Magnesium in PDB 4wc0: Trna-Processing Enzyme with Atp

The structure of Trna-Processing Enzyme with Atp, PDB code: 4wc0 was solved by S.Yamashita, K.Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.82 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.710, 109.060, 85.090, 90.00, 109.84, 90.00
R / Rfree (%)	21.3 / 26.3

The binding sites of Magnesium atom in the Trna-Processing Enzyme with Atp (pdb code 4wc0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Trna-Processing Enzyme with Atp, PDB code: 4wc0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Trna-Processing Enzyme with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trna-Processing Enzyme with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:56.8 occ:1.00 O2B A:ATP401 2.3 88.3 1.0 O3G A:ATP401 2.7 0.2 1.0 O2A A:ATP401 3.3 99.5 1.0 O1G A:ATP401 3.5 0.7 1.0 PG A:ATP401 3.6 96.5 1.0 PB A:ATP401 3.7 72.7 1.0 O3B A:ATP401 4.1 90.9 1.0 PA A:ATP401 4.5 78.2 1.0 O3A A:ATP401 4.6 56.6 1.0 OD2 A:ASP33 4.6 88.3 1.0 O1B A:ATP401 4.8 55.6 1.0 C5' A:ATP401 4.8 66.4 1.0 O5' A:ATP401 4.9 56.1 1.0 O2G A:ATP401 5.0 61.9 1.0

Magnesium binding site 2 out of 2 in the Trna-Processing Enzyme with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trna-Processing Enzyme with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:58.5 occ:1.00 O1B B:ATP401 2.2 0.0 1.0 O3G B:ATP401 3.6 0.0 1.0 PB B:ATP401 3.7 0.5 1.0 O1A B:ATP401 3.7 70.4 1.0 O1G B:ATP401 3.8 0.1 1.0 PG B:ATP401 4.2 0.9 1.0 C5' B:ATP401 4.3 99.8 1.0 N B:VAL19 4.4 97.0 1.0 O2B B:ATP401 4.4 76.0 1.0 O3B B:ATP401 4.4 92.8 1.0 C B:GLY18 4.4 59.3 1.0 CA B:GLY18 4.5 66.9 1.0 NH2 B:ARG21 4.6 89.0 1.0 CG2 B:VAL19 4.6 0.9 1.0 O B:ASP31 4.6 59.7 1.0 O3A B:ATP401 4.7 80.9 1.0 PA B:ATP401 4.7 72.1 1.0 OD2 B:ASP22 4.7 83.0 1.0 N B:GLY18 4.8 85.5 1.0 O5' B:ATP401 4.9 90.5 1.0 O B:GLY18 4.9 76.3 1.0

S.Yamashita, A.Martinez, K.Tomita. Measurement of Acceptor-T Psi C Helix Length of Trna For Terminal A76-Addition By A-Adding Enzyme. Structure V. 23 830 2015.
ISSN: ISSN 0969-2126
PubMed: 25914059
DOI: 10.1016/J.STR.2015.03.013