Atomistry » Magnesium » PDB 3gx3-3hd1 » 3h0l
Atomistry »
  Magnesium »
    PDB 3gx3-3hd1 »
      3h0l »

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

Go back to Magnesium Binding Sites List in 3h0l
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

Go back to Magnesium Binding Sites List in 3h0l
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

Go back to Magnesium Binding Sites List in 3h0l
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

Go back to Magnesium Binding Sites List in 3h0l
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

Go back to Magnesium Binding Sites List in 3h0l
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

Go back to Magnesium Binding Sites List in 3h0l
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

Go back to Magnesium Binding Sites List in 3h0l
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

Go back to Magnesium Binding Sites List in 3h0l
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: Wed Aug 14 15:02:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy