7 47.2 1.0 CE D:LYS312 4.8 47.3 1.0 O1B D:DGT703 4.9 66.8 1.0 O3G D:DGT703 4.9 66.0 1.0 O1G D:DGT703 4.9 65.8 1.0 CA D:ALA302 5.0 55.6 1.0 CB D:ASP311 5.0 48.8 1.0

Magnesium binding site 9 out of 16 in the Crystal Structure of Pig SAMHD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg702 b:84.7 occ:1.00 NH2 E:ARG206 2.7 57.6 1.0 O2G E:DGT701 2.9 68.5 1.0 O2B E:DGT701 3.2 67.1 1.0 OD2 E:ASP309 3.2 54.3 1.0 CZ E:ARG206 4.0 56.6 1.0 NZ E:LYS312 4.0 53.0 1.0 CG E:ASP309 4.0 53.7 1.0 OD1 E:ASP309 4.1 53.1 1.0 PG E:DGT701 4.3 67.8 1.0 PB E:DGT701 4.5 66.4 1.0 O3B E:DGT701 4.6 66.7 1.0 OD1 E:ASP311 4.7 54.6 1.0 O E:ASN303 4.7 55.8 1.0 NE E:ARG206 4.8 56.3 1.0 CA E:ALA302 4.8 54.4 1.0 NH1 E:ARG206 4.8 56.0 1.0 N E:ASN303 4.9 54.6 1.0 CB E:ALA302 5.0 55.1 1.0 O E:GLY307 5.0 52.8 1.0 O1G E:DGT701 5.0 68.3 1.0

Magnesium binding site 10 out of 16 in the Crystal Structure of Pig SAMHD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Pig SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg705 b:57.7 occ:1.00 O1G G:DGT706 2.0 53.4 1.0 O2G C:DGT706 2.0 48.1 1.0 O1B C:DGT706 2.0 49.4 1.0 O1B G:DGT706 2.5 52.3 1.0 O2A G:DGT706 2.6 54.4 1.0 PG C:DGT706 3.2 47.5 1.0 PG G:DGT706 3.3 53.0 1.0 PB C:DGT706 3.3 48.8 1.0 NZ E:LYS116 3.6 55.9 1.0 O3' G:DGT706 3.7 54.9 1.0 PB G:DGT706 3.7 52.6 1.0 O3B C:DGT706 3.7 47.8 1.0 O1G C:DGT706 3.8 47.9 1.0 O3G G:DGT706 3.8 52.2 1.0 PA G:DGT706 3.9 54.5 1.0 O3B G:DGT706 3.9 52.9 1.0 O3A G:DGT706 4.2 53.6 1.0 O3A C:DGT706 4.3 49.5 1.0 O2B C:DGT706 4.4 48.5 1.0 C5' G:DGT706 4.4 54.3 1.0 O2G G:DGT706 4.4 53.8 1.0 C3' G:DGT706 4.4 55.5 1.0 O3G C:DGT706 4.4 46.4 1.0 O5' G:DGT706 4.7 54.9 1.0 CE E:LYS116 4.8 57.0 1.0 O2B G:DGT706 4.9 51.9 1.0 C4' G:DGT706 4.9 55.0 1.0 CG E:LYS116 4.9 57.5 1.0 O1A G:DGT706 5.0 55.3 1.0 CD E:LYS116 5.0 57.6 1.0

J.Kong, M.M.Wang, S.Y.He, X.Peng, X.H.Qin. Structural Characterization and Directed Modification of Sus Scrofa SAMHD1 Reveal the Mechanism Underlying Deoxynucleotide Regulation. Febs J. V. 286 3844 2019.
ISSN: ISSN 1742-464X
PubMed: 31152619
DOI: 10.1111/FEBS.14943