Magnesium in PDB 8qxl: Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed

Other elements in 8qxl:

The structure of Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 10 in 8qxl

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Magnesium binding site 1 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:10.0
occ:1.00
 CE1 A:HIS233 2.6 11.8 1.0
OD1 A:ASP207 2.7 6.8 1.0
O5' A:3PO706 2.7 16.5 0.2
NE2 A:HIS233 3.3 11.8 1.0
ND1 A:HIS233 3.7 11.8 1.0
CG A:ASP207 3.8 6.8 1.0
OE2 A:GLU234 3.9 14.8 1.0
PA A:3PO706 4.1 16.5 0.2
O A:HIS206 4.2 5.4 1.0
CD2 A:HIS206 4.2 5.4 1.0
OD2 A:ASP207 4.4 6.8 1.0
NE2 A:HIS210 4.4 7.8 1.0
FE A:FE702 4.5 11.7 1.0
O1A A:3PO706 4.5 16.5 0.2
OD2 A:ASP311 4.5 7.2 1.0
CD A:GLU234 4.6 14.8 1.0
CD2 A:HIS233 4.6 11.8 1.0
CG A:GLU234 4.6 14.8 1.0
C A:HIS206 4.8 5.4 1.0
CG A:HIS233 4.8 11.8 1.0
OH A:TYR315 4.9 8.1 1.0
CA A:ASP207 4.9 6.8 1.0
CE1 A:HIS210 5.0 7.8 1.0
NE2 A:HIS206 5.0 5.4 1.0
CB A:ASP207 5.0 6.8 1.0

Magnesium binding site 2 out of 10 in 8qxl

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Magnesium binding site 2 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:2.3
occ:1.00
 O3B A:GTP701 2.6 7.8 1.0
NZ A:LYS116 3.0 6.1 1.0
O2G A:GTP701 3.2 7.8 1.0
O2A A:GTP701 3.2 7.8 1.0
O1G D:DTP701 3.2 7.8 1.0
O3B D:DTP701 3.3 7.8 1.0
PG A:GTP701 3.5 7.8 1.0
O5' A:GTP701 3.7 7.8 1.0
PG D:DTP701 3.8 7.8 1.0
PB A:GTP701 3.8 7.8 1.0
O3' A:GTP701 3.9 7.8 1.0
PA A:GTP701 3.9 7.8 1.0
O1B A:GTP701 4.1 7.8 1.0
O1B D:DTP701 4.3 7.8 1.0
O3A A:GTP701 4.3 7.8 1.0
NZ D:LYS523 4.4 19.1 1.0
O3G D:DTP701 4.4 7.8 1.0
PB D:DTP701 4.4 7.8 1.0
O3G A:GTP701 4.4 7.8 1.0
C3' A:GTP701 4.4 7.8 1.0
CE A:LYS116 4.4 6.1 1.0
CG A:LYS116 4.6 6.1 1.0
O1G A:GTP701 4.6 7.8 1.0
C5' A:GTP701 4.7 7.8 1.0
CD A:LYS116 4.8 6.1 1.0
O3A D:DTP701 5.0 7.8 1.0

Magnesium binding site 3 out of 10 in 8qxl

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Magnesium binding site 3 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:7.8
occ:1.00
 CE1 B:HIS233 2.4 8.8 1.0
OD1 B:ASP207 2.7 7.8 1.0
NE2 B:HIS233 3.0 8.8 1.0
O1A B:DCP805 3.1 16.9 1.0
ND1 B:HIS233 3.6 8.8 1.0
O2A B:DCP805 3.7 16.9 1.0
CG B:ASP207 3.8 7.8 1.0
PA B:DCP805 3.8 16.9 1.0
O2B B:DCP805 3.8 16.9 1.0
OD2 B:ASP207 4.0 7.8 1.0
FE B:FE801 4.1 11.2 1.0
O3A B:DCP805 4.2 16.9 1.0
CD2 B:HIS233 4.3 8.8 1.0
O B:HIS206 4.4 11.6 1.0
NE2 B:HIS210 4.4 4.8 1.0
OE2 B:GLU234 4.5 7.0 1.0
CD2 B:HIS206 4.5 11.6 1.0
PB B:DCP805 4.6 16.9 1.0
CG B:HIS233 4.6 8.8 1.0
CD B:GLU234 4.7 7.0 1.0
OD2 B:ASP311 4.8 11.0 1.0
CG B:GLU234 4.9 7.0 1.0
CD2 B:HIS210 5.0 4.8 1.0

Magnesium binding site 4 out of 10 in 8qxl

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Magnesium binding site 4 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:7.8
occ:1.00
 O3G B:DCP805 3.4 16.9 1.0
O2B B:DCP805 3.6 16.9 1.0
OD2 B:ASP309 4.1 11.0 1.0
OG B:SER302 4.4 14.2 1.0
CB B:SER302 4.7 14.2 1.0
PB B:DCP805 4.8 16.9 1.0
NZ B:LYS312 4.9 4.6 1.0
PG B:DCP805 4.9 16.9 1.0
O1B B:DCP805 4.9 16.9 1.0

Magnesium binding site 5 out of 10 in 8qxl

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Magnesium binding site 5 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:8.1
occ:1.00
 O1B A:GTP707 2.1 7.8 1.0
O1G A:DTP708 2.1 10.7 1.0
O1G A:GTP707 2.4 7.8 1.0
NZ B:LYS116 2.9 11.5 1.0
O1B A:DTP708 3.3 10.7 1.0
PB A:GTP707 3.4 7.8 1.0
PG A:GTP707 3.5 7.8 1.0
PG A:DTP708 3.6 10.7 1.0
O3B A:GTP707 3.7 7.8 1.0
O5' A:GTP707 3.8 7.8 1.0
O3G A:GTP707 3.9 7.8 1.0
O3' A:GTP707 4.0 7.8 1.0
O2A A:GTP707 4.1 7.8 1.0
O3B A:DTP708 4.2 10.7 1.0
O3A A:GTP707 4.2 7.8 1.0
CE B:LYS116 4.2 11.5 1.0
PB A:DTP708 4.2 10.7 1.0
PA A:GTP707 4.3 7.8 1.0
CG B:LYS116 4.4 11.5 1.0
O2G A:DTP708 4.5 10.7 1.0
CD B:LYS116 4.5 11.5 1.0
O2B A:GTP707 4.5 7.8 1.0
C3' A:GTP707 4.5 7.8 1.0
O3G A:DTP708 4.6 10.7 1.0
C5' A:GTP707 4.7 7.8 1.0
O2G A:GTP707 4.8 7.8 1.0
O3A A:DTP708 4.8 10.7 1.0

Magnesium binding site 6 out of 10 in 8qxl

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Magnesium binding site 6 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg703

b:11.7
occ:1.00
 O1B C:3PO706 2.3 67.7 1.0
CE1 C:HIS233 2.9 10.3 1.0
O2B C:3PO706 3.0 67.7 1.0
NE2 C:HIS233 3.2 10.3 1.0
PB C:3PO706 3.2 67.7 1.0
OD1 C:ASP207 3.5 5.8 1.0
ND1 C:HIS233 4.2 10.3 1.0
OE2 C:GLU234 4.2 12.8 1.0
O1G C:3PO706 4.3 67.7 1.0
O3B C:3PO706 4.3 67.7 1.0
OH C:TYR315 4.4 8.5 1.0
CG C:ASP207 4.4 5.8 1.0
FE C:FE702 4.4 14.4 1.0
O3A C:3PO706 4.4 67.7 1.0
OD2 C:ASP207 4.5 5.8 1.0
CD2 C:HIS233 4.5 10.3 1.0
CD C:GLU234 4.6 12.8 1.0
NE2 C:HIS210 4.7 4.3 1.0
PG C:3PO706 4.7 67.7 1.0
CD2 C:HIS206 4.8 5.5 1.0
O5' C:DCZ705 4.9 18.8 0.2
O C:HIS206 4.9 5.5 1.0
O2G C:3PO706 4.9 67.7 1.0

Magnesium binding site 7 out of 10 in 8qxl

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Magnesium binding site 7 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg704

b:8.5
occ:1.00
 O3B C:GTP701 2.5 7.8 1.0
O1B B:DTP806 2.6 7.8 1.0
O3G B:DTP806 2.6 7.8 1.0
O1B C:GTP701 3.5 7.8 1.0
PG C:GTP701 3.6 7.8 1.0
O2G C:GTP701 3.6 7.8 1.0
PB C:GTP701 3.6 7.8 1.0
O5' C:GTP701 3.7 7.8 1.0
NZ C:LYS116 3.8 12.7 1.0
O3' C:GTP701 3.8 7.8 1.0
PB B:DTP806 3.8 7.8 1.0
O2A C:GTP701 3.9 7.8 1.0
PG B:DTP806 3.9 7.8 1.0
O1G C:GTP701 4.0 7.8 1.0
O3B B:DTP806 4.1 7.8 1.0
NZ B:LYS523 4.1 19.6 1.0
PA C:GTP701 4.2 7.8 1.0
O2G B:DTP806 4.3 7.8 1.0
O3A C:GTP701 4.4 7.8 1.0
C3' C:GTP701 4.5 7.8 1.0
CD C:LYS116 4.6 12.7 1.0
CE C:LYS116 4.6 12.7 1.0
O3A B:DTP806 4.7 7.8 1.0
C5' C:GTP701 4.8 7.8 1.0
O2B C:GTP701 4.8 7.8 1.0
O3G C:GTP701 4.9 7.8 1.0
CG C:LYS116 4.9 12.7 1.0

Magnesium binding site 8 out of 10 in 8qxl

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Magnesium binding site 8 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg704

b:11.2
occ:1.00
 NE2 D:HIS233 2.2 10.8 1.0
O2A D:DCP707 2.3 25.8 1.0
CE1 D:HIS233 2.3 10.8 1.0
OD1 D:ASP207 3.2 7.8 1.0
O1B D:DCP707 3.5 25.8 1.0
CD2 D:HIS233 3.5 10.8 1.0
ND1 D:HIS233 3.6 10.8 1.0
PA D:DCP707 3.7 25.8 1.0
NE2 D:HIS210 3.9 7.8 1.0
O3A D:DCP707 4.1 25.8 1.0
CG D:ASP207 4.2 7.8 1.0
CG D:HIS233 4.2 10.8 1.0
OD2 D:ASP207 4.3 7.8 1.0
PB D:DCP707 4.4 25.8 1.0
O1A D:DCP707 4.5 25.8 1.0
CE1 D:HIS210 4.6 7.8 1.0
OE2 D:GLU234 4.6 10.0 1.0
O5' D:DCP707 4.7 25.8 1.0
FE D:FE703 4.7 13.7 1.0
CD2 D:HIS210 4.8 7.8 1.0
CD D:GLU234 4.9 10.0 1.0

Magnesium binding site 9 out of 10 in 8qxl

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Magnesium binding site 9 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg705

b:12.9
occ:1.00
 O2B D:DCP707 3.0 25.8 1.0
O1B D:DCP707 3.1 25.8 1.0
O1G D:DCP707 3.2 25.8 1.0
PB D:DCP707 3.5 25.8 1.0
O3B D:DCP707 4.1 25.8 1.0
OD2 D:ASP309 4.2 8.6 1.0
PG D:DCP707 4.2 25.8 1.0
OG D:SER302 4.6 5.8 1.0
O2G D:DCP707 4.7 25.8 1.0
NZ D:LYS312 5.0 3.6 1.0
O3A D:DCP707 5.0 25.8 1.0

Magnesium binding site 10 out of 10 in 8qxl

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Magnesium binding site 10 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State II - Hemi-Relaxed


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 State II - Hemi-Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg706

b:13.5
occ:1.00
 O3G A:DTP709 2.2 12.8 1.0
O1B D:GTP702 2.2 8.3 1.0
O1B A:DTP709 2.6 12.8 1.0
O1G D:GTP702 3.3 8.3 1.0
NZ D:LYS116 3.4 13.2 1.0
PG A:DTP709 3.6 12.8 1.0
PB D:GTP702 3.7 8.3 1.0
O3' D:GTP702 3.7 8.3 1.0
PB A:DTP709 3.7 12.8 1.0
O3B A:DTP709 3.9 12.8 1.0
O5' D:GTP702 4.1 8.3 1.0
O3B D:GTP702 4.2 8.3 1.0
CG D:LYS116 4.3 13.2 1.0
O2A D:GTP702 4.4 8.3 1.0
C3' D:GTP702 4.4 8.3 1.0
PG D:GTP702 4.4 8.3 1.0
O2G A:DTP709 4.4 12.8 1.0
O3A D:GTP702 4.5 8.3 1.0
CE D:LYS116 4.6 13.2 1.0
PA D:GTP702 4.6 8.3 1.0
O3A A:DTP709 4.6 12.8 1.0
O1G A:DTP709 4.6 12.8 1.0
CD D:LYS116 4.6 13.2 1.0
O2B D:GTP702 4.7 8.3 1.0
C5' D:GTP702 4.7 8.3 1.0
O2B A:DTP709 4.9 12.8 1.0

Reference:

O.J.Acton, D.Sheppard, E.R.Morris, S.Kunzelmann, S.J.Caswell, A.Nans, A.Burgess, G.Kelly, P.B.Rosenthal, I.A.Taylor. Platform-Directed Allostery and Quaternary Structure Dynamics of SAMHD1 Catalysis To Be Published.
Page generated: Fri Oct 4 17:04:05 2024

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