Manganese in PDB 1e24: Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+

All present enzymatic activity of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+:
6.1.1.6;

The structure of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+, PDB code: 1e24 was solved by G.Desogus, F.Todone, P.Brick, S.Onesti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.0 / 2.35
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.600, 143.600, 177.230, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 24.9

The binding sites of Manganese atom in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+ (pdb code 1e24). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+, PDB code: 1e24:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn515 b:40.5 occ:1.00 O1B A:ATP512 2.2 48.7 1.0 OE2 A:GLU414 2.2 29.7 1.0 OE2 A:GLU421 2.3 21.3 1.0 O1A A:ATP512 2.5 41.2 1.0 CD A:GLU421 3.1 18.7 1.0 OE1 A:GLU421 3.2 18.8 1.0 CD A:GLU414 3.3 22.9 1.0 MN A:MN517 3.4 50.5 1.0 PB A:ATP512 3.4 41.4 1.0 PA A:ATP512 3.5 40.0 1.0 OE1 A:GLU414 3.7 27.4 1.0 O3A A:ATP512 3.7 43.8 1.0 NH2 A:ARG412 4.0 12.2 1.0 O2A A:ATP512 4.1 43.7 1.0 O A:HOH2360 4.2 26.7 1.0 ND2 A:ASN424 4.2 15.9 1.0 O A:HOH2357 4.3 36.5 1.0 O2B A:ATP512 4.4 45.5 1.0 CG A:ASN424 4.5 14.9 1.0 CB A:ASN424 4.5 11.4 1.0 CG A:GLU421 4.5 18.3 1.0 O3B A:ATP512 4.6 44.6 1.0 CG A:GLU414 4.6 17.4 1.0 O3' A:ATP512 4.6 25.1 1.0 O3G A:ATP512 4.7 46.1 1.0 O A:HOH2295 4.8 23.9 1.0 O5' A:ATP512 4.9 36.6 1.0 C3' A:ATP512 4.9 25.7 1.0

Manganese binding site 2 out of 3 in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn516 b:58.9 occ:1.00 O1G A:ATP512 2.2 46.4 1.0 O2B A:ATP512 2.6 45.5 1.0 O A:HOH2200 3.2 44.4 1.0 PG A:ATP512 3.3 43.3 1.0 O3B A:ATP512 3.3 44.6 1.0 PB A:ATP512 3.5 41.4 1.0 O A:HOH2198 3.7 39.7 1.0 NE2 A:HIS270 3.9 32.4 1.0 O3G A:ATP512 3.9 46.1 1.0 OE2 A:GLU264 4.3 34.0 1.0 O A:HOH2201 4.5 39.1 1.0 O1B A:ATP512 4.5 48.7 1.0 O2G A:ATP512 4.5 42.7 1.0 CD2 A:HIS270 4.5 28.5 1.0 O3A A:ATP512 4.7 43.8 1.0 CE1 A:HIS270 4.8 27.1 1.0 OE1 A:GLU264 4.8 41.1 1.0 N7 A:ATP512 4.8 26.6 1.0 CD A:GLU264 4.9 37.0 1.0

Manganese binding site 3 out of 3 in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and Atp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn517 b:50.5 occ:1.00 OE1 A:GLU421 2.2 18.8 1.0 O3G A:ATP512 2.3 46.1 1.0 O1B A:ATP512 2.6 48.7 1.0 CD A:GLU421 3.3 18.7 1.0 MN A:MN515 3.4 40.5 1.0 O A:HOH2360 3.6 26.7 1.0 PG A:ATP512 3.7 43.3 1.0 PB A:ATP512 3.8 41.4 1.0 OE2 A:GLU421 3.8 21.3 1.0 OE2 A:GLU380 3.9 41.3 1.0 O3B A:ATP512 4.0 44.6 1.0 O A:HOH2264 4.0 30.8 1.0 OE1 A:GLU414 4.1 27.4 1.0 O A:HOH2266 4.1 33.0 1.0 OD1 A:ASP376 4.3 35.7 1.0 O2B A:ATP512 4.5 45.5 1.0 CG A:GLU421 4.5 18.3 1.0 OE2 A:GLU414 4.5 29.7 1.0 O1G A:ATP512 4.6 46.4 1.0 O2G A:ATP512 4.6 42.7 1.0 OD2 A:ASP376 4.6 33.6 1.0 CB A:GLU421 4.7 17.8 1.0 CD A:GLU414 4.7 22.9 1.0 CG A:ASP376 4.9 32.0 1.0 O A:HOH2263 4.9 34.2 1.0

G.Desogus, F.Todone, P.Brick, S.Onesti. Active Site of Lysyl-Trna Synthetase: Structural Studies of the Adenylation Reaction Biochemistry V. 39 8418 2000.
ISSN: ISSN 0006-2960
PubMed: 10913247
DOI: 10.1021/BI0006722