Magnesium in PDB 8qxj: Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp

The structure of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp (pdb code 8qxj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp, PDB code: 8qxj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:7.2 occ:1.00 OD1 A:ASP207 2.0 5.7 1.0 O2A A:DZ4701 2.5 2.9 1.0 NE2 A:HIS233 2.8 5.9 1.0 CG A:ASP207 3.1 5.7 1.0 PA A:DZ4701 3.5 2.9 1.0 OD2 A:ASP207 3.6 5.7 1.0 O1B A:DZ4701 3.6 2.9 1.0 CD2 A:HIS233 3.6 5.9 1.0 O1A A:DZ4701 3.6 2.9 1.0 CE1 A:HIS233 3.8 5.9 1.0 CD2 A:HIS206 3.8 4.9 1.0 FE A:FE702 4.0 11.7 1.0 O A:HIS206 4.2 4.9 1.0 N3A A:DZ4701 4.2 2.9 1.0 OE2 A:GLU234 4.3 6.0 1.0 NE2 A:HIS206 4.3 4.9 1.0 NE2 A:HIS210 4.3 4.1 1.0 CB A:ASP207 4.4 5.7 1.0 CA A:ASP207 4.6 5.7 1.0 PB A:DZ4701 4.6 2.9 1.0 C A:HIS206 4.7 4.9 1.0 CG A:HIS233 4.8 5.9 1.0 CG A:HIS206 4.8 4.9 1.0 ND1 A:HIS233 4.9 5.9 1.0 CD2 A:HIS210 4.9 4.1 1.0 CD A:GLU234 4.9 6.0 1.0 N A:ASP207 4.9 5.7 1.0 O5' A:DZ4701 4.9 2.9 1.0 CG A:GLU234 5.0 6.0 1.0 NH2 A:ARG164 5.0 3.3 1.0

Magnesium binding site 2 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:5.9 occ:1.00 O3B A:DZ4701 2.5 2.9 1.0 PG A:DZ4701 3.5 2.9 1.0 O1B A:DZ4701 3.5 2.9 1.0 O2G A:DZ4701 3.6 2.9 1.0 PB A:DZ4701 3.6 2.9 1.0 O3G A:DZ4701 3.8 2.9 1.0 O A:HOH853 4.2 8.9 1.0 OD2 A:ASP309 4.3 4.9 1.0 OG A:SER302 4.5 7.4 1.0 N3A A:DZ4701 4.6 2.9 1.0 NZ A:LYS312 4.6 3.5 1.0 O2B A:DZ4701 4.8 2.9 1.0 O1G A:DZ4701 4.9 2.9 1.0 OD2 A:ASP311 4.9 1.9 1.0

Magnesium binding site 3 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:3.9 occ:1.00 O3G B:GTP701 2.0 7.5 1.0 O1B B:GTP701 2.0 7.5 1.0 O1G D:DZ4701 2.0 7.5 1.0 O2A B:GTP701 2.1 7.5 1.0 O2B D:DZ4701 3.0 7.5 1.0 O1B D:DZ4701 3.1 7.5 1.0 PB B:GTP701 3.3 7.5 1.0 PG B:GTP701 3.3 7.5 1.0 PG D:DZ4701 3.4 7.5 1.0 PB D:DZ4701 3.4 7.5 1.0 PA B:GTP701 3.4 7.5 1.0 O3B B:GTP701 3.7 7.5 1.0 NZ A:LYS116 3.7 7.9 1.0 O3A B:GTP701 3.8 7.5 1.0 O3' B:GTP701 3.8 7.5 1.0 O3B D:DZ4701 3.8 7.5 1.0 O1G B:GTP701 3.9 7.5 1.0 O3G D:DZ4701 4.1 7.5 1.0 O D:HOH809 4.1 6.0 1.0 C5' B:GTP701 4.2 7.5 1.0 O5' B:GTP701 4.3 7.5 1.0 C3' B:GTP701 4.4 7.5 1.0 O2G B:GTP701 4.4 7.5 1.0 O2G D:DZ4701 4.5 7.5 1.0 O2B B:GTP701 4.5 7.5 1.0 O1A B:GTP701 4.5 7.5 1.0 NZ D:LYS523 4.7 11.5 1.0 C4' B:GTP701 4.8 7.5 1.0

Magnesium binding site 4 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:7.5 occ:1.00 OD1 B:ASP207 2.3 4.0 1.0 O2A B:DZ4702 2.5 3.3 1.0 NE2 B:HIS233 2.8 5.5 1.0 CG B:ASP207 3.4 4.0 1.0 PA B:DZ4702 3.5 3.3 1.0 O1B B:DZ4702 3.6 3.3 1.0 O1A B:DZ4702 3.6 3.3 1.0 CD2 B:HIS233 3.6 5.5 1.0 OD2 B:ASP207 3.7 4.0 1.0 CE1 B:HIS233 3.8 5.5 1.0 CD2 B:HIS206 3.8 3.1 1.0 O B:HIS206 4.0 3.1 1.0 FE B:FE703 4.0 8.8 1.0 N3A B:DZ4702 4.2 3.3 1.0 OE2 B:GLU234 4.3 5.7 1.0 NE2 B:HIS210 4.3 4.8 1.0 NE2 B:HIS206 4.3 3.1 1.0 PB B:DZ4702 4.6 3.3 1.0 CB B:ASP207 4.7 4.0 1.0 C B:HIS206 4.8 3.1 1.0 CG B:HIS233 4.8 5.5 1.0 ND1 B:HIS233 4.9 5.5 1.0 CD2 B:HIS210 4.9 4.8 1.0 CA B:ASP207 4.9 4.0 1.0 CD B:GLU234 4.9 5.7 1.0 CG B:HIS206 4.9 3.1 1.0 NH2 B:ARG164 4.9 4.5 1.0 O5' B:DZ4702 5.0 3.3 1.0 CG B:GLU234 5.0 5.7 1.0

Magnesium binding site 5 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:4.6 occ:1.00 O3B B:DZ4702 2.5 3.3 1.0 PG B:DZ4702 3.5 3.3 1.0 O1B B:DZ4702 3.5 3.3 1.0 O2G B:DZ4702 3.6 3.3 1.0 PB B:DZ4702 3.6 3.3 1.0 O3G B:DZ4702 3.8 3.3 1.0 OD2 B:ASP309 4.3 4.9 1.0 OG B:SER302 4.4 7.2 1.0 N3A B:DZ4702 4.6 3.3 1.0 NZ B:LYS312 4.6 3.2 1.0 O2B B:DZ4702 4.8 3.3 1.0 O1G B:DZ4702 4.9 3.3 1.0 OD2 B:ASP311 4.9 2.1 1.0

Magnesium binding site 6 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg706 b:3.5 occ:1.00 O1B A:GTP706 1.9 7.5 1.0 O2B C:DZ4701 2.0 7.5 1.0 O3G A:GTP706 2.2 7.5 1.0 O1G C:DZ4701 2.3 7.5 1.0 PB A:GTP706 3.3 7.5 1.0 PB C:DZ4701 3.4 7.5 1.0 PG A:GTP706 3.4 7.5 1.0 O5' A:GTP706 3.4 7.5 1.0 O2A A:GTP706 3.5 7.5 1.0 PG C:DZ4701 3.6 7.5 1.0 NZ B:LYS116 3.7 7.7 1.0 O3B A:GTP706 3.8 7.5 1.0 PA A:GTP706 3.8 7.5 1.0 O1G A:GTP706 4.0 7.5 1.0 O3B C:DZ4701 4.0 7.5 1.0 O3A A:GTP706 4.0 7.5 1.0 O3' A:GTP706 4.0 7.5 1.0 O A:HOH823 4.0 5.6 1.0 O3G C:DZ4701 4.2 7.5 1.0 O1B C:DZ4701 4.3 7.5 1.0 O2B A:GTP706 4.4 7.5 1.0 N3A C:DZ4701 4.4 7.5 1.0 C5' A:GTP706 4.6 7.5 1.0 CE B:LYS116 4.6 7.7 1.0 O2G A:GTP706 4.6 7.5 1.0 NZ C:LYS523 4.7 11.6 1.0 C3' A:GTP706 4.7 7.5 1.0 O2G C:DZ4701 4.7 7.5 1.0 CD B:LYS116 4.9 7.7 1.0

Magnesium binding site 7 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:7.4 occ:1.00 OD1 C:ASP207 2.3 3.5 1.0 O2A C:DZ4702 2.5 2.8 1.0 NE2 C:HIS233 2.7 5.2 1.0 CG C:ASP207 3.4 3.5 1.0 PA C:DZ4702 3.5 2.8 1.0 O1B C:DZ4702 3.6 2.8 1.0 CD2 C:HIS233 3.6 5.2 1.0 O1A C:DZ4702 3.6 2.8 1.0 OD2 C:ASP207 3.7 3.5 1.0 CE1 C:HIS233 3.8 5.2 1.0 CD2 C:HIS206 3.8 2.3 1.0 O C:HIS206 4.0 2.3 1.0 FE C:FE703 4.0 7.5 1.0 N3A C:DZ4702 4.2 2.8 1.0 OE2 C:GLU234 4.3 6.0 1.0 NE2 C:HIS210 4.3 3.4 1.0 NE2 C:HIS206 4.3 2.3 1.0 PB C:DZ4702 4.6 2.8 1.0 CB C:ASP207 4.7 3.5 1.0 C C:HIS206 4.8 2.3 1.0 CG C:HIS233 4.8 5.2 1.0 CD2 C:HIS210 4.8 3.4 1.0 ND1 C:HIS233 4.9 5.2 1.0 CD C:GLU234 4.9 6.0 1.0 CA C:ASP207 4.9 3.5 1.0 CG C:HIS206 4.9 2.3 1.0 NH2 C:ARG164 4.9 3.6 1.0 O5' C:DZ4702 4.9 2.8 1.0 CG C:GLU234 5.0 6.0 1.0

Magnesium binding site 8 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg705 b:4.3 occ:1.00 O3B C:DZ4702 2.5 2.8 1.0 PG C:DZ4702 3.5 2.8 1.0 O1B C:DZ4702 3.5 2.8 1.0 O2G C:DZ4702 3.6 2.8 1.0 PB C:DZ4702 3.6 2.8 1.0 O3G C:DZ4702 3.8 2.8 1.0 OD2 C:ASP309 4.3 3.4 1.0 OG C:SER302 4.5 5.8 1.0 N3A C:DZ4702 4.6 2.8 1.0 NZ C:LYS312 4.6 3.0 1.0 O2B C:DZ4702 4.8 2.8 1.0 O1G C:DZ4702 4.9 2.8 1.0 OD2 C:ASP311 4.9 2.6 1.0

Magnesium binding site 9 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg706 b:4.1 occ:1.00 O1B D:GTP702 1.9 7.5 1.0 O2B B:DZ4707 2.0 7.5 1.0 O3G D:GTP702 2.2 7.5 1.0 O1G B:DZ4707 2.3 7.5 1.0 PB D:GTP702 3.3 7.5 1.0 PB B:DZ4707 3.4 7.5 1.0 PG D:GTP702 3.4 7.5 1.0 O5' D:GTP702 3.4 7.5 1.0 O2A D:GTP702 3.5 7.5 1.0 PG B:DZ4707 3.6 7.5 1.0 NZ C:LYS116 3.6 7.6 1.0 O3B D:GTP702 3.8 7.5 1.0 PA D:GTP702 3.8 7.5 1.0 O1G D:GTP702 4.0 7.5 1.0 O3B B:DZ4707 4.0 7.5 1.0 O3' D:GTP702 4.0 7.5 1.0 O3A D:GTP702 4.0 7.5 1.0 O D:HOH826 4.0 4.7 1.0 O3G B:DZ4707 4.2 7.5 1.0 O1B B:DZ4707 4.3 7.5 1.0 O2B D:GTP702 4.4 7.5 1.0 N3A B:DZ4707 4.4 7.5 1.0 C5' D:GTP702 4.6 7.5 1.0 O2G D:GTP702 4.6 7.5 1.0 C3' D:GTP702 4.7 7.5 1.0 NZ B:LYS523 4.7 10.9 1.0 O2G B:DZ4707 4.7 7.5 1.0 CE C:LYS116 4.9 7.6 1.0

Magnesium binding site 10 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg705 b:8.5 occ:1.00 OD1 D:ASP207 2.3 4.0 1.0 O2A D:DZ4703 2.5 3.8 1.0 NE2 D:HIS233 2.7 6.2 1.0 CG D:ASP207 3.4 4.0 1.0 PA D:DZ4703 3.5 3.8 1.0 O1B D:DZ4703 3.6 3.8 1.0 O1A D:DZ4703 3.6 3.8 1.0 CD2 D:HIS233 3.6 6.2 1.0 CE1 D:HIS233 3.7 6.2 1.0 OD2 D:ASP207 3.8 4.0 1.0 CD2 D:HIS206 3.9 7.5 1.0 O D:HIS206 4.0 7.5 1.0 FE D:FE704 4.0 8.2 1.0 N3A D:DZ4703 4.2 3.8 1.0 NE2 D:HIS206 4.3 7.5 1.0 OE2 D:GLU234 4.3 5.3 1.0 NE2 D:HIS210 4.3 7.8 1.0 PB D:DZ4703 4.6 3.8 1.0 CB D:ASP207 4.7 4.0 1.0 C D:HIS206 4.8 7.5 1.0 CG D:HIS233 4.8 6.2 1.0 ND1 D:HIS233 4.9 6.2 1.0 CD2 D:HIS210 4.9 7.8 1.0 CA D:ASP207 4.9 4.0 1.0 CD D:GLU234 4.9 5.3 1.0 CG D:HIS206 4.9 7.5 1.0 O5' D:DZ4703 5.0 3.8 1.0 CG D:GLU234 5.0 5.3 1.0

O.J.Acton, D.Sheppard, S.Kunzelmann, S.J.Caswell, A.Nans, A.Burgess, G.Kelly, E.R.Morris, P.B.Rosenthal, I.A.Taylor. Platform-Directed Allostery and Quaternary Structure Dynamics of SAMHD1 Catalysis To Be Published.