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Magnesium in PDB 4bzb: Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 Mutant Catalytic Core

Protein crystallography data

The structure of Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 Mutant Catalytic Core, PDB code: 4bzb was solved by X.Ji, H.Yang, Y.Wu, J.Yan, J.Mehrens, M.Delucia, C.Hao, A.M.Gronenborn, J.Skowronski, J.Ahn, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.73 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.203, 146.746, 98.723, 90.00, 114.42, 90.00
R / Rfree (%) 18.871 / 20.612

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 4bzb

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 Mutant Catalytic Core


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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-Bound SAMHD1 Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg750

b:42.8
occ:1.00
 O3G A:DGT700 1.9 42.5 1.0
O2B A:DGT700 1.9 42.4 1.0
O A:HOH2052 2.1 36.6 1.0
O A:HOH2222 2.1 39.2 1.0
O A:HOH2053 2.2 43.8 1.0
O A:HOH2084 2.2 39.7 1.0
PG A:DGT700 3.2 42.3 1.0
PB A:DGT700 3.3 44.0 1.0
O3B A:DGT700 3.6 42.9 1.0
NZ A:LYS312 3.7 32.5 1.0
O1G A:DGT700 3.8 43.2 1.0
OD2 A:ASP309 4.0 34.6 1.0
NH2 A:ARG206 4.1 35.6 1.0
NH1 A:ARG206 4.1 35.5 1.0
O A:HOH2081 4.2 46.9 1.0
O1B A:DGT700 4.2 43.0 1.0
O A:HOH2065 4.3 43.5 1.0
O3A A:DGT700 4.3 42.9 1.0
O A:HOH2223 4.3 46.2 1.0
O2G A:DGT700 4.4 41.5 1.0
OD1 A:ASP309 4.5 33.9 1.0
CZ A:ARG206 4.6 35.3 1.0
CG A:ASP309 4.6 34.4 1.0
OD2 A:ASP311 4.7 35.5 1.0
O A:HOH2085 4.8 42.9 1.0
CE A:LYS312 4.9 32.3 1.0
CG A:LYS312 5.0 31.2 1.0
OG A:SER302 5.0 41.2 1.0

Magnesium binding site 2 out of 8 in 4bzb

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 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-Bound SAMHD1 Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg850

b:29.0
occ:1.00
 O3G A:DGT900 1.9 32.7 1.0
O2B A:DGT800 1.9 28.5 1.0
O2G A:DGT800 2.0 28.8 1.0
O2A A:DGT900 2.0 28.4 1.0
O A:HOH2226 2.1 24.8 1.0
O2B A:DGT900 2.1 32.4 1.0
PB A:DGT900 3.2 33.1 1.0
PG A:DGT900 3.2 34.2 1.0
PB A:DGT800 3.3 28.3 1.0
PA A:DGT900 3.4 28.9 1.0
PG A:DGT800 3.4 29.6 1.0
O3B A:DGT900 3.5 33.1 1.0
O3A A:DGT900 3.7 30.2 1.0
NZ D:LYS116 3.7 34.3 1.0
O3B A:DGT800 3.7 29.2 1.0
NZ C:LYS523 3.9 42.6 1.0
O3' A:DGT900 4.0 27.2 1.0
O3G A:DGT800 4.1 28.3 1.0
O1G A:DGT900 4.1 32.6 1.0
O1B A:DGT800 4.2 28.0 1.0
O2G A:DGT900 4.2 35.2 1.0
C5' A:DGT900 4.3 27.2 1.0
O5' A:DGT900 4.3 27.7 1.0
O3A A:DGT800 4.4 28.4 1.0
O A:HOH2227 4.4 29.9 1.0
O1A A:DGT900 4.5 28.4 1.0
O1G A:DGT800 4.5 30.9 1.0
C3' A:DGT900 4.5 27.1 1.0
O D:HOH2002 4.6 45.6 1.0
O1B A:DGT900 4.6 32.8 1.0
CE C:LYS523 4.8 42.8 1.0
C4' A:DGT900 4.9 26.9 1.0
CE D:LYS116 4.9 34.2 1.0

Magnesium binding site 3 out of 8 in 4bzb

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 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-Bound SAMHD1 Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg750

b:30.9
occ:1.00
 O2B B:DGT700 1.9 30.8 1.0
O1G B:DGT700 1.9 31.6 1.0
O B:HOH2052 2.1 27.4 1.0
O B:HOH2261 2.1 31.4 1.0
O B:HOH2053 2.2 26.8 1.0
O B:HOH2098 2.3 27.8 1.0
PB B:DGT700 3.2 32.6 1.0
PG B:DGT700 3.2 31.1 1.0
O3B B:DGT700 3.6 32.2 1.0
NZ B:LYS312 3.8 25.8 1.0
O3G B:DGT700 3.9 30.8 1.0
NH2 B:ARG206 4.0 28.9 1.0
OD2 B:ASP309 4.0 26.0 1.0
NH1 B:ARG206 4.1 28.9 1.0
O B:HOH2092 4.1 32.8 1.0
O1B B:DGT700 4.2 33.0 1.0
O B:HOH2074 4.2 36.0 1.0
O B:HOH2262 4.3 31.6 1.0
O B:HOH2054 4.3 36.4 1.0
O3A B:DGT700 4.3 33.0 1.0
O2G B:DGT700 4.4 30.1 1.0
OD1 B:ASP309 4.5 25.9 1.0
CZ B:ARG206 4.5 28.5 1.0
OD2 B:ASP311 4.7 29.9 1.0
CG B:ASP309 4.7 25.7 1.0
OG B:SER302 4.9 34.1 1.0
O B:HOH2099 5.0 29.4 1.0
CE B:LYS312 5.0 25.4 1.0

Magnesium binding site 4 out of 8 in 4bzb

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 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-Bound SAMHD1 Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg850

b:24.7
occ:1.00
 O1G B:DGT900 1.9 28.7 1.0
O2G B:DGT800 1.9 27.2 1.0
O2B B:DGT800 1.9 25.9 1.0
O1B B:DGT900 2.0 29.0 1.0
O B:HOH2265 2.1 24.8 1.0
O1A B:DGT900 2.1 26.4 1.0
PB B:DGT900 3.2 29.5 1.0
PG B:DGT900 3.2 30.5 1.0
PB B:DGT800 3.2 25.2 1.0
PG B:DGT800 3.3 26.9 1.0
PA B:DGT900 3.4 26.6 1.0
O3B B:DGT900 3.5 29.8 1.0
O3B B:DGT800 3.7 26.2 1.0
NZ C:LYS116 3.7 32.4 1.0
O3A B:DGT900 3.7 28.5 1.0
NZ D:LYS523 3.9 39.7 1.0
O B:HOH2270 3.9 48.5 1.0
O3' B:DGT900 4.0 25.4 1.0
O3G B:DGT800 4.0 25.8 1.0
O1B B:DGT800 4.2 25.8 1.0
O B:HOH2266 4.2 41.9 1.0
C5' B:DGT900 4.2 24.9 1.0
O3G B:DGT900 4.2 29.1 1.0
O2G B:DGT900 4.2 31.7 1.0
O B:HOH2267 4.2 44.4 1.0
O3A B:DGT800 4.3 25.0 1.0
O5' B:DGT900 4.3 26.5 1.0
O1G B:DGT800 4.4 26.6 1.0
O B:HOH2268 4.4 24.2 1.0
C3' B:DGT900 4.5 24.5 1.0
O2B B:DGT900 4.5 29.7 1.0
O2A B:DGT900 4.6 27.5 1.0
O C:HOH2002 4.7 40.4 1.0
C4' B:DGT900 4.8 24.7 1.0
CE C:LYS116 4.9 32.8 1.0

Magnesium binding site 5 out of 8 in 4bzb

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 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-Bound SAMHD1 Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg750

b:44.7
occ:1.00
 O3G C:DGT700 1.8 42.0 1.0
O1B C:DGT700 1.9 42.1 1.0
O C:HOH2046 2.1 33.3 1.0
O C:HOH2068 2.1 38.1 1.0
O C:HOH2152 2.2 45.7 1.0
O C:HOH2045 2.3 40.9 1.0
PG C:DGT700 3.2 41.5 1.0
PB C:DGT700 3.2 43.0 1.0
O3B C:DGT700 3.5 42.6 1.0
NZ C:LYS312 3.7 31.2 1.0
O1G C:DGT700 4.0 41.9 1.0
OD2 C:ASP309 4.0 32.4 1.0
NH2 C:ARG206 4.0 33.9 1.0
NH1 C:ARG206 4.1 32.7 1.0
O2B C:DGT700 4.2 43.3 1.0
O C:HOH2064 4.2 44.0 1.0
O3A C:DGT700 4.3 42.6 1.0
O2G C:DGT700 4.3 40.7 1.0
O C:HOH2153 4.3 43.9 1.0
O C:HOH2047 4.4 49.4 1.0
OD1 C:ASP309 4.5 32.6 1.0
CZ C:ARG206 4.6 33.3 1.0
OD2 C:ASP311 4.6 35.8 1.0
CG C:ASP309 4.7 32.5 1.0
CE C:LYS312 4.9 30.6 1.0
CG C:LYS312 5.0 29.4 1.0
OG C:SER302 5.0 40.7 1.0

Magnesium binding site 6 out of 8 in 4bzb

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 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-Bound SAMHD1 Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg850

b:27.3
occ:1.00
 O2G C:DGT900 1.9 35.8 1.0
O1B C:DGT800 1.9 30.7 1.0
O3G C:DGT800 1.9 31.5 1.0
O1B C:DGT900 2.0 34.7 1.0
O B:HOH2003 2.1 29.9 1.0
O2A C:DGT900 2.1 31.0 1.0
PB C:DGT900 3.1 35.4 1.0
PB C:DGT800 3.2 30.9 1.0
PG C:DGT900 3.2 36.9 1.0
PG C:DGT800 3.3 31.3 1.0
PA C:DGT900 3.4 31.4 1.0
O3B C:DGT900 3.5 36.1 1.0
O3B C:DGT800 3.6 31.8 1.0
O3A C:DGT900 3.7 33.5 1.0
NZ B:LYS116 3.8 35.6 1.0
O3' C:DGT900 4.0 30.4 1.0
O1G C:DGT800 4.0 31.2 1.0
NZ A:LYS523 4.1 47.8 1.0
C5' C:DGT900 4.1 30.2 1.0
O2B C:DGT800 4.1 30.9 1.0
O1G C:DGT900 4.1 38.6 1.0
O3G C:DGT900 4.2 36.1 1.0
O C:HOH2156 4.3 51.5 1.0
O5' C:DGT900 4.3 30.9 1.0
O3A C:DGT800 4.3 29.8 1.0
O C:HOH2155 4.3 44.0 1.0
O2G C:DGT800 4.4 31.1 1.0
O B:HOH2004 4.5 31.9 1.0
O2B C:DGT900 4.5 35.6 1.0
C3' C:DGT900 4.5 29.8 1.0
O1A C:DGT900 4.6 32.1 1.0
O B:HOH2002 4.7 46.8 1.0
C4' C:DGT900 4.8 29.9 1.0
CE B:LYS116 5.0 35.8 1.0

Magnesium binding site 7 out of 8 in 4bzb

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 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-Bound SAMHD1 Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg750

b:32.5
occ:1.00
 O2B D:DGT700 1.9 33.2 1.0
O1G D:DGT700 1.9 31.9 1.0
O D:HOH2217 2.1 31.2 1.0
O D:HOH2050 2.1 28.0 1.0
O D:HOH2087 2.2 30.2 1.0
O D:HOH2049 2.2 32.4 1.0
PB D:DGT700 3.1 33.2 1.0
PG D:DGT700 3.2 31.2 1.0
O3B D:DGT700 3.5 32.3 1.0
NZ D:LYS312 3.8 24.4 1.0
O3G D:DGT700 3.9 31.3 1.0
NH2 D:ARG206 4.0 30.3 1.0
OD2 D:ASP309 4.1 26.5 1.0
O1B D:DGT700 4.1 34.2 1.0
NH1 D:ARG206 4.1 29.0 1.0
O D:HOH2218 4.2 34.9 1.0
O D:HOH2083 4.3 42.2 1.0
O3A D:DGT700 4.3 34.2 1.0
O D:HOH2064 4.3 39.3 1.0
O2G D:DGT700 4.4 30.6 1.0
O D:HOH2051 4.4 38.5 1.0
OD1 D:ASP309 4.5 26.0 1.0
CZ D:ARG206 4.6 29.6 1.0
OD2 D:ASP311 4.7 28.2 1.0
CG D:ASP309 4.7 26.0 1.0
O D:HOH2088 4.9 34.5 1.0
OG D:SER302 4.9 32.2 1.0
CE D:LYS312 5.0 23.8 1.0

Magnesium binding site 8 out of 8 in 4bzb

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Magnesium binding site 8 out of 8 in the Crystal Structure of the Tetrameric Dgtp-Bound SAMHD1 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-Bound SAMHD1 Mutant Catalytic Core within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg850

b:24.2
occ:1.00
 O3G D:DGT900 1.9 29.5 1.0
O1B D:DGT800 2.0 23.8 1.0
O3G D:DGT800 2.0 24.0 1.0
O2B D:DGT900 2.0 27.3 1.0
O A:HOH2004 2.1 25.1 1.0
O2A D:DGT900 2.2 24.2 1.0
PB D:DGT900 3.2 28.3 1.0
PG D:DGT900 3.2 30.5 1.0
PB D:DGT800 3.3 24.0 1.0
PG D:DGT800 3.3 23.7 1.0
PA D:DGT900 3.4 25.0 1.0
O3B D:DGT900 3.5 29.6 1.0
O3B D:DGT800 3.6 23.5 1.0
O3A D:DGT900 3.7 25.8 1.0
NZ A:LYS116 3.7 30.5 1.0
O3' D:DGT900 3.9 24.2 1.0
NZ B:LYS523 4.0 37.1 1.0
O1G D:DGT800 4.0 22.9 1.0
O B:HOH2232 4.1 45.6 1.0
O2G D:DGT900 4.2 29.7 1.0
O2B D:DGT800 4.2 23.5 1.0
O D:HOH2220 4.2 38.9 1.0
O1G D:DGT900 4.2 30.8 1.0
C5' D:DGT900 4.3 23.4 1.0
O D:HOH2221 4.3 41.1 1.0
O3A D:DGT800 4.3 23.8 1.0
O5' D:DGT900 4.4 24.2 1.0
O A:HOH2005 4.5 23.8 1.0
C3' D:DGT900 4.5 23.8 1.0
O2G D:DGT800 4.5 24.0 1.0
O1B D:DGT900 4.5 28.1 1.0
O A:HOH2002 4.6 44.5 1.0
O1A D:DGT900 4.6 25.1 1.0
C4' D:DGT900 4.9 23.6 1.0
CE A:LYS116 4.9 31.4 1.0

Reference:

X.Ji, Y.Wu, J.Yan, J.Mehrens, H.Yang, M.Delucia, C.Hao, A.M.Gronenborn, J.Skowronski, J.Ahn, Y.Xiong. Mechanism of Allosteric Activation of SAMHD1 By Dgtp Nat.Struct.Mol.Biol. V. 20 1304 2013.
ISSN: ISSN 1545-9993
PubMed: 24141705
DOI: 10.1038/NSMB.2692
Page generated: Thu Aug 15 16:38:03 2024

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