Magnesium in PDB 1i9v: Crystal Structure Analysis of A Trna-Neomycin Complex

The structure of Crystal Structure Analysis of A Trna-Neomycin Complex, PDB code: 1i9v was solved by N.E.Mikkelsen, K.Johansson, A.Virtanen, L.A.Kirsebom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.900, 32.900, 63.100, 90.00, 90.50, 90.00
R / Rfree (%)	22.8 / 27.5

The binding sites of Magnesium atom in the Crystal Structure Analysis of A Trna-Neomycin Complex (pdb code 1i9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure Analysis of A Trna-Neomycin Complex, PDB code: 1i9v:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure Analysis of A Trna-Neomycin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of A Trna-Neomycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:31.4 occ:1.00 OP2 A:A21 2.5 28.1 1.0 OP1 A:G20 2.6 28.1 1.0 P A:A21 3.5 28.2 1.0 OP1 A:A21 3.7 26.4 1.0 P A:G20 4.0 30.2 1.0 O3' A:G20 4.5 29.9 1.0 OP2 A:G20 4.7 30.3 1.0 C5' A:G20 4.7 27.6 1.0 O5' A:G20 4.7 27.5 1.0 O5' A:A21 4.8 26.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure Analysis of A Trna-Neomycin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of A Trna-Neomycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:30.7 occ:1.00 OP1 A:G19 2.0 28.3 1.0 O A:HOH127 2.4 28.9 1.0 P A:G19 3.1 27.2 1.0 O5' A:G19 3.6 26.8 1.0 OP2 A:G19 3.7 25.9 1.0 N7 A:G20 4.0 23.7 1.0 C5' A:G19 4.2 25.1 1.0 O6 A:G20 4.3 20.7 1.0 O3' A:G18 4.5 27.7 1.0 O4 A:U59 4.7 31.1 1.0 C5 A:G20 4.8 21.8 1.0 N3 A:C60 4.9 28.0 1.0 C6 A:G20 5.0 20.9 1.0 C8 A:G20 5.0 24.4 1.0 N4 A:C60 5.0 31.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure Analysis of A Trna-Neomycin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Analysis of A Trna-Neomycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:47.1 occ:1.00 O A:HOH130 2.0 24.9 1.0 OP2 A:U12 2.9 40.2 1.0 C5 A:U12 3.8 36.5 1.0 O A:HOH110 3.9 13.9 1.0 P A:U12 4.2 41.2 1.0 C6 A:U12 4.3 37.4 1.0 OP2 A:C11 4.3 37.2 1.0 O5' A:C11 4.4 34.0 1.0 OP2 A:A9 4.5 25.0 1.0 O5' A:U12 4.6 40.9 1.0 C3' A:C11 4.6 37.2 1.0 C5 A:C13 4.6 21.9 1.0 OP2 A:U8 4.8 29.0 1.0 C4 A:U12 4.8 35.2 1.0 P A:C11 4.9 37.1 1.0 O3' A:C11 4.9 38.0 1.0

N.E.Mikkelsen, K.Johansson, A.Virtanen, L.A.Kirsebom. Aminoglycoside Binding Displaces A Divalent Metal Ion in A Trna-Neomycin B Complex. Nat.Struct.Biol. V. 8 510 2001.
ISSN: ISSN 1072-8368
PubMed: 11373618
DOI: 10.1038/88569