Magnesium in PDB 3hdg: Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes

The structure of Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes, PDB code: 3hdg was solved by S.Eswaramoorthy, S.K.Burley, S.Swaminathan, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.53 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.331, 77.059, 75.087, 90.00, 102.67, 90.00
R / Rfree (%)	22.3 / 27

The binding sites of Magnesium atom in the Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes (pdb code 3hdg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes, PDB code: 3hdg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes


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 N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:32.6 occ:1.00 OD1 A:ASP16 1.9 28.1 1.0 OD1 B:ASP17 1.9 33.9 1.0 OD2 A:ASP59 2.0 30.3 1.0 O A:HOH140 2.0 39.2 1.0 O A:HOH139 2.2 26.3 1.0 OE2 A:GLU15 2.3 33.9 1.0 CG A:ASP16 3.0 26.0 1.0 CG B:ASP17 3.0 30.4 1.0 CG A:ASP59 3.1 27.7 1.0 CD A:GLU15 3.3 30.4 1.0 OD2 A:ASP16 3.4 26.5 1.0 OD2 B:ASP17 3.5 30.8 1.0 OE1 A:GLU15 3.6 33.7 1.0 OD1 A:ASP59 3.9 30.7 1.0 N A:ASP16 4.0 23.6 1.0 OD2 B:ASP19 4.0 43.4 1.0 O A:ARG61 4.0 32.5 1.0 NZ A:LYS109 4.0 49.1 1.0 CB A:ASP59 4.1 26.2 1.0 N A:ASP17 4.1 22.6 1.0 CB A:ASP16 4.3 22.4 1.0 CB B:ASP17 4.3 26.5 1.0 CA A:ASP16 4.5 24.2 1.0 N B:THR18 4.6 30.1 1.0 CG A:GLU15 4.6 27.4 1.0 CA B:ASP17 4.6 26.1 1.0 C A:ASP16 4.7 23.9 1.0 CB A:ASP17 4.7 26.5 1.0 N B:ASP19 4.9 34.2 1.0 CG A:MSE62 4.9 32.4 1.0 CG B:ASP19 4.9 39.4 1.0 C B:ASP17 5.0 27.9 1.0 C A:GLU15 5.0 23.7 1.0 CB B:ASP19 5.0 36.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes


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 N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:32.2 occ:1.00 OD1 A:ASP17 1.9 30.6 1.0 OD2 B:ASP59 2.0 31.9 1.0 OD1 B:ASP16 2.0 30.3 1.0 OE2 B:GLU15 2.1 28.5 1.0 O B:HOH139 2.2 32.9 1.0 O A:HOH1 2.3 31.4 1.0 CG A:ASP17 3.0 27.8 1.0 CD B:GLU15 3.1 29.1 1.0 CG B:ASP16 3.1 28.7 1.0 CG B:ASP59 3.1 28.4 1.0 OE1 B:GLU15 3.4 30.9 1.0 OD1 B:ASP59 3.6 31.8 1.0 OD2 A:ASP17 3.6 28.0 1.0 OD2 B:ASP16 3.6 28.4 1.0 N B:ASP17 3.9 25.1 1.0 N B:ASP16 3.9 25.4 1.0 OD2 A:ASP19 4.0 43.6 1.0 CB A:ASP17 4.0 26.5 1.0 CA A:ASP17 4.2 24.5 1.0 CB B:ASP17 4.3 26.5 1.0 CB B:ASP16 4.3 27.1 1.0 N A:THR18 4.3 25.3 1.0 CB B:ASP59 4.4 28.5 1.0 NZ B:LYS109 4.4 38.9 1.0 CA B:ASP16 4.4 25.1 1.0 CG B:GLU15 4.4 27.6 1.0 C B:ASP16 4.5 25.4 1.0 O B:ARG61 4.6 30.9 1.0 C A:ASP17 4.7 25.2 1.0 CA B:ASP17 4.7 26.1 1.0 CG A:ASP19 4.8 39.4 1.0 C B:GLU15 4.8 25.8 1.0 N A:ASP19 4.9 28.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes


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 N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:33.8 occ:1.00 OE2 D:GLU15 1.8 33.4 1.0 O D:HOH141 1.9 36.1 1.0 O D:HOH142 2.0 40.7 1.0 OD2 D:ASP59 2.1 38.3 1.0 OD1 D:ASP16 2.2 32.3 1.0 OD1 E:ASP17 2.3 37.0 1.0 CD D:GLU15 2.8 31.2 1.0 CG D:ASP59 3.0 34.1 1.0 CG D:ASP16 3.2 31.2 1.0 OE1 D:GLU15 3.3 33.2 1.0 OD1 D:ASP59 3.5 33.6 1.0 CG E:ASP17 3.5 38.4 1.0 N D:ASP16 3.8 30.5 1.0 OD2 D:ASP16 3.8 30.9 1.0 N D:ASP17 3.9 35.4 1.0 CG D:GLU15 4.1 30.9 1.0 CB D:ASP59 4.2 32.5 1.0 CB D:ASP17 4.3 36.9 1.0 CB D:ASP16 4.4 30.0 1.0 CA D:ASP16 4.4 32.0 1.0 CB E:ASP17 4.4 34.7 1.0 OD2 E:ASP17 4.4 40.9 1.0 CA E:ASP17 4.4 35.0 1.0 OD2 E:ASP19 4.4 44.8 1.0 C D:ASP16 4.5 34.1 1.0 O D:ARG61 4.5 35.4 1.0 C D:GLU15 4.7 30.8 1.0 CA D:ASP17 4.7 35.5 1.0 N E:THR18 4.7 32.4 1.0 CA D:GLU15 4.8 30.0 1.0 CB D:GLU15 4.9 29.3 1.0 C E:ASP17 5.0 34.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg204 b:43.0 occ:1.00 OD1 E:ASP16 1.8 37.6 1.0 O D:HOH139 1.8 36.9 1.0 O D:HOH140 2.1 41.4 1.0 OD2 E:ASP59 2.4 38.6 1.0 OD1 D:ASP17 2.4 42.8 1.0 CG E:ASP16 2.6 34.9 1.0 OD2 E:ASP16 2.7 35.5 1.0 CG D:ASP17 2.9 40.0 1.0 OD2 D:ASP17 3.1 40.3 1.0 OE2 E:GLU15 3.1 33.2 1.0 CG E:ASP59 3.5 38.4 1.0 OD2 D:ASP19 4.0 41.6 1.0 O E:ARG61 4.0 40.1 1.0 N D:THR18 4.0 34.9 1.0 CA D:ASP17 4.0 35.5 1.0 CB E:ASP16 4.0 33.7 1.0 CB D:ASP17 4.0 36.9 1.0 OD1 E:ASP59 4.1 36.1 1.0 CD E:GLU15 4.2 32.2 1.0 C D:ASP17 4.3 35.3 1.0 N E:ASP16 4.3 32.6 1.0 N E:ASP17 4.5 35.2 1.0 N D:ASP19 4.5 31.5 1.0 CA E:ASP16 4.5 33.4 1.0 C E:ASP16 4.6 34.0 1.0 OE1 E:GLU15 4.6 33.2 1.0 CB E:ASP59 4.6 35.7 1.0 CG D:ASP19 4.8 40.0 1.0 CB E:ASP17 4.9 34.7 1.0 CB D:ASP19 4.9 35.5 1.0 CA D:THR18 4.9 33.9 1.0 CB D:THR18 5.0 35.7 1.0

S.Eswaramoorthy, S.K.Burley, S.Swaminathan. Crystal Structure of the N-Terminal Domain of An Uncharacterized Protein (WS1339) From Wolinella Succinogenes To Be Published.