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Magnesium in PDB 3h0l: 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: 3h0l 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) 40.50 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 127.482, 131.012, 154.668, 90.02, 90.00, 89.91
R / Rfree (%) 24 / 27.3

Other elements in 3h0l:

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 3h0l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus, PDB code: 3h0l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3h0l

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Magnesium binding site 1 out of 8 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:Mg801

b:10.8
occ:1.00
 OE1 B:GLU153 1.9 41.6 1.0
NE2 B:HIS14 2.0 39.8 1.0
OE2 B:GLU127 2.5 25.1 1.0
CD2 B:HIS14 3.0 39.7 1.0
CE1 B:HIS14 3.1 41.8 1.0
CD B:GLU153 3.1 39.1 1.0
OE1 B:GLU127 3.2 33.0 1.0
CD B:GLU127 3.2 32.2 1.0
CG B:GLU153 3.9 35.9 1.0
OE2 B:GLU153 4.0 42.9 1.0
CG B:HIS14 4.2 39.0 1.0
ND1 B:HIS14 4.2 37.9 1.0
NZ B:LYS81 4.2 38.4 1.0
CB B:GLU153 4.2 34.4 1.0
OE1 B:GLN93 4.3 35.9 1.0
NE2 B:GLN93 4.4 32.4 1.0
CG B:GLU127 4.7 31.2 1.0
NE2 B:HIS125 4.8 35.7 1.0
CD B:GLN93 4.8 34.4 1.0

Magnesium binding site 2 out of 8 in 3h0l

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Magnesium binding site 2 out of 8 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
E:Mg802

b:19.2
occ:1.00
 NE2 E:HIS14 2.0 40.2 1.0
OE1 E:GLU153 2.1 42.7 1.0
OE2 E:GLU127 2.3 27.5 1.0
CD2 E:HIS14 3.0 39.6 1.0
CE1 E:HIS14 3.0 41.1 1.0
CD E:GLU127 3.2 33.0 1.0
OE1 E:GLU127 3.3 33.0 1.0
CD E:GLU153 3.4 42.4 1.0
ND1 E:HIS14 4.1 39.1 1.0
CG E:HIS14 4.1 39.9 1.0
CG E:GLU153 4.2 36.5 1.0
OE1 E:GLN93 4.3 37.3 1.0
OE2 E:GLU153 4.3 43.9 1.0
NZ E:LYS81 4.3 38.1 1.0
CB E:GLU153 4.3 34.1 1.0
NE2 E:GLN93 4.5 34.2 1.0
CG E:GLU127 4.6 32.1 1.0
CD E:GLN93 4.8 34.2 1.0
NE2 E:HIS125 5.0 37.7 1.0

Magnesium binding site 3 out of 8 in 3h0l

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Magnesium binding site 3 out of 8 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
H:Mg803

b:11.0
occ:1.00
 OE1 H:GLU153 1.9 42.0 1.0
NE2 H:HIS14 2.0 38.8 1.0
OE2 H:GLU127 2.5 22.9 1.0
CE1 H:HIS14 2.8 41.3 1.0
OE1 H:GLU127 3.0 30.4 1.0
CD H:GLU153 3.1 43.0 1.0
CD H:GLU127 3.1 31.2 1.0
CD2 H:HIS14 3.1 38.8 1.0
OE2 H:GLU153 3.8 44.4 1.0
ND1 H:HIS14 4.0 39.4 1.0
CG H:GLU153 4.1 36.4 1.0
CG H:HIS14 4.2 38.5 1.0
CB H:GLU153 4.2 35.4 1.0
NZ H:LYS81 4.2 35.9 1.0
OE1 H:GLN93 4.3 34.5 1.0
NE2 H:GLN93 4.4 35.7 1.0
CG H:GLU127 4.6 30.9 1.0
NE2 H:HIS125 4.8 38.0 1.0
CD H:GLN93 4.8 35.4 1.0

Magnesium binding site 4 out of 8 in 3h0l

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Magnesium binding site 4 out of 8 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
K:Mg804

b:11.7
occ:1.00
 OE1 K:GLU153 2.0 38.9 1.0
NE2 K:HIS14 2.0 38.7 1.0
OE2 K:GLU127 2.4 24.6 1.0
CD2 K:HIS14 3.0 40.0 1.0
CE1 K:HIS14 3.1 40.9 1.0
CD K:GLU127 3.1 31.9 1.0
OE1 K:GLU127 3.1 30.4 1.0
CD K:GLU153 3.2 39.8 1.0
CG K:GLU153 4.0 34.8 1.0
ND1 K:HIS14 4.1 38.8 1.0
CG K:HIS14 4.1 39.6 1.0
OE2 K:GLU153 4.2 42.3 1.0
CB K:GLU153 4.3 34.6 1.0
NE2 K:GLN93 4.3 31.9 1.0
OE1 K:GLN93 4.4 34.8 1.0
NZ K:LYS81 4.5 37.0 1.0
CG K:GLU127 4.6 30.5 1.0
NE2 K:HIS125 4.8 36.4 1.0
CD K:GLN93 4.9 31.0 1.0

Magnesium binding site 5 out of 8 in 3h0l

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Magnesium binding site 5 out of 8 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
N:Mg805

b:16.7
occ:1.00
 OE1 N:GLU153 1.9 38.5 1.0
NE2 N:HIS14 2.0 39.8 1.0
OE2 N:GLU127 2.4 25.5 1.0
OE1 N:GLU127 2.9 31.2 1.0
CE1 N:HIS14 2.9 42.1 1.0
CD N:GLU127 3.0 30.3 1.0
CD2 N:HIS14 3.0 40.0 1.0
CD N:GLU153 3.1 41.4 1.0
OE2 N:GLU153 4.0 45.2 1.0
CG N:GLU153 4.0 36.1 1.0
ND1 N:HIS14 4.1 37.6 1.0
NE2 N:GLN93 4.1 33.9 1.0
CG N:HIS14 4.1 39.5 1.0
OE1 N:GLN93 4.2 35.0 1.0
CB N:GLU153 4.2 34.6 1.0
NZ N:LYS81 4.3 36.9 1.0
CG N:GLU127 4.4 32.1 1.0
CD N:GLN93 4.6 33.7 1.0
NE2 N:HIS125 4.7 38.9 1.0

Magnesium binding site 6 out of 8 in 3h0l

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Magnesium binding site 6 out of 8 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
Q:Mg806

b:21.1
occ:1.00
 NE2 Q:HIS14 2.0 39.0 1.0
OE1 Q:GLU153 2.0 39.4 1.0
OE2 Q:GLU127 2.3 26.3 1.0
CE1 Q:HIS14 3.0 40.1 1.0
CD2 Q:HIS14 3.1 40.0 1.0
CD Q:GLU153 3.2 40.4 1.0
CD Q:GLU127 3.2 33.0 1.0
OE1 Q:GLU127 3.3 34.0 1.0
OE2 Q:GLU153 3.9 44.0 1.0
CG Q:GLU153 4.1 34.8 1.0
ND1 Q:HIS14 4.1 38.1 1.0
CG Q:HIS14 4.2 39.6 1.0
NZ Q:LYS81 4.3 36.6 1.0
CB Q:GLU153 4.3 34.5 1.0
NE2 Q:GLN93 4.4 33.7 1.0
OE1 Q:GLN93 4.5 34.7 1.0
CG Q:GLU127 4.6 30.9 1.0
CD Q:GLN93 4.9 32.7 1.0
NE2 Q:HIS125 4.9 36.1 1.0

Magnesium binding site 7 out of 8 in 3h0l

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Magnesium binding site 7 out of 8 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
T:Mg807

b:15.1
occ:1.00
 NE2 T:HIS14 1.9 40.1 1.0
OE1 T:GLU153 2.0 41.8 1.0
OE2 T:GLU127 2.3 25.8 1.0
CE1 T:HIS14 2.8 40.9 1.0
CD2 T:HIS14 3.0 39.3 1.0
CD T:GLU127 3.2 30.9 1.0
CD T:GLU153 3.2 42.0 1.0
OE1 T:GLU127 3.4 29.2 1.0
ND1 T:HIS14 4.0 38.7 1.0
CG T:GLU153 4.1 36.2 1.0
OE1 T:GLN93 4.1 36.6 1.0
CG T:HIS14 4.1 39.6 1.0
NZ T:LYS81 4.1 35.5 1.0
OE2 T:GLU153 4.1 42.5 1.0
CB T:GLU153 4.2 35.0 1.0
NE2 T:GLN93 4.4 34.7 1.0
CD T:GLN93 4.6 34.7 1.0
CG T:GLU127 4.6 31.2 1.0
NE2 T:HIS125 4.9 38.1 1.0

Magnesium binding site 8 out of 8 in 3h0l

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Magnesium binding site 8 out of 8 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 8 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg808

b:18.1
occ:1.00
 OE1 W:GLU153 2.0 40.4 1.0
NE2 W:HIS14 2.0 39.8 1.0
OE2 W:GLU127 2.3 29.8 1.0
CE1 W:HIS14 3.0 41.0 1.0
CD2 W:HIS14 3.0 40.0 1.0
CD W:GLU153 3.1 41.6 1.0
CD W:GLU127 3.2 33.3 1.0
OE1 W:GLU127 3.4 34.0 1.0
OE2 W:GLU153 4.0 44.5 1.0
CG W:GLU153 4.0 36.1 1.0
ND1 W:HIS14 4.1 37.9 1.0
CG W:HIS14 4.1 39.3 1.0
CB W:GLU153 4.2 34.2 1.0
OE1 W:GLN93 4.4 34.9 1.0
NZ W:LYS81 4.5 40.1 1.0
NE2 W:GLN93 4.6 31.6 1.0
CG W:GLU127 4.6 32.1 1.0
NE2 W:HIS125 4.7 35.5 1.0
CD W:GLN93 5.0 33.7 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 08:12:55 2020

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