Magnesium in PDB 1ixy: Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex

All present enzymatic activity of Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex:
2.4.1.27;

The structure of Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex, PDB code: 1ixy was solved by L.Lariviere, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.900, 56.400, 99.100, 90.00, 90.30, 90.00
R / Rfree (%)	20.9 / 28.2

The binding sites of Magnesium atom in the Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex (pdb code 1ixy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex, PDB code: 1ixy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:38.8 occ:1.00 O A:HOH937 1.9 36.8 1.0 O A:HOH939 2.3 34.3 1.0 O A:HOH938 2.3 40.6 1.0 OE1 A:GLU163 2.6 32.1 1.0 CD A:GLU163 3.5 33.9 1.0 O1B A:UDP400 3.6 29.6 1.0 OE2 A:GLU163 3.7 35.8 1.0 O A:HOH701 3.8 39.3 1.0 O A:THR99 3.8 26.1 1.0 OE2 A:GLU22 4.1 41.0 1.0 OG1 A:THR99 4.3 25.9 1.0 C A:THR99 4.5 29.4 1.0 CB A:THR99 4.6 27.1 1.0 O2B A:UDP400 4.7 30.9 1.0 PB A:UDP400 4.8 34.9 1.0 OH A:TYR261 4.8 46.6 1.0 CG A:GLU163 4.9 32.5 1.0

Magnesium binding site 2 out of 3 in the Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:52.5 occ:1.00 O B:HOH911 1.9 39.9 1.0 O B:HOH912 2.2 43.9 1.0 O B:HOH910 2.2 40.4 1.0 OE1 B:GLU163 2.7 39.1 1.0 O1B B:UDP401 3.2 28.7 1.0 O B:HOH702 3.3 28.5 1.0 CD B:GLU163 3.6 40.0 1.0 OE2 B:GLU163 3.7 43.2 1.0 OE1 B:GLU22 3.9 41.0 1.0 PB B:UDP401 4.6 32.5 1.0 CB B:LEU268 4.6 36.1 1.0 O B:THR99 4.7 32.6 1.0 O5' B:UDP401 4.8 27.4 1.0 CD B:GLU22 4.8 39.3 1.0 O2B B:UDP401 4.9 31.5 1.0 CG B:GLU163 5.0 38.6 1.0 OG1 B:THR99 5.0 25.3 1.0

Magnesium binding site 3 out of 3 in the Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex of T4 Phage Bgt with Udp and A 13 Mer Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg700 b:49.8 occ:1.00 O B:HOH909 1.9 22.8 1.0 O B:HOH908 2.0 33.7 1.0 OE2 B:GLU305 2.0 32.2 1.0 O B:HOH905 2.0 56.0 1.0 CD B:GLU305 2.9 37.0 1.0 OE1 B:GLU305 3.1 34.8 1.0 NH2 B:ARG309 4.0 28.7 1.0 O B:TYR299 4.1 32.7 1.0 CG B:GLU305 4.3 37.4 1.0 ND2 B:ASN301 4.4 49.2 1.0

L.Lariviere, S.Morera. A Base-Flipping Mechanism For the T4 Phage Beta-Glucosyltransferase and Identification of A Transition-State Analog J.Mol.Biol. V. 324 483 2002.
ISSN: ISSN 0022-2836
PubMed: 12445783
DOI: 10.1016/S0022-2836(02)01091-4