Magnesium in PDB 2gt4: Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2

The structure of Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2, PDB code: 2gt4 was solved by S.B.Gabelli, M.A.Bianchet, H.F.Azurmendi, A.S.Mildvan, L.A.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.61 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.785, 93.893, 66.103, 90.00, 91.23, 90.00
R / Rfree (%)	18.6 / 22.6

The binding sites of Magnesium atom in the Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2 (pdb code 2gt4). 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 of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2, PDB code: 2gt4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:34.9 occ:1.00 O2A A:GDD201 2.2 39.1 1.0 O A:GLY50 2.2 32.5 1.0 O A:HOH455 2.3 41.1 1.0 O A:HOH411 2.4 55.5 1.0 OE2 A:GLU70 2.4 46.4 1.0 O2B A:GDD201 2.6 41.7 1.0 CD A:GLU70 3.1 44.2 1.0 OE1 A:GLU70 3.3 43.5 1.0 C A:GLY50 3.4 31.7 1.0 PA A:GDD201 3.5 42.1 1.0 PB A:GDD201 3.8 40.8 1.0 O3A A:GDD201 3.9 41.0 1.0 O A:HOH476 4.0 52.9 1.0 CA A:GLY51 4.1 30.9 1.0 NH1 A:ARG37 4.1 59.2 1.0 C11 A:GDD201 4.1 38.3 1.0 N A:GLY51 4.2 31.5 1.0 O A:HOH464 4.3 44.5 1.0 CG A:GLU70 4.3 41.1 1.0 O5' A:GDD201 4.3 41.8 1.0 N A:GLY50 4.4 32.0 1.0 O1B A:GDD201 4.4 40.1 1.0 O A:HOH402 4.4 39.5 1.0 CA A:GLY50 4.5 31.9 1.0 C5' A:GDD201 4.5 41.6 1.0 O A:HOH465 4.7 62.7 1.0 O1A A:GDD201 4.7 41.7 1.0 O51 A:GDD201 4.7 38.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:28.7 occ:1.00 O B:HOH417 1.9 52.3 1.0 OE2 B:GLU70 2.2 39.0 1.0 O2A B:GDD201 2.2 32.7 1.0 O B:GLY50 2.2 29.3 1.0 O2B B:GDD201 2.2 34.5 1.0 O B:HOH402 2.3 34.4 1.0 CD B:GLU70 3.1 40.8 1.0 O4 B:BMA202 3.3 70.0 1.0 O B:HOH468 3.4 47.9 1.0 C B:GLY50 3.4 29.1 1.0 PA B:GDD201 3.5 34.5 1.0 OE1 B:GLU70 3.5 41.3 1.0 PB B:GDD201 3.5 34.5 1.0 O3A B:GDD201 3.8 35.5 1.0 CA B:GLY51 4.1 29.5 1.0 C11 B:GDD201 4.1 33.7 1.0 N B:GLY51 4.2 28.7 1.0 O1B B:GDD201 4.2 35.5 1.0 C5' B:GDD201 4.2 35.2 1.0 O5' B:GDD201 4.3 33.7 1.0 N B:GLY50 4.4 28.9 1.0 CG B:GLU70 4.4 40.0 1.0 O B:HOH403 4.5 36.6 1.0 CA B:GLY50 4.5 28.8 1.0 C4 B:BMA202 4.6 69.2 1.0 O1A B:GDD201 4.6 36.2 1.0 C3 B:BMA202 4.8 70.1 1.0 O3B B:GDD201 4.8 34.6 1.0 O51 B:GDD201 4.8 33.4 1.0 O3 B:BMA202 4.8 71.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp-Mannose and Mg+2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:23.2 occ:1.00 O C:GLY50 2.2 26.4 1.0 O2B C:GDD201 2.2 30.9 1.0 OE2 C:GLU70 2.2 33.1 1.0 O2A C:GDD201 2.2 32.2 1.0 O C:HOH425 2.4 31.0 1.0 O C:HOH413 2.7 49.9 1.0 CD C:GLU70 2.9 36.8 1.0 O4 C:BMA202 3.1 65.3 1.0 OE1 C:GLU70 3.2 37.4 1.0 C C:GLY50 3.4 27.4 1.0 PB C:GDD201 3.5 32.7 1.0 PA C:GDD201 3.5 35.3 1.0 O3A C:GDD201 3.8 34.4 1.0 CA C:GLY51 3.9 26.7 1.0 O C:HOH403 4.0 36.1 1.0 C11 C:GDD201 4.1 33.5 1.0 N C:GLY51 4.1 26.6 1.0 O1B C:GDD201 4.2 33.7 1.0 CG C:GLU70 4.2 35.8 1.0 C5' C:GDD201 4.3 37.0 1.0 N C:GLY50 4.3 29.3 1.0 O5' C:GDD201 4.3 36.0 1.0 CA C:GLY50 4.4 27.9 1.0 O C:HOH402 4.5 35.8 1.0 C4 C:BMA202 4.5 63.7 1.0 O1A C:GDD201 4.7 37.9 1.0 O3B C:GDD201 4.7 33.0 1.0 O C:HOH507 4.7 58.2 1.0 C6 C:BMA202 4.8 61.6 1.0 O51 C:GDD201 4.9 33.2 1.0 C21 C:GDD201 5.0 33.3 1.0

S.B.Gabelli, H.F.Azurmendi, M.A.Bianchet, L.M.Amzel, A.S.Mildvan. X-Ray, uc(Nmr), and Mutational Studies of the Catalytic Cycle of the Gdp-Mannose Mannosyl Hydrolase Reaction. Biochemistry V. 45 11290 2006.
ISSN: ISSN 0006-2960
PubMed: 16981689
DOI: 10.1021/BI061239G