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Magnesium in PDB 6dw5: SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket

Protein crystallography data

The structure of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket, PDB code: 6dw5 was solved by K.M.Knecht, O.Buzovetsky, C.Schneider, D.Thomas, V.Srikanth, L.Kaderali, F.Tofoleanu, K.Reiss, N.Ferreiros, G.Geisslinger, V.S.Batista, X.Ji, J.Cinatl, O.T.Keppler, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.41 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.686, 142.901, 98.907, 90.00, 113.92, 90.00
R / Rfree (%) 17.3 / 20.5

Other elements in 6dw5:

The structure of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Nickel (Ni) 1 atom
Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket (pdb code 6dw5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket, PDB code: 6dw5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6dw5

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Magnesium binding site 1 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:24.7
occ:1.00
 O1G A:DTP703 2.0 26.0 1.0
O2G B:GTP703 2.0 29.3 1.0
O1B A:DTP703 2.0 22.7 1.0
O2A B:GTP703 2.2 24.2 1.0
O2B B:GTP703 2.2 26.8 1.0
O B:HOH860 2.2 21.3 1.0
PB B:GTP703 3.1 29.4 1.0
PB A:DTP703 3.2 21.6 1.0
PG B:GTP703 3.2 30.6 1.0
PG A:DTP703 3.2 25.7 1.0
PA B:GTP703 3.4 24.1 1.0
O3B B:GTP703 3.4 29.4 1.0
O3B A:DTP703 3.5 23.5 1.0
O3A B:GTP703 3.6 25.8 1.0
NZ B:LYS116 3.8 34.4 1.0
NZ A:LYS523 3.9 43.9 1.0
O3' B:GTP703 4.0 23.9 1.0
O B:HOH920 4.0 34.6 1.0
O2G A:DTP703 4.1 24.3 1.0
O2B A:DTP703 4.1 20.9 1.0
O3G B:GTP703 4.2 30.5 1.0
O1G B:GTP703 4.2 29.9 1.0
O5' B:GTP703 4.3 23.9 1.0
C5' B:GTP703 4.3 23.4 1.0
O B:HOH844 4.3 31.4 1.0
O3A A:DTP703 4.3 22.2 1.0
O1B B:GTP703 4.5 30.8 1.0
O3G A:DTP703 4.5 26.6 1.0
O B:HOH885 4.5 24.0 1.0
O1A B:GTP703 4.5 24.2 1.0
C3' B:GTP703 4.6 22.9 1.0
C4' B:GTP703 4.9 22.7 1.0
CE A:LYS523 5.0 44.2 1.0

Magnesium binding site 2 out of 10 in 6dw5

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Magnesium binding site 2 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:20.8
occ:1.00
 O1G D:GTP703 2.0 23.6 1.0
O1A D:GTP703 2.0 21.9 1.0
O D:HOH863 2.1 18.0 1.0
O1B B:DTP704 2.1 18.7 1.0
O2G B:DTP704 2.1 21.1 1.0
O1B D:GTP703 2.1 22.9 1.0
PB D:GTP703 3.2 24.8 1.0
PG D:GTP703 3.2 26.6 1.0
PB B:DTP704 3.3 20.5 1.0
PG B:DTP704 3.3 22.4 1.0
PA D:GTP703 3.3 21.1 1.0
O3B D:GTP703 3.4 24.6 1.0
O3A D:GTP703 3.6 22.1 1.0
O3B B:DTP704 3.6 20.8 1.0
NZ A:LYS116 3.7 34.4 1.0
NZ B:LYS523 3.9 35.8 1.0
O D:HOH918 3.9 35.5 1.0
O3' D:GTP703 3.9 18.0 1.0
O2G D:GTP703 4.0 27.2 1.0
O1G B:DTP704 4.1 22.2 1.0
O3G D:GTP703 4.1 26.4 1.0
O2B B:DTP704 4.2 19.5 1.0
C5' D:GTP703 4.2 18.8 1.0
O5' D:GTP703 4.2 19.6 1.0
O D:HOH857 4.4 32.7 1.0
O D:HOH928 4.4 24.0 1.0
O3A B:DTP704 4.4 19.6 1.0
O2B D:GTP703 4.5 27.2 1.0
O3G B:DTP704 4.5 24.5 1.0
O B:HOH830 4.5 35.3 1.0
O2A D:GTP703 4.5 19.4 1.0
C3' D:GTP703 4.6 17.6 1.0
C4' D:GTP703 4.9 17.2 1.0

Magnesium binding site 3 out of 10 in 6dw5

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Magnesium binding site 3 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg707

b:62.5
occ:1.00
 O1G A:GTF701 2.2 56.2 1.0
PG A:GTF701 2.9 67.5 1.0
OH A:TYR315 2.9 22.5 1.0
O2G A:GTF701 3.1 62.3 1.0
NE2 A:HIS370 3.1 26.7 1.0
F2 A:GTF701 3.2 57.3 1.0
NE A:ARG366 3.5 23.6 1.0
O3B A:GTF701 3.5 66.0 1.0
NH2 A:ARG366 3.6 28.8 1.0
CE1 A:HIS370 3.7 28.5 1.0
CZ A:TYR315 3.8 21.7 1.0
C5' A:GTF701 3.9 50.7 1.0
CZ A:ARG366 3.9 27.9 1.0
C6 A:GTF701 3.9 44.4 1.0
O3G A:GTF701 4.2 61.9 1.0
CD2 A:HIS370 4.3 24.9 1.0
CE2 A:TYR315 4.3 20.6 1.0
O5' A:GTF701 4.5 64.3 1.0
CD A:ARG366 4.5 23.9 1.0
C5 A:GTF701 4.6 44.2 1.0
C2' A:GTF701 4.6 46.7 1.0
CE1 A:TYR315 4.7 20.1 1.0
CG A:ARG366 4.7 21.7 1.0

Magnesium binding site 4 out of 10 in 6dw5

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Magnesium binding site 4 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg708

b:53.2
occ:1.00
 O2A A:GTF701 2.5 85.4 1.0
O A:HOH847 2.5 46.3 1.0
OD2 A:ASP311 2.6 28.5 1.0
O3B A:GTF701 2.6 66.0 1.0
O3G A:GTF701 3.0 61.9 1.0
O1B A:GTF701 3.1 53.6 1.0
PG A:GTF701 3.3 67.5 1.0
CG A:ASP311 3.4 25.9 1.0
PB A:GTF701 3.4 62.3 1.0
CE2 A:TYR315 3.5 20.6 1.0
O A:HOH814 3.5 57.9 1.0
O1G A:GTF701 3.6 56.2 1.0
NH2 A:ARG206 3.7 28.8 1.0
PA A:GTF701 3.9 76.8 1.0
CB A:ASP311 3.9 23.8 1.0
O A:HOH836 4.0 32.8 1.0
CD2 A:TYR315 4.1 18.7 1.0
C5' A:GTF701 4.2 50.7 1.0
O3A A:GTF701 4.2 75.5 1.0
CG A:LYS312 4.2 27.4 1.0
O5' A:GTF701 4.3 64.3 1.0
N A:LYS312 4.3 19.6 1.0
CZ A:ARG206 4.4 30.8 1.0
OD1 A:ASP311 4.4 27.3 1.0
C A:ASP311 4.5 19.4 1.0
NH1 A:ARG206 4.5 30.0 1.0
CZ A:TYR315 4.5 21.7 1.0
OD1 A:ASP309 4.6 27.7 1.0
O2G A:GTF701 4.7 62.3 1.0
NZ A:LYS312 4.7 32.8 1.0
O A:HOH818 4.7 45.6 1.0
CA A:LYS312 4.8 21.4 1.0
OH A:TYR315 4.8 22.5 1.0
O1A A:GTF701 4.8 59.0 1.0
O2B A:GTF701 4.8 59.2 1.0
CA A:ASP311 4.9 21.5 1.0
O A:HOH806 4.9 42.3 1.0

Magnesium binding site 5 out of 10 in 6dw5

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Magnesium binding site 5 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:66.4
occ:1.00
 O1B B:GTF701 2.2 82.8 1.0
OE2 B:GLU234 2.8 46.2 1.0
PB B:GTF701 3.2 82.1 1.0
O2B B:GTF701 3.2 73.8 1.0
O B:HOH810 3.6 41.5 1.0
O B:HOH811 3.6 38.8 1.0
O B:HOH835 3.8 56.3 1.0
CD B:GLU234 3.9 42.0 1.0
O3A B:GTF701 4.1 94.6 1.0
NE2 B:HIS233 4.3 35.5 1.0
OE1 B:GLU234 4.3 41.0 1.0
O3B B:GTF701 4.7 78.7 1.0
CE1 B:HIS233 4.7 36.2 1.0
O3G B:GTF701 4.7 59.3 1.0

Magnesium binding site 6 out of 10 in 6dw5

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Magnesium binding site 6 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg703

b:18.1
occ:1.00
 O1G A:GTP702 2.0 19.6 1.0
O1A A:GTP702 2.0 18.3 1.0
O2G C:DTP702 2.1 19.3 1.0
O2B C:DTP702 2.1 16.1 1.0
O1B A:GTP702 2.2 19.5 1.0
O A:HOH921 2.2 12.5 1.0
PB A:GTP702 3.2 20.4 1.0
PG C:DTP702 3.2 19.6 1.0
PB C:DTP702 3.2 17.6 1.0
PG A:GTP702 3.3 21.7 1.0
O3B C:DTP702 3.4 18.3 1.0
PA A:GTP702 3.4 18.2 1.0
O3B A:GTP702 3.4 19.6 1.0
O3A A:GTP702 3.7 18.4 1.0
NZ C:LYS523 3.8 29.8 1.0
NZ D:LYS116 3.9 23.7 1.0
O A:HOH830 3.9 29.1 1.0
O3' A:GTP702 4.0 17.3 1.0
O1B C:DTP702 4.0 16.9 1.0
O1G C:DTP702 4.1 19.8 1.0
O3G A:GTP702 4.2 20.9 1.0
O2G A:GTP702 4.2 21.1 1.0
C5' A:GTP702 4.3 16.0 1.0
O5' A:GTP702 4.3 16.8 1.0
O D:HOH911 4.3 17.3 1.0
O3G C:DTP702 4.4 18.9 1.0
O3A C:DTP702 4.4 16.8 1.0
O2B A:GTP702 4.6 21.6 1.0
O2A A:GTP702 4.6 17.8 1.0
C3' A:GTP702 4.6 15.8 1.0
O C:HOH904 4.9 21.4 1.0
C4' A:GTP702 4.9 15.6 1.0

Magnesium binding site 7 out of 10 in 6dw5

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Magnesium binding site 7 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg704

b:22.9
occ:1.00
 O2G B:GTP702 1.9 27.5 1.0
O2A B:GTP702 2.0 23.4 1.0
O1G D:DTP701 2.1 24.6 1.0
O1B D:DTP701 2.1 22.6 1.0
O2B B:GTP702 2.1 25.6 1.0
O B:HOH852 2.2 21.3 1.0
PB B:GTP702 3.1 27.1 1.0
PG B:GTP702 3.1 29.1 1.0
PB D:DTP701 3.3 22.2 1.0
O3B B:GTP702 3.3 27.6 1.0
PA B:GTP702 3.3 23.5 1.0
PG D:DTP701 3.4 24.4 1.0
O3B D:DTP701 3.6 22.8 1.0
O3A B:GTP702 3.6 24.7 1.0
NZ C:LYS116 3.7 32.5 1.0
NZ D:LYS523 3.8 43.1 1.0
O B:HOH921 4.0 38.7 1.0
O3' B:GTP702 4.0 21.5 1.0
O1G B:GTP702 4.1 29.0 1.0
O2G D:DTP701 4.1 23.5 1.0
O3G B:GTP702 4.1 29.6 1.0
O2B D:DTP701 4.1 21.7 1.0
O5' B:GTP702 4.2 22.2 1.0
O D:HOH825 4.3 33.7 1.0
C5' B:GTP702 4.3 21.2 1.0
O B:HOH910 4.5 21.3 1.0
O1B B:GTP702 4.5 28.7 1.0
O3A D:DTP701 4.5 21.5 1.0
O1A B:GTP702 4.5 22.4 1.0
O3G D:DTP701 4.6 25.5 1.0
C3' B:GTP702 4.6 20.2 1.0
C4' B:GTP702 4.9 20.4 1.0

Magnesium binding site 8 out of 10 in 6dw5

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Magnesium binding site 8 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg704

b:57.2
occ:1.00
 O D:HOH811 1.9 44.2 1.0
O D:HOH836 2.1 41.5 1.0
O D:HOH812 2.2 43.2 1.0
O1B D:GTF702 2.4 51.5 1.0
O1G D:GTF702 3.2 45.5 1.0
NZ D:LYS312 3.4 28.5 1.0
PB D:GTF702 3.4 57.0 1.0
OD2 D:ASP309 3.5 30.6 1.0
O3B D:GTF702 3.5 54.5 1.0
PG D:GTF702 3.6 47.3 1.0
NH1 D:ARG206 4.0 28.0 1.0
O3G D:GTF702 4.0 47.9 1.0
OD1 D:ASP309 4.1 28.0 1.0
NH2 D:ARG206 4.1 27.8 1.0
CG D:ASP309 4.2 27.6 1.0
O3A D:GTF702 4.4 67.8 1.0
CZ D:ARG206 4.5 27.3 1.0
O D:HOH807 4.6 38.5 1.0
O2B D:GTF702 4.6 49.3 1.0
CE D:LYS312 4.6 26.9 1.0
O D:HOH805 4.7 48.9 1.0
CG D:LYS312 4.7 24.2 1.0
OG D:SER302 4.9 40.6 1.0

Magnesium binding site 9 out of 10 in 6dw5

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Magnesium binding site 9 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg705

b:57.1
occ:1.00
 O2G D:GTF702 1.8 53.8 1.0
NE2 D:HIS370 2.9 28.1 1.0
PG D:GTF702 3.0 47.3 1.0
O3G D:GTF702 3.3 47.9 1.0
F2 D:GTF702 3.4 52.7 1.0
OH D:TYR315 3.4 26.8 1.0
CE1 D:HIS370 3.5 29.4 1.0
O3B D:GTF702 3.5 54.5 1.0
C6 D:GTF702 3.6 44.6 1.0
O5' D:GTF702 3.7 50.2 1.0
NH2 D:ARG366 3.9 25.6 1.0
C5' D:GTF702 3.9 42.2 1.0
NE D:ARG366 4.0 23.8 1.0
CZ D:TYR315 4.1 23.3 1.0
C5 D:GTF702 4.1 42.1 1.0
O1G D:GTF702 4.1 45.5 1.0
CD2 D:HIS370 4.2 27.7 1.0
CZ D:ARG366 4.4 26.2 1.0
CE2 D:TYR315 4.5 22.1 1.0
C2' D:GTF702 4.7 43.4 1.0
N1 D:GTF702 4.7 44.6 1.0
ND1 D:HIS370 4.8 29.2 1.0
CE1 D:TYR315 4.9 21.4 1.0
PB D:GTF702 5.0 57.0 1.0

Magnesium binding site 10 out of 10 in 6dw5

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Magnesium binding site 10 out of 10 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg706

b:49.2
occ:1.00
 O2A D:GTF702 1.7 70.5 1.0
O D:HOH923 2.2 31.9 1.0
PA D:GTF702 2.5 67.5 1.0
O3A D:GTF702 2.7 67.8 1.0
NE2 D:HIS210 2.8 20.3 1.0
O1A D:GTF702 2.9 69.5 1.0
OD1 D:ASN207 3.1 22.4 1.0
O D:HOH804 3.3 33.9 1.0
CE1 D:HIS233 3.4 34.2 1.0
NH1 D:ARG164 3.4 16.1 1.0
NH2 D:ARG206 3.7 27.8 1.0
CD2 D:HIS210 3.7 19.3 1.0
NE2 D:HIS233 3.8 32.4 1.0
CE1 D:HIS210 3.8 20.8 1.0
ND1 D:HIS233 3.9 29.8 1.0
O5' D:GTF702 4.1 50.2 1.0
PB D:GTF702 4.1 57.0 1.0
CG D:ASN207 4.1 20.6 1.0
CZ D:ARG164 4.4 16.3 1.0
OD1 D:ASP311 4.4 32.1 1.0
NE2 D:HIS215 4.5 36.8 1.0
CD2 D:HIS233 4.5 34.5 1.0
OD2 D:ASP311 4.5 29.1 1.0
O1B D:GTF702 4.5 51.5 1.0
C5' D:GTF702 4.6 42.2 1.0
CG D:HIS233 4.6 31.0 1.0
O2B D:GTF702 4.6 49.3 1.0
ND2 D:ASN207 4.7 19.9 1.0
CZ D:ARG206 4.7 27.3 1.0
NE D:ARG206 4.8 28.9 1.0
O D:HOH808 4.8 32.4 1.0
CG D:ASP311 4.8 27.6 1.0
CE1 D:HIS215 4.9 37.0 1.0
ND1 D:HIS210 4.9 20.1 1.0
CG D:HIS210 4.9 19.6 1.0
NH2 D:ARG164 4.9 17.8 1.0
C4' D:GTF702 5.0 40.6 1.0

Reference:

K.M.Knecht, O.Buzovetsky, C.Schneider, D.Thomas, V.Srikanth, L.Kaderali, F.Tofoleanu, K.Reiss, N.Ferreiros, G.Geisslinger, V.S.Batista, X.Ji, J.Cinatl Jr., O.T.Keppler, Y.Xiong. The Structural Basis For Cancer Drug Interactions with the Catalytic and Allosteric Sites of SAMHD1. Proc. Natl. Acad. Sci. V. 115 10022 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30305425
DOI: 10.1073/PNAS.1805593115
Page generated: Mon Sep 30 23:42:57 2024

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