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Magnesium in PDB 8qxm: Cryo-Em Structure of Tetrameric Human SAMHD1 State III - Relaxed

Other elements in 8qxm:

The structure of Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed (pdb code 8qxm). 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 III - Relaxed, PDB code: 8qxm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8qxm

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Magnesium binding site 1 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:5.1
occ:1.00
 OD1 A:ASP207 2.4 5.4 1.0
NE2 A:HIS233 2.7 7.9 1.0
CE1 A:HIS233 3.3 7.9 1.0
CG A:ASP207 3.5 5.4 1.0
OD2 A:ASP207 3.8 5.4 1.0
CD2 A:HIS233 3.9 7.9 1.0
FE A:FE801 4.1 12.8 1.0
OE2 A:GLU234 4.2 9.0 1.0
OH A:TYR315 4.3 8.9 1.0
CD2 A:HIS206 4.4 5.0 1.0
OD2 A:ASP311 4.4 8.5 1.0
O A:HIS206 4.5 5.0 1.0
NE2 A:HIS210 4.6 5.0 1.0
ND1 A:HIS233 4.6 7.9 1.0
CD A:GLU234 4.7 9.0 1.0
CB A:ASP207 4.8 5.4 1.0
CG A:HIS233 4.9 7.9 1.0
CA A:ASP207 5.0 5.4 1.0

Magnesium binding site 2 out of 10 in 8qxm

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Magnesium binding site 2 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:5.1
occ:1.00
 O1B B:GTP701 2.0 5.1 1.0
O1G D:DTP701 2.4 5.1 1.0
O1G B:GTP701 2.4 5.1 1.0
O1B D:DTP701 2.7 5.1 1.0
O2A B:GTP701 2.9 5.1 1.0
PB B:GTP701 3.3 5.1 1.0
NZ A:LYS116 3.4 7.4 1.0
PG D:DTP701 3.5 5.1 1.0
PG B:GTP701 3.6 5.1 1.0
O3B B:GTP701 3.6 5.1 1.0
O3' B:GTP701 3.8 5.1 1.0
PB D:DTP701 3.9 5.1 1.0
O3B D:DTP701 3.9 5.1 1.0
O3G D:DTP701 4.1 5.1 1.0
PA B:GTP701 4.1 5.1 1.0
O3A B:GTP701 4.1 5.1 1.0
O3G B:GTP701 4.4 5.1 1.0
O2B B:GTP701 4.4 5.1 1.0
C3' B:GTP701 4.6 5.1 1.0
NZ D:LYS523 4.6 13.2 1.0
O2G B:GTP701 4.7 5.1 1.0
O3A D:DTP701 4.7 5.1 1.0
CE A:LYS116 4.8 7.4 1.0
C5' B:GTP701 4.8 5.1 1.0
O2G D:DTP701 4.8 5.1 1.0
CG A:LYS116 4.8 7.4 1.0
O5' B:GTP701 4.9 5.1 1.0

Magnesium binding site 3 out of 10 in 8qxm

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Magnesium binding site 3 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:5.1
occ:1.00
 O1A B:DCP707 2.8 12.5 1.0
NE2 B:HIS233 3.1 6.0 1.0
OD1 B:ASP207 3.1 5.1 1.0
O2B B:DCP707 3.3 12.5 1.0
O2A B:DCP707 3.4 12.5 1.0
PA B:DCP707 3.6 12.5 1.0
OE2 B:GLU234 3.9 6.6 1.0
CD2 B:HIS233 3.9 6.0 1.0
CE1 B:HIS233 4.1 6.0 1.0
CG B:ASP207 4.1 5.1 1.0
FE B:FE703 4.1 10.3 1.0
O3A B:DCP707 4.2 12.5 1.0
OD2 B:ASP311 4.3 5.1 1.0
OD2 B:ASP207 4.4 5.1 1.0
CD2 B:HIS206 4.4 5.1 1.0
PB B:DCP707 4.4 12.5 1.0
O B:HIS206 4.5 5.1 1.0
NE2 B:HIS210 4.7 6.1 1.0
CD B:GLU234 4.8 6.6 1.0
NE2 B:HIS206 4.9 5.1 1.0

Magnesium binding site 4 out of 10 in 8qxm

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Magnesium binding site 4 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:3.8
occ:1.00
 O2B B:DCP707 3.1 12.5 1.0
O1G B:DCP707 3.4 12.5 1.0
PB B:DCP707 4.0 12.5 1.0
O3B B:DCP707 4.1 12.5 1.0
PG B:DCP707 4.1 12.5 1.0
O3G B:DCP707 4.2 12.5 1.0
OD2 B:ASP309 4.3 7.6 1.0
O1B B:DCP707 4.4 12.5 1.0
OD2 B:ASP311 4.9 5.1 1.0

Magnesium binding site 5 out of 10 in 8qxm

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Magnesium binding site 5 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:8.8
occ:1.00
 O1G C:DTP701 2.0 16.5 1.0
O1B B:GTP702 2.0 11.1 1.0
O1G B:GTP702 2.7 11.1 1.0
O1B C:DTP701 3.2 16.5 1.0
NZ B:LYS116 3.3 10.7 1.0
PB B:GTP702 3.4 11.1 1.0
PG C:DTP701 3.4 16.5 1.0
O3B B:GTP702 3.7 11.1 1.0
O5' B:GTP702 3.8 11.1 1.0
O3' B:GTP702 3.8 11.1 1.0
PG B:GTP702 3.8 11.1 1.0
O3B C:DTP701 4.0 16.5 1.0
CD B:LYS116 4.0 10.7 1.0
O2A B:GTP702 4.1 11.1 1.0
PB C:DTP701 4.1 16.5 1.0
O3A B:GTP702 4.2 11.1 1.0
PA B:GTP702 4.2 11.1 1.0
CE B:LYS116 4.3 10.7 1.0
O3G C:DTP701 4.3 16.5 1.0
O2G C:DTP701 4.4 16.5 1.0
O2B B:GTP702 4.4 11.1 1.0
C3' B:GTP702 4.5 11.1 1.0
O3A C:DTP701 4.6 16.5 1.0
C5' B:GTP702 4.7 11.1 1.0
O3G B:GTP702 4.7 11.1 1.0
O2G B:GTP702 4.9 11.1 1.0

Magnesium binding site 6 out of 10 in 8qxm

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Magnesium binding site 6 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg704

b:5.1
occ:1.00
 OD1 C:ASP207 2.6 5.1 1.0
NE2 C:HIS233 2.8 6.4 1.0
CE1 C:HIS233 3.6 6.4 1.0
CG C:ASP207 3.6 5.1 1.0
CD2 C:HIS233 3.9 6.4 1.0
OD2 C:ASP207 3.9 5.1 1.0
OE2 C:GLU234 4.0 7.2 1.0
FE C:FE703 4.1 10.9 1.0
CE1 C:HIS210 4.3 6.3 1.0
O C:HIS206 4.3 3.5 1.0
OH C:TYR315 4.4 8.7 1.0
OD2 C:ASP311 4.4 8.1 1.0
CD2 C:HIS206 4.5 3.5 1.0
CD C:GLU234 4.6 7.2 1.0
NE2 C:HIS210 4.7 6.3 1.0
ND1 C:HIS233 4.8 6.4 1.0
NE2 C:HIS206 4.9 3.5 1.0
CG C:HIS233 5.0 6.4 1.0
CB C:ASP207 5.0 5.1 1.0

Magnesium binding site 7 out of 10 in 8qxm

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Magnesium binding site 7 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:2.4
occ:1.00
 O1B C:GTP702 2.0 5.1 1.0
O1G C:GTP702 2.2 5.1 1.0
O1G B:DTP708 2.3 5.1 1.0
O1B B:DTP708 2.6 5.1 1.0
PB C:GTP702 3.2 5.1 1.0
PG C:GTP702 3.4 5.1 1.0
O3B C:GTP702 3.4 5.1 1.0
PG B:DTP708 3.5 5.1 1.0
NZ C:LYS116 3.7 6.0 1.0
O5' C:GTP702 3.7 5.1 1.0
PB B:DTP708 3.8 5.1 1.0
O2A C:GTP702 3.8 5.1 1.0
O3B B:DTP708 3.9 5.1 1.0
O3A C:GTP702 4.0 5.1 1.0
O3' C:GTP702 4.1 5.1 1.0
PA C:GTP702 4.1 5.1 1.0
O3G B:DTP708 4.1 5.1 1.0
O3G C:GTP702 4.3 5.1 1.0
O2B C:GTP702 4.3 5.1 1.0
O2G C:GTP702 4.5 5.1 1.0
NZ B:LYS523 4.6 13.1 1.0
C5' C:GTP702 4.7 5.1 1.0
O3A B:DTP708 4.7 5.1 1.0
O2G B:DTP708 4.8 5.1 1.0
C3' C:GTP702 4.8 5.1 1.0
CG C:LYS116 4.9 6.0 1.0
CE C:LYS116 4.9 6.0 1.0
O2B B:DTP708 5.0 5.1 1.0

Magnesium binding site 8 out of 10 in 8qxm

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Magnesium binding site 8 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg706

b:12.7
occ:1.00
 O1B A:DTP804 1.8 18.2 1.0
O1G A:DTP804 1.8 18.2 1.0
O1B D:GTP702 2.1 10.3 1.0
PB A:DTP804 2.3 18.2 1.0
O3B A:DTP804 2.5 18.2 1.0
PG A:DTP804 2.6 18.2 1.0
O3A A:DTP804 2.7 18.2 1.0
O3' D:GTP702 3.2 10.3 1.0
O5' D:GTP702 3.5 10.3 1.0
PB D:GTP702 3.6 10.3 1.0
O3G A:DTP804 3.7 18.2 1.0
O2G A:DTP804 3.8 18.2 1.0
O2B A:DTP804 3.8 18.2 1.0
C5' D:GTP702 3.9 10.3 1.0
C3' D:GTP702 4.0 10.3 1.0
C4' D:GTP702 4.1 10.3 1.0
O3B D:GTP702 4.1 10.3 1.0
O3A D:GTP702 4.3 10.3 1.0
PA A:DTP804 4.3 18.2 1.0
PA D:GTP702 4.5 10.3 1.0
O2B D:GTP702 4.6 10.3 1.0
O5' A:DTP804 4.7 18.2 1.0
O1A A:DTP804 5.0 18.2 1.0

Magnesium binding site 9 out of 10 in 8qxm

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Magnesium binding site 9 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg704

b:5.1
occ:1.00
 O1A D:DCP706 2.8 12.3 1.0
OD1 D:ASP207 2.9 4.5 1.0
NE2 D:HIS233 3.0 5.4 1.0
O2B D:DCP706 3.3 12.3 1.0
O2A D:DCP706 3.5 12.3 1.0
PA D:DCP706 3.6 12.3 1.0
CE1 D:HIS233 3.8 5.4 1.0
CG D:ASP207 3.8 4.5 1.0
OE2 D:GLU234 3.9 6.3 1.0
OD2 D:ASP207 4.0 4.5 1.0
CD2 D:HIS233 4.1 5.4 1.0
FE D:FE703 4.1 7.5 1.0
O3A D:DCP706 4.2 12.3 1.0
CD2 D:HIS206 4.2 2.4 1.0
PB D:DCP706 4.4 12.3 1.0
O D:HIS206 4.5 2.4 1.0
CD D:GLU234 4.7 6.3 1.0
NE2 D:HIS206 4.7 2.4 1.0
NE2 D:HIS210 4.8 5.2 1.0
ND1 D:HIS233 5.0 5.4 1.0

Magnesium binding site 10 out of 10 in 8qxm

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Magnesium binding site 10 out of 10 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State III - 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 III - Relaxed within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg705

b:7.3
occ:1.00
 O2B D:DCP706 3.1 12.3 1.0
O1G D:DCP706 3.5 12.3 1.0
PB D:DCP706 4.0 12.3 1.0
O3B D:DCP706 4.0 12.3 1.0
OD2 D:ASP309 4.1 8.3 1.0
PG D:DCP706 4.1 12.3 1.0
O3G D:DCP706 4.2 12.3 1.0
O1B D:DCP706 4.3 12.3 1.0
OG D:SER302 4.4 7.9 1.0
NZ D:LYS312 4.7 7.3 1.0
OD2 D:ASP311 4.9 5.1 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 17:07:15 2024

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