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Magnesium in PDB 3h0m: Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus

Protein crystallography data

The structure of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus, PDB code: 3h0m was solved by J.Wu, W.Bu, K.Sheppard, M.Kitabatake, D.Soll, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.37 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 128.248, 129.856, 155.069, 90.01, 89.96, 90.11
R / Rfree (%) 25.4 / 30.5

Other elements in 3h0m:

The structure of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus (pdb code 3h0m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus, PDB code: 3h0m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3h0m

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Magnesium binding site 1 out of 7 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg479

b:57.2
occ:0.50
NE2 B:HIS14 2.0 44.1 1.0
OE2 B:GLU127 2.2 35.9 1.0
OE1 B:GLU153 2.8 47.7 1.0
CD2 B:HIS14 2.9 46.2 1.0
CD B:GLU127 3.1 42.4 1.0
CE1 B:HIS14 3.1 48.5 1.0
OE1 B:GLU127 3.3 44.5 1.0
CD B:GLU153 3.3 49.2 1.0
CG B:GLU153 3.9 44.4 1.0
OE2 B:GLU153 3.9 49.7 1.0
CG B:HIS14 4.1 46.7 1.0
ND1 B:HIS14 4.2 45.8 1.0
NZ B:LYS81 4.2 46.9 1.0
CB B:GLU153 4.3 43.5 1.0
OE1 B:GLN93 4.4 46.0 1.0
NE2 B:GLN93 4.5 42.1 1.0
CG B:GLU127 4.5 42.2 1.0
CD B:GLN93 4.9 43.2 1.0
NE2 B:HIS125 4.9 44.1 1.0

Magnesium binding site 2 out of 7 in 3h0m

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Magnesium binding site 2 out of 7 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg479

b:61.1
occ:0.50
NE2 H:HIS14 2.0 45.7 1.0
OE1 H:GLU153 2.2 46.9 1.0
OE2 H:GLU127 2.4 36.5 1.0
CE1 H:HIS14 2.9 47.7 1.0
CD2 H:HIS14 3.1 45.6 1.0
CD H:GLU153 3.1 50.1 1.0
CD H:GLU127 3.3 42.0 1.0
OE1 H:GLU127 3.4 42.7 1.0
OE2 H:GLU153 3.8 50.8 1.0
ND1 H:HIS14 4.0 47.9 1.0
CG H:GLU153 4.1 44.8 1.0
CB H:GLU153 4.2 44.4 1.0
CG H:HIS14 4.2 46.5 1.0
NZ H:LYS81 4.3 43.5 1.0
OE1 H:GLN93 4.7 45.3 1.0
NE2 H:GLN93 4.7 45.5 1.0
CG H:GLU127 4.7 42.6 1.0

Magnesium binding site 3 out of 7 in 3h0m

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Magnesium binding site 3 out of 7 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg479

b:53.9
occ:0.50
NE2 K:HIS14 1.7 42.2 1.0
OE2 K:GLU127 2.4 35.5 1.0
OE1 K:GLU153 2.6 43.3 1.0
CE1 K:HIS14 2.7 47.8 1.0
CD2 K:HIS14 2.8 46.9 1.0
CD K:GLU127 3.4 42.5 1.0
CD K:GLU153 3.6 46.4 1.0
OE1 K:GLU127 3.6 43.3 1.0
ND1 K:HIS14 3.8 46.3 1.0
CG K:HIS14 3.9 47.4 1.0
CG K:GLU153 4.1 43.3 1.0
CB K:GLU153 4.4 43.6 1.0
OE2 K:GLU153 4.5 50.1 1.0
NZ K:LYS81 4.6 46.2 1.0
NE2 K:GLN93 4.7 42.0 1.0
OE1 K:GLN93 4.7 44.4 1.0
CG K:GLU127 4.8 41.8 1.0

Magnesium binding site 4 out of 7 in 3h0m

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Magnesium binding site 4 out of 7 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg479

b:86.3
occ:0.50
NE2 N:HIS14 1.9 46.0 1.0
OE2 N:GLU127 2.2 38.1 1.0
OE1 N:GLU153 2.8 46.2 1.0
CE1 N:HIS14 2.9 48.9 1.0
CD2 N:HIS14 3.0 47.2 1.0
CD N:GLU127 3.0 41.9 1.0
OE1 N:GLU127 3.1 44.5 1.0
CD N:GLU153 3.3 48.5 1.0
CG N:GLU153 3.9 44.4 1.0
OE2 N:GLU153 3.9 52.1 1.0
ND1 N:HIS14 4.0 45.2 1.0
CG N:HIS14 4.1 47.4 1.0
CB N:GLU153 4.2 43.7 1.0
OE1 N:GLN93 4.4 46.1 1.0
NZ N:LYS81 4.4 45.5 1.0
CG N:GLU127 4.4 43.1 1.0
NE2 N:GLN93 4.5 43.1 1.0
CD N:GLN93 4.9 43.1 1.0
NE2 N:HIS125 4.9 47.2 1.0

Magnesium binding site 5 out of 7 in 3h0m

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Magnesium binding site 5 out of 7 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg479

b:61.4
occ:0.50
NE2 Q:HIS14 1.8 45.1 1.0
OE2 Q:GLU127 2.2 39.2 1.0
OE1 Q:GLU153 2.3 45.2 1.0
CD2 Q:HIS14 2.7 47.5 1.0
CE1 Q:HIS14 2.9 47.2 1.0
CD Q:GLU127 3.2 43.9 1.0
CD Q:GLU153 3.3 47.3 1.0
OE1 Q:GLU127 3.5 46.1 1.0
CG Q:HIS14 3.9 47.5 1.0
ND1 Q:HIS14 3.9 45.6 1.0
OE2 Q:GLU153 4.1 50.1 1.0
CG Q:GLU153 4.2 42.8 1.0
CB Q:GLU153 4.3 43.5 1.0
NE2 Q:GLN93 4.6 43.0 1.0
CG Q:GLU127 4.6 41.9 1.0
NZ Q:LYS81 4.6 44.6 1.0
OE1 Q:GLN93 4.7 44.4 1.0

Magnesium binding site 6 out of 7 in 3h0m

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Magnesium binding site 6 out of 7 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg479

b:60.2
occ:0.50
OE1 T:GLU153 1.9 47.1 1.0
NE2 T:HIS14 2.1 45.3 1.0
OE2 T:GLU127 2.4 39.9 1.0
CD2 T:HIS14 2.8 46.7 1.0
CD T:GLU153 3.0 48.7 1.0
CE1 T:HIS14 3.2 48.0 1.0
CD T:GLU127 3.3 43.2 1.0
OE1 T:GLU127 3.5 42.2 1.0
CG T:GLU153 3.6 44.7 1.0
CB T:GLU153 3.9 44.0 1.0
OE2 T:GLU153 4.0 48.9 1.0
CG T:HIS14 4.1 47.4 1.0
ND1 T:HIS14 4.2 46.1 1.0
NZ T:LYS81 4.4 43.8 1.0
OE1 T:GLN93 4.5 46.3 1.0
CG T:GLU127 4.7 42.4 1.0
NE2 T:HIS125 4.9 46.9 1.0
NE2 T:GLN93 4.9 44.5 1.0

Magnesium binding site 7 out of 7 in 3h0m

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Magnesium binding site 7 out of 7 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg479

b:75.9
occ:0.50
NE2 W:HIS14 1.8 46.0 1.0
OE2 W:GLU127 2.0 40.4 1.0
OE1 W:GLU153 2.2 46.9 1.0
CD2 W:HIS14 2.7 46.9 1.0
CD W:GLU127 2.9 44.5 1.0
CD W:GLU153 2.9 48.9 1.0
CE1 W:HIS14 3.0 48.1 1.0
OE1 W:GLU127 3.2 47.0 1.0
CG W:GLU153 3.5 44.7 1.0
CB W:GLU153 3.7 43.1 1.0
OE2 W:GLU153 3.8 51.8 1.0
CG W:HIS14 3.9 47.1 1.0
ND1 W:HIS14 4.0 45.6 1.0
CG W:GLU127 4.3 43.0 1.0
NE2 W:HIS125 4.5 44.3 1.0
NE2 W:GLN93 4.8 42.5 1.0
OE1 W:GLN93 4.8 45.2 1.0
CA W:GLU153 4.8 43.6 1.0
NZ W:LYS81 4.9 48.3 1.0

Reference:

J.Wu, W.Bu, K.Sheppard, M.Kitabatake, S.T.Kwon, D.Soll, J.L.Smith. Insights Into Trna-Dependent Amidotransferase Evolution and Catalysis From the Structure of the Aquifex Aeolicus Enzyme J.Mol.Biol. V. 391 703 2009.
ISSN: ISSN 0022-2836
PubMed: 19520089
DOI: 10.1016/J.JMB.2009.06.014
Page generated: Mon Dec 14 08:12:59 2020

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