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Magnesium in PDB 4qfz: Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core

Protein crystallography data

The structure of Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qfz was solved by L.M.I.Koharudin, Y.Wu, M.Delucia, J.Mehrens, A.M.Gronenborn, J.Ahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.98 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.831, 146.738, 98.941, 90.00, 114.29, 90.00
R / Rfree (%) 20.9 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core (pdb code 4qfz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qfz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4qfz

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Magnesium binding site 1 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:33.0
occ:0.65
 O2G B:TTP702 2.1 34.6 0.6
O3G D:DGT702 2.1 33.1 0.5
O1B B:TTP702 2.1 35.0 0.6
O2A D:DGT702 2.3 27.8 0.5
O2B D:DGT702 2.3 26.8 0.5
PG B:TTP702 3.2 35.4 0.6
PB B:TTP702 3.3 30.4 0.6
PG D:DGT702 3.4 34.9 0.5
PB D:DGT702 3.4 34.3 0.5
O3B B:TTP702 3.5 36.4 0.6
PA D:DGT702 3.6 30.2 0.5
O1G B:TTP702 3.7 36.8 0.6
NZ A:LYS116 3.7 30.1 0.6
O3B D:DGT702 3.8 35.7 0.5
O3' D:DGT702 3.9 28.4 0.5
O3A D:DGT702 4.0 32.2 0.5
O2G D:DGT702 4.2 33.8 0.5
O2B B:TTP702 4.2 34.5 0.6
NZ B:LYS523 4.3 44.8 0.6
O D:HOH802 4.3 32.8 0.7
C5' D:DGT702 4.3 31.2 0.5
O3A B:TTP702 4.4 36.9 0.6
O1G D:DGT702 4.4 35.4 0.5
O3G B:TTP702 4.5 36.5 0.6
O5' D:DGT702 4.5 32.8 0.5
C3' D:DGT702 4.5 30.6 0.5
O1A D:DGT702 4.7 30.2 0.5
O1B D:DGT702 4.7 28.1 0.5
CE A:LYS116 4.9 34.8 0.6
C4' D:DGT702 4.9 32.5 0.5

Magnesium binding site 2 out of 9 in 4qfz

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Magnesium binding site 2 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:60.0
occ:0.89
 O1G A:TTP702 2.1 48.8 0.6
O1B A:TTP702 2.3 44.4 0.6
NZ A:LYS312 3.4 46.1 0.6
PG A:TTP702 3.5 49.3 0.6
OD2 A:ASP309 3.5 45.7 0.6
PB A:TTP702 3.5 51.3 0.6
O3B A:TTP702 3.8 52.5 0.6
OD1 A:ASP309 4.0 41.2 0.6
NH1 A:ARG206 4.1 38.8 0.6
O A:HOH839 4.1 57.0 0.8
CG A:ASP309 4.2 43.8 0.6
O3G A:TTP702 4.3 48.8 0.6
O2G A:TTP702 4.5 49.9 0.6
NH2 A:ARG206 4.5 47.5 0.6
O3A A:TTP702 4.5 55.9 0.6
O2B A:TTP702 4.5 51.8 0.6
CG A:LYS312 4.7 45.1 0.6
CE A:LYS312 4.7 44.8 0.6
OD2 A:ASP311 4.7 45.7 0.6
CZ A:ARG206 4.8 41.8 0.6

Magnesium binding site 3 out of 9 in 4qfz

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Magnesium binding site 3 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:44.9
occ:0.69
 O2G C:DGT703 1.9 46.9 0.6
O1G A:TTP703 2.0 45.6 0.7
O1B A:TTP703 2.1 44.9 0.7
O1A C:DGT703 2.2 40.3 0.6
O1B C:DGT703 2.2 42.9 0.6
PG C:DGT703 3.2 44.6 0.6
PG A:TTP703 3.2 45.2 0.7
PB C:DGT703 3.3 45.6 0.6
PB A:TTP703 3.4 43.9 0.7
PA C:DGT703 3.5 43.0 0.6
NZ B:LYS116 3.6 42.8 0.7
O3B C:DGT703 3.6 47.2 0.6
O3B A:TTP703 3.6 49.6 0.7
O3A C:DGT703 3.8 48.1 0.6
O3' C:DGT703 3.9 38.3 0.6
O3G A:TTP703 4.0 46.0 0.7
NZ A:LYS523 4.1 49.9 0.6
O1G C:DGT703 4.1 50.1 0.6
O3G C:DGT703 4.2 45.0 0.6
C5' C:DGT703 4.3 38.4 0.6
O3A A:TTP703 4.3 44.6 0.7
O2G A:TTP703 4.4 50.9 0.7
O2B A:TTP703 4.4 39.1 0.7
O C:HOH845 4.4 44.4 0.7
O5' C:DGT703 4.5 43.6 0.6
O2A C:DGT703 4.5 41.9 0.6
C3' C:DGT703 4.5 38.9 0.6
O2B C:DGT703 4.6 47.4 0.6
CE B:LYS116 4.8 40.6 0.7
C4' C:DGT703 4.9 40.7 0.6

Magnesium binding site 4 out of 9 in 4qfz

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Magnesium binding site 4 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:55.5
occ:0.79
 O2B B:TTP701 2.0 42.5 0.6
O2G B:TTP701 2.3 37.5 0.6
O B:HOH803 2.5 38.7 0.8
PB B:TTP701 3.3 41.2 0.6
O B:HOH857 3.4 50.1 0.8
PG B:TTP701 3.5 39.7 0.6
O3B B:TTP701 3.8 42.2 0.6
NZ B:LYS312 4.0 34.5 0.7
O1G B:TTP701 4.0 37.6 0.6
O1B B:TTP701 4.0 41.5 0.6
O B:HOH840 4.0 43.8 0.8
OD2 B:ASP309 4.2 38.7 0.6
NH1 B:ARG206 4.2 36.1 0.7
NH2 B:ARG206 4.2 39.1 0.7
O3A B:TTP701 4.5 45.7 0.6
O3G B:TTP701 4.7 39.2 0.6
O B:HOH856 4.7 43.0 0.8
CZ B:ARG206 4.7 41.2 0.7
OD1 B:ASP309 4.7 33.4 0.6
CG B:ASP309 4.9 32.9 0.6
OG B:SER302 4.9 44.0 0.5

Magnesium binding site 5 out of 9 in 4qfz

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Magnesium binding site 5 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:35.7
occ:0.58
 O2G C:DGT702 1.9 42.4 0.6
O2B D:TTP701 2.0 37.0 0.6
O1G D:TTP701 2.0 34.8 0.6
O1B C:DGT702 2.1 34.1 0.6
O1A C:DGT702 2.2 34.9 0.6
O D:HOH867 2.2 36.3 0.8
PB C:DGT702 3.1 36.5 0.6
PB D:TTP701 3.2 34.1 0.6
PG C:DGT702 3.2 40.2 0.6
PG D:TTP701 3.2 40.4 0.6
O3B D:TTP701 3.4 41.0 0.6
PA C:DGT702 3.4 35.8 0.6
O3B C:DGT702 3.5 40.1 0.6
O3A C:DGT702 3.6 37.5 0.6
O1B D:TTP701 3.9 35.9 0.6
O3' C:DGT702 4.0 35.5 0.6
C5' C:DGT702 4.0 35.2 0.6
NZ D:LYS523 4.1 44.6 0.6
NZ C:LYS116 4.1 34.3 0.6
O2G D:TTP701 4.1 38.4 0.6
O3G C:DGT702 4.1 34.8 0.6
O1G C:DGT702 4.2 40.8 0.6
O5' C:DGT702 4.2 37.2 0.6
O3G D:TTP701 4.3 37.8 0.6
O3A D:TTP701 4.4 42.8 0.6
O2B C:DGT702 4.4 37.6 0.6
O2A C:DGT702 4.5 34.9 0.6
C3' C:DGT702 4.5 35.5 0.6
C4' C:DGT702 4.8 36.5 0.6

Magnesium binding site 6 out of 9 in 4qfz

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Magnesium binding site 6 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg706

b:60.5
occ:0.87
 O2B C:TTP704 2.1 49.2 0.6
O3G C:TTP704 2.2 48.8 0.6
O C:HOH847 2.5 45.8 0.8
PB C:TTP704 3.4 49.5 0.6
PG C:TTP704 3.4 48.5 0.6
NZ C:LYS312 3.6 45.1 0.7
O3B C:TTP704 3.8 49.6 0.6
O1G C:TTP704 3.9 48.2 0.6
OD2 C:ASP309 4.1 46.4 0.6
O1B C:TTP704 4.1 51.8 0.6
O C:HOH835 4.1 53.2 0.8
O C:HOH833 4.2 53.3 0.8
NH2 C:ARG206 4.3 48.0 0.7
NH1 C:ARG206 4.5 40.7 0.7
O3A C:TTP704 4.6 54.5 0.6
O2G C:TTP704 4.6 48.2 0.6
O C:HOH828 4.8 48.8 0.7
OD1 C:ASP309 4.9 43.7 0.6
CE C:LYS312 4.9 44.0 0.7
CZ C:ARG206 4.9 43.7 0.7
CG C:ASP309 4.9 46.0 0.6

Magnesium binding site 7 out of 9 in 4qfz

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Magnesium binding site 7 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg704

b:48.1
occ:0.80
 O1B D:TTP703 1.9 44.4 0.6
O3G D:TTP703 2.1 41.1 0.6
O D:HOH864 2.4 44.0 0.8
O D:HOH857 2.4 43.6 0.8
PB D:TTP703 3.2 45.0 0.6
PG D:TTP703 3.3 42.1 0.6
O3B D:TTP703 3.5 42.8 0.6
NZ D:LYS312 3.7 39.1 0.7
O D:HOH830 3.9 44.2 0.7
O2G D:TTP703 3.9 43.7 0.6
O2B D:TTP703 3.9 40.3 0.6
O D:HOH861 4.1 45.8 0.7
NH2 D:ARG206 4.2 42.6 0.7
NH1 D:ARG206 4.2 35.4 0.7
OD2 D:ASP309 4.3 39.7 0.7
O3A D:TTP703 4.4 48.7 0.6
O1G D:TTP703 4.5 42.4 0.6
CZ D:ARG206 4.7 41.2 0.7
O D:HOH835 4.8 42.8 0.7
OD1 D:ASP309 4.8 40.8 0.7
OD2 D:ASP311 4.9 40.7 0.6
CG D:ASP309 5.0 41.2 0.7

Magnesium binding site 8 out of 9 in 4qfz

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Magnesium binding site 8 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg705

b:76.9
occ:0.81
 CD D:LYS405 3.4 63.2 0.6
CG D:LYS405 3.6 62.6 0.6
CE D:LYS405 4.1 66.8 0.6
O D:LYS406 4.6 59.1 0.6
NZ D:LYS405 4.7 72.7 0.6

Magnesium binding site 9 out of 9 in 4qfz

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Magnesium binding site 9 out of 9 in the Crystal Structure of the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Dttp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg706

b:43.0
occ:0.64
 O2G C:TTP701 2.0 32.1 0.6
O3G A:DGT701 2.0 36.3 0.6
O2A A:DGT701 2.1 33.5 0.6
O2B C:TTP701 2.2 34.8 0.6
O2B A:DGT701 2.2 36.4 0.6
PB A:DGT701 3.2 41.6 0.6
PG A:DGT701 3.3 39.1 0.6
PG C:TTP701 3.3 44.9 0.6
PB C:TTP701 3.4 37.9 0.6
PA A:DGT701 3.4 36.4 0.6
O3B A:DGT701 3.6 36.7 0.6
NZ D:LYS116 3.6 39.0 0.7
O3B C:TTP701 3.6 45.6 0.6
O3A A:DGT701 3.7 36.9 0.6
O3' A:DGT701 3.9 35.0 0.6
O1G C:TTP701 4.1 44.0 0.6
O2G A:DGT701 4.1 32.4 0.6
O1B C:TTP701 4.3 41.7 0.6
O1G A:DGT701 4.3 41.0 0.6
C5' A:DGT701 4.3 33.2 0.6
O3G C:TTP701 4.3 44.6 0.6
O5' A:DGT701 4.4 38.5 0.6
O D:HOH863 4.4 40.8 0.7
O1A A:DGT701 4.4 37.1 0.6
O3A C:TTP701 4.4 41.6 0.6
O1B A:DGT701 4.5 38.5 0.6
C3' A:DGT701 4.6 35.1 0.6
C4' A:DGT701 4.9 34.0 0.6
CE D:LYS116 4.9 41.1 0.7

Reference:

L.M.Koharudin, Y.Wu, M.Delucia, J.Mehrens, A.M.Gronenborn, J.Ahn. Structural Basis of Allosteric Activation of Sterile Alpha Motif and Histidine-Aspartate Domain Containing Protein 1 (SAMHD1) By Nucleoside Triphosphates. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25288794
DOI: 10.1074/JBC.M114.591958
Page generated: Tue Aug 20 01:55:44 2024

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