Magnesium in PDB 3i76: The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement

The structure of The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement, PDB code: 3i76 was solved by J.B.Bonanno, M.Dickey, K.T.Bain, B.K.Tang, R.Romero, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.685, 67.964, 271.404, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.9

The structure of The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement (pdb code 3i76). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement, PDB code: 3i76:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:16.4 occ:1.00 O A:HOH246 2.0 16.3 1.0 OD2 A:ASP10 2.0 16.3 1.0 OD1 A:ASP181 2.0 17.7 1.0 O A:HOH250 2.0 13.7 1.0 O A:HOH248 2.0 18.6 1.0 O A:ASP12 2.1 15.1 1.0 CG A:ASP10 3.0 16.3 1.0 CG A:ASP181 3.0 19.7 1.0 C A:ASP12 3.3 16.8 1.0 OD2 A:ASP181 3.3 21.0 1.0 OD1 A:ASP10 3.3 18.2 1.0 O A:HOH277 3.9 31.6 1.0 N A:ASP12 4.0 15.5 1.0 CA A:ASP12 4.1 15.9 1.0 OG1 A:THR14 4.1 15.9 1.0 OD2 A:ASP186 4.1 23.1 1.0 O A:HOH295 4.2 23.2 1.0 CB A:ASP10 4.3 16.2 1.0 CB A:ASP12 4.3 16.1 1.0 CB A:ASP181 4.4 19.6 1.0 N A:ASP13 4.4 17.5 1.0 O2 A:GOL243 4.4 29.1 1.0 O A:HOH276 4.4 34.1 1.0 O A:HOH284 4.5 14.2 1.0 N A:ASP181 4.5 18.5 1.0 CB A:ASP13 4.7 17.5 1.0 CL A:CL1002 4.7 23.0 1.0 N A:THR14 4.8 17.1 1.0 N A:SER182 4.8 19.8 1.0 C A:ASP13 4.8 16.6 1.0 CA A:ASP13 4.8 17.2 1.0 C A:VAL11 4.9 16.2 1.0 CA A:ASP181 4.9 18.9 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:15.1 occ:1.00 O B:HOH246 2.0 12.9 1.0 O B:HOH245 2.0 15.8 1.0 OD1 B:ASP181 2.0 14.3 1.0 O B:HOH244 2.1 14.4 1.0 O B:ASP12 2.1 13.6 1.0 OD2 B:ASP10 2.2 14.2 1.0 CG B:ASP181 3.1 16.7 1.0 CG B:ASP10 3.1 12.9 1.0 C B:ASP12 3.3 13.4 1.0 OD2 B:ASP181 3.4 13.7 1.0 OD1 B:ASP10 3.5 15.6 1.0 CA B:ASP12 4.0 13.6 1.0 OG1 B:THR14 4.0 10.9 1.0 OD2 B:ASP186 4.1 14.9 1.0 N B:ASP12 4.1 13.7 1.0 O B:HOH267 4.2 24.3 1.0 CB B:ASP12 4.3 12.9 1.0 O B:HOH313 4.3 20.9 1.0 CB B:ASP10 4.3 15.0 1.0 N B:ASP13 4.4 13.5 1.0 CB B:ASP181 4.4 16.4 1.0 CL B:CL1002 4.5 22.3 1.0 O B:HOH292 4.5 33.0 1.0 N B:ASP181 4.5 15.1 1.0 CB B:ASP13 4.7 14.5 1.0 C B:ASP13 4.7 14.1 1.0 CA B:ASP13 4.7 13.9 1.0 N B:THR14 4.8 12.4 1.0 N B:SER182 4.8 16.0 1.0 CB B:SER182 4.9 16.3 1.0 C B:VAL11 4.9 13.4 1.0 CA B:ASP181 4.9 15.6 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg243 b:37.1 occ:1.00 O B:HOH275 2.0 37.5 1.0 O B:HOH276 2.1 38.0 1.0 O B:HOH274 2.2 34.8 1.0 O B:HOH278 2.4 51.2 1.0 NE2 B:HIS99 2.5 21.8 1.0 O B:HOH272 2.6 26.9 1.0 CE1 B:HIS99 3.4 23.5 1.0 CD2 B:HIS99 3.5 21.3 1.0 O B:HOH281 4.1 34.2 1.0 NE2 B:GLN100 4.3 26.3 1.0 ND1 B:HIS99 4.5 19.9 1.0 CG B:HIS99 4.6 17.7 1.0 O B:HOH295 4.9 23.6 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of the Orthorhombic Form of the Putative Had- Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:16.0 occ:1.00 O C:HOH245 2.0 15.3 1.0 O C:HOH243 2.0 17.9 1.0 O C:ASP12 2.1 16.1 1.0 OD2 C:ASP10 2.1 16.7 1.0 O C:HOH244 2.1 13.6 1.0 OD1 C:ASP181 2.2 15.9 1.0 CG C:ASP10 3.0 16.7 1.0 CG C:ASP181 3.1 18.7 1.0 C C:ASP12 3.3 16.0 1.0 OD2 C:ASP181 3.3 21.0 1.0 OD1 C:ASP10 3.4 18.1 1.0 CA C:ASP12 4.0 17.3 1.0 OD2 C:ASP186 4.0 20.3 1.0 OG1 C:THR14 4.1 17.0 1.0 N C:ASP12 4.1 18.2 1.0 O C:HOH294 4.3 27.0 1.0 CB C:ASP12 4.3 16.9 1.0 CB C:ASP10 4.3 18.3 1.0 O C:HOH257 4.3 23.4 1.0 N C:ASP13 4.4 15.5 1.0 CB C:ASP181 4.5 18.9 1.0 CL C:CL1002 4.5 27.4 1.0 N C:ASP181 4.6 18.4 1.0 O C:HOH644 4.7 43.0 1.0 C C:ASP13 4.7 16.0 1.0 CB C:ASP13 4.7 16.4 1.0 N C:SER182 4.7 18.9 1.0 CA C:ASP13 4.8 15.8 1.0 N C:THR14 4.8 16.3 1.0 C C:VAL11 4.9 18.5 1.0 CB C:SER182 4.9 19.2 1.0 CA C:ASP181 5.0 18.7 1.0

J.B.Bonanno, M.Dickey, K.T.Bain, B.K.Tang, R.Romero, J.M.Sauder, S.K.Burley, S.C.Almo. The Crystal Structure of the Orthorhombic Form of the Putative Had-Hydrolase Yfnb From Bacillus Subtilis Bound to Magnesium Reveals Interdomain Movement To Be Published.