Manganese in PDB 3h0r: Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus

The structure of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus, PDB code: 3h0r 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)	48.97 / 3.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	127.377, 130.411, 153.973, 89.89, 90.21, 89.95
R / Rfree (%)	26.3 / 30.6

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

Zinc

(Zn)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus (pdb code 3h0r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus, PDB code: 3h0r:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn480 b:44.1 occ:1.00 NE2 B:HIS14 2.1 48.6 1.0 OE1 B:GLU153 2.6 50.0 1.0 OE2 B:GLU127 2.9 45.7 1.0 CE1 B:HIS14 3.0 50.0 1.0 CD2 B:HIS14 3.2 48.9 1.0 CD B:GLU153 3.4 49.5 1.0 O B:HOH484 3.4 23.2 1.0 OE1 B:GLU127 3.5 49.4 1.0 CD B:GLU127 3.6 46.6 1.0 OE2 B:GLU153 3.7 50.1 1.0 NZ B:LYS81 4.1 47.4 1.0 ND1 B:HIS14 4.2 48.2 1.0 O B:HOH485 4.2 29.1 1.0 CG B:HIS14 4.3 48.8 1.0 OE1 B:GLN93 4.3 47.9 1.0 CG B:GLU153 4.5 46.5 1.0 NE2 B:GLN93 4.7 44.7 1.0 CB B:GLU153 4.8 45.6 1.0 CD B:GLN93 4.9 44.7 1.0

Manganese binding site 2 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 B:Mn481 b:56.9 occ:0.50 OE1 B:GLU12 2.7 60.9 1.0 CD B:GLU12 3.2 56.4 1.0 OD1 B:ASN197 3.3 62.4 1.0 OE2 B:GLU12 3.4 59.2 1.0 CD B:GLU213 3.5 77.1 1.0 CG B:GLU213 3.6 75.8 1.0 OE1 B:GLU213 3.7 77.3 1.0 ND2 B:ASN197 3.9 61.2 1.0 OE2 B:GLU213 3.9 77.3 1.0 CG B:ASN197 4.0 61.2 1.0 C5' B:ADP479 4.0 75.0 0.7 NH1 B:ARG211 4.2 83.8 1.0 CG B:GLU12 4.3 55.5 1.0 O1B B:ADP479 4.4 82.2 0.7 O3A B:ADP479 4.4 81.6 0.7 C4' B:ADP479 4.6 72.6 0.7 O4' B:ADP479 4.8 71.9 0.7 O5' B:ADP479 4.8 78.6 0.7

Manganese binding site 3 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 E:Mn480 b:53.9 occ:1.00 NE2 E:HIS14 2.2 49.9 1.0 OE2 E:GLU127 2.5 48.0 1.0 OE1 E:GLU153 2.6 49.5 1.0 CE1 E:HIS14 3.1 49.8 1.0 O E:HOH483 3.1 23.2 1.0 CD2 E:HIS14 3.2 49.4 1.0 CD E:GLU127 3.4 49.7 1.0 OE1 E:GLU127 3.5 50.1 1.0 CD E:GLU153 3.7 49.4 1.0 ND1 E:HIS14 4.2 48.8 1.0 OE1 E:GLN93 4.3 47.3 1.0 CG E:GLU153 4.3 46.7 1.0 CG E:HIS14 4.3 49.3 1.0 NZ E:LYS81 4.4 47.2 1.0 NE2 E:GLN93 4.5 46.3 1.0 OE2 E:GLU153 4.6 50.6 1.0 CB E:GLU153 4.6 45.4 1.0 O E:HOH484 4.7 29.1 1.0 CG E:GLU127 4.8 46.1 1.0 CD E:GLN93 4.9 44.9 1.0

Manganese binding site 4 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 E:Mn481 b:85.8 occ:0.50 OE1 E:GLU12 2.9 61.6 1.0 OE2 E:GLU213 3.1 77.8 1.0 OE1 E:GLU213 3.1 78.6 1.0 O E:HOH482 3.3 23.2 1.0 CD E:GLU213 3.3 76.9 1.0 OE2 E:GLU12 3.5 58.5 1.0 CD E:GLU12 3.6 56.9 1.0 O1G E:ATP479 3.7 85.3 0.5 O2G E:ATP479 4.0 85.2 0.5 PG E:ATP479 4.3 85.7 0.5 O3B E:ATP479 4.3 81.6 0.5 OD1 E:ASN197 4.5 64.2 1.0 NH1 E:ARG211 4.6 83.7 1.0 CG E:GLU213 4.6 76.1 1.0 NH2 E:ARG211 4.9 84.3 1.0 OD2 E:ASP195 4.9 62.9 1.0

Manganese binding site 5 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 H:Mn480 b:50.8 occ:1.00 OXT H:ASP482 1.9 82.5 1.0 NE2 H:HIS14 2.1 49.1 1.0 OE1 H:GLU153 2.1 50.7 1.0 OE2 H:GLU127 2.2 44.1 1.0 O H:HOH484 2.5 23.2 1.0 C H:ASP482 2.7 81.6 1.0 CE1 H:HIS14 3.0 48.8 1.0 CD H:GLU127 3.1 45.8 1.0 CD H:GLU153 3.1 51.2 1.0 CD2 H:HIS14 3.2 47.8 1.0 O H:ASP482 3.2 81.9 1.0 OE1 H:GLU127 3.3 46.7 1.0 CA H:ASP482 3.6 80.7 1.0 N H:ASP482 3.7 81.0 1.0 CG H:GLU153 3.9 46.8 1.0 OE2 H:GLU153 4.0 51.0 1.0 ND1 H:HIS14 4.2 49.1 1.0 CB H:GLU153 4.2 46.3 1.0 CG H:HIS14 4.3 48.5 1.0 NE2 H:GLN93 4.4 45.6 1.0 NZ H:LYS81 4.4 47.4 1.0 OE1 H:GLN93 4.4 46.8 1.0 CG H:GLU127 4.5 45.8 1.0 NE2 H:HIS125 4.8 46.8 1.0 CD H:GLN93 4.9 45.5 1.0

Manganese binding site 6 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 H:Mn481 b:75.8 occ:0.50 OE1 H:GLU12 2.5 60.9 1.0 OE2 H:GLU213 2.6 77.8 1.0 OD2 H:ASP482 2.9 71.5 1.0 CG H:ASP482 3.1 76.5 1.0 CB H:ASP482 3.2 79.8 1.0 O2G H:ATP479 3.3 49.5 0.5 CD H:GLU12 3.5 56.2 1.0 CD H:GLU213 3.6 76.7 1.0 OE2 H:GLU12 3.7 57.9 1.0 OE1 H:GLU213 3.9 78.2 1.0 O1G H:ATP479 3.9 50.1 0.5 OD1 H:ASP482 4.0 74.4 1.0 CE H:LYS215 4.0 77.6 1.0 O H:ASP482 4.2 81.9 1.0 PG H:ATP479 4.2 51.1 0.5 NZ H:LYS215 4.3 77.6 1.0 OD2 H:ASP195 4.4 62.1 1.0 CA H:ASP482 4.6 80.7 1.0 CG H:GLU12 4.8 55.2 1.0 C H:ASP482 4.8 81.6 1.0 CG H:GLU213 5.0 75.8 1.0

Manganese binding site 7 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 K:Mn480 b:46.0 occ:1.00 NE2 K:HIS14 2.1 46.6 1.0 OE2 K:GLU127 2.3 42.6 1.0 OE1 K:GLU153 2.3 47.1 1.0 O K:HOH485 2.6 32.1 1.0 CE1 K:HIS14 3.0 49.7 1.0 CD2 K:HIS14 3.1 48.8 1.0 O K:HOH482 3.2 23.2 1.0 CD K:GLU127 3.3 46.5 1.0 O K:HOH483 3.3 23.2 1.0 CD K:GLU153 3.5 48.4 1.0 OE1 K:GLU127 3.6 48.0 1.0 ND1 K:HIS14 4.2 48.6 1.0 CG K:HIS14 4.2 49.1 1.0 NE2 K:GLN93 4.3 44.1 1.0 OE1 K:GLN93 4.3 43.0 1.0 CG K:GLU153 4.3 45.4 1.0 OE2 K:GLU153 4.4 50.6 1.0 NZ K:LYS81 4.4 48.5 1.0 CB K:GLU153 4.5 45.2 1.0 CG K:GLU127 4.6 45.8 1.0 CD K:GLN93 4.7 43.4 1.0 O K:HOH484 4.9 23.2 1.0

Manganese binding site 8 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 K:Mn481 b:63.0 occ:0.50 OE1 K:GLU12 2.2 60.9 1.0 CD K:GLU12 3.1 56.1 1.0 CD K:GLU213 3.4 77.1 1.0 OE2 K:GLU213 3.4 77.2 1.0 OE1 K:GLU213 3.5 77.5 1.0 OE2 K:GLU12 3.5 56.9 1.0 CE K:LYS215 3.5 77.5 1.0 O1G K:ATP479 3.8 58.9 0.5 NZ K:LYS215 4.1 77.4 1.0 CG K:GLU213 4.1 75.6 1.0 O3G K:ATP479 4.1 57.6 0.5 CB K:ASP195 4.3 59.3 1.0 PG K:ATP479 4.3 57.7 0.5 OD2 K:ASP195 4.3 62.2 1.0 CG K:GLU12 4.5 54.9 1.0 O2G K:ATP479 4.6 58.6 0.5 OD1 K:ASN197 4.6 62.2 1.0 ND2 K:ASN197 4.6 61.3 1.0 CG K:ASP195 4.8 60.5 1.0 CB K:GLU12 4.8 52.8 1.0 CD K:LYS215 4.9 75.6 1.0

Manganese binding site 9 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ N:Mn480 b:49.2 occ:1.00 NE2 N:HIS14 2.1 48.9 1.0 OE1 N:GLU153 2.4 49.1 1.0 OE2 N:GLU127 2.4 44.8 1.0 O N:HOH485 3.0 23.2 1.0 CE1 N:HIS14 3.0 49.2 1.0 OXT N:ASP482 3.0 82.5 1.0 CD2 N:HIS14 3.2 49.1 1.0 CD N:GLU127 3.2 46.3 1.0 CD N:GLU153 3.3 48.4 1.0 OE1 N:GLU127 3.3 48.9 1.0 C N:ASP482 3.4 81.6 1.0 O N:ASP482 3.8 81.9 1.0 N N:ASP482 3.9 81.0 1.0 CG N:GLU153 3.9 46.4 1.0 OE2 N:GLU153 4.1 51.8 1.0 ND1 N:HIS14 4.1 48.1 1.0 OE1 N:GLN93 4.2 46.8 1.0 CA N:ASP482 4.2 80.7 1.0 CG N:HIS14 4.3 48.7 1.0 CB N:GLU153 4.4 45.8 1.0 NE2 N:GLN93 4.5 44.8 1.0 NZ N:LYS81 4.5 48.4 1.0 CG N:GLU127 4.6 46.4 1.0 CD N:GLN93 4.7 44.7 1.0 O N:HOH484 4.8 23.2 1.0 NE2 N:HIS125 5.0 47.0 1.0

Manganese binding site 10 out of 16 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ N:Mn481 b:86.9 occ:0.50 OE2 N:GLU213 2.9 77.7 1.0 OE1 N:GLU12 2.9 60.7 1.0 OE2 N:GLU12 3.0 59.1 1.0 OD2 N:ASP482 3.1 71.5 1.0 CG N:ASP482 3.2 76.5 1.0 CD N:GLU12 3.2 56.5 1.0 CB N:ASP482 3.4 79.8 1.0 CD N:GLU213 3.7 76.5 1.0 OE1 N:GLU213 3.8 78.2 1.0 OD1 N:ASP482 3.9 74.4 1.0 O1B N:ATP479 4.1 66.6 0.5 C N:ASP482 4.2 81.6 1.0 OXT N:ASP482 4.3 82.5 1.0 O N:ASP482 4.4 81.9 1.0 CA N:ASP482 4.5 80.7 1.0 CG N:GLU12 4.6 55.0 1.0 OD2 N:ASP195 4.7 62.2 1.0 O N:HOH484 4.7 23.2 1.0 O3G N:ATP479 5.0 65.3 0.5 CG N:GLU213 5.0 75.7 1.0

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