Magnesium in PDB 1nmp: Structural Genomics, Ybgi Protein, Unknown Function

The structure of Structural Genomics, Ybgi Protein, Unknown Function, PDB code: 1nmp was solved by J.E.Ladner, G.Obmolova, A.Teplyakov, P.P.Khil, R.D.Camerini-Otero, G.L.Gilliland, Structure 2 Function Project (S2F), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 2.20
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	156.730, 156.730, 57.610, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 25.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Structural Genomics, Ybgi Protein, Unknown Function (pdb code 1nmp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Structural Genomics, Ybgi Protein, Unknown Function, PDB code: 1nmp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:55.0 occ:1.00 MG A:MG302 2.2 24.8 1.0 OE2 A:GLU219 2.5 18.3 1.0 OE1 A:GLU219 2.7 17.5 1.0 O A:HOH367 2.8 19.5 1.0 NE2 A:HIS64 2.9 17.2 1.0 NE2 A:HIS215 3.0 16.2 1.0 CD A:GLU219 3.0 16.8 1.0 NE2 A:HIS63 3.2 2.5 1.0 CE1 A:HIS64 3.6 18.5 1.0 CE1 A:HIS215 3.7 16.6 1.0 NE2 A:HIS97 3.8 17.9 1.0 CD2 A:HIS63 3.8 4.8 1.0 CD2 A:HIS64 3.9 15.3 1.0 CD2 A:HIS215 4.0 15.3 1.0 OD1 A:ASP101 4.2 15.4 1.0 CD2 A:HIS97 4.2 16.5 1.0 CE1 A:HIS63 4.3 3.5 1.0 CA A:GLY173 4.4 10.8 1.0 CG A:GLU219 4.5 15.6 1.0 OD2 A:ASP101 4.6 17.0 1.0 N A:GLY174 4.7 12.4 1.0 O A:THR172 4.8 12.3 1.0 ND1 A:HIS64 4.8 17.1 1.0 CG A:ASP101 4.9 15.7 1.0 ND1 A:HIS215 4.9 15.9 1.0 O A:HOH379 5.0 17.5 1.0 CE1 A:HIS97 5.0 17.1 1.0

Magnesium binding site 2 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:24.8 occ:1.00 OD1 A:ASP101 2.1 15.4 1.0 OE1 A:GLU219 2.2 17.5 1.0 MG A:MG301 2.2 55.0 1.0 NE2 A:HIS63 2.4 2.5 1.0 OD2 A:ASP101 2.5 17.0 1.0 CG A:ASP101 2.6 15.7 1.0 CD A:GLU219 3.1 16.8 1.0 CE1 A:HIS63 3.1 3.5 1.0 OE2 A:GLU219 3.4 18.3 1.0 CD2 A:HIS63 3.6 4.8 1.0 O A:HOH367 3.8 19.5 1.0 NE2 A:HIS97 4.0 17.9 1.0 OG1 A:THR172 4.1 10.4 1.0 CD2 A:HIS97 4.1 16.5 1.0 CB A:ASP101 4.2 13.9 1.0 ND2 A:ASN108 4.3 11.2 1.0 O A:THR172 4.3 12.3 1.0 O A:HOH380 4.3 34.3 1.0 CG A:GLU219 4.3 15.6 1.0 ND1 A:HIS63 4.4 5.1 1.0 NE2 A:HIS64 4.5 17.2 1.0 O A:HOH379 4.6 17.5 1.0 CG A:HIS63 4.6 6.6 1.0 C A:THR172 4.9 11.5 1.0 NE2 A:HIS215 5.0 16.2 1.0

Magnesium binding site 3 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:41.6 occ:1.00 O B:HOH380 2.1 23.4 1.0 OE1 B:GLU219 2.2 12.3 1.0 NE2 B:HIS63 2.6 5.1 1.0 OD1 B:ASP101 2.6 15.9 1.0 OD2 B:ASP101 2.7 18.2 1.0 CG B:ASP101 3.1 15.4 1.0 CD B:GLU219 3.1 12.7 1.0 O B:HOH381 3.3 23.7 1.0 OE2 B:GLU219 3.4 16.0 1.0 CE1 B:HIS63 3.5 6.6 1.0 CD2 B:HIS63 3.6 6.2 1.0 NE2 B:HIS97 3.7 17.8 1.0 NE2 B:HIS64 4.2 16.2 1.0 CD2 B:HIS97 4.2 13.3 1.0 O B:HOH356 4.3 20.7 1.0 O B:THR172 4.4 11.4 1.0 ND2 B:ASN108 4.4 11.2 1.0 OG1 B:THR172 4.4 11.6 1.0 CG B:GLU219 4.4 13.0 1.0 NE2 B:HIS215 4.5 12.8 1.0 CB B:ASP101 4.6 14.7 1.0 ND1 B:HIS63 4.6 8.0 1.0 CG B:HIS63 4.8 8.3 1.0 CA B:GLY173 4.8 12.9 1.0 CE1 B:HIS64 4.8 16.4 1.0 CE1 B:HIS97 4.8 16.6 1.0 C B:THR172 4.8 11.8 1.0

Magnesium binding site 4 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:58.4 occ:1.00 NE2 C:HIS215 2.4 13.3 1.0 OE2 C:GLU219 2.5 9.5 1.0 NE2 C:HIS64 2.5 15.8 1.0 MG C:MG302 2.8 27.0 1.0 CE1 C:HIS64 3.1 12.3 1.0 CE1 C:HIS215 3.1 9.8 1.0 CD C:GLU219 3.2 8.3 1.0 OE1 C:GLU219 3.2 8.7 1.0 CD2 C:HIS215 3.5 11.0 1.0 CD2 C:HIS64 3.7 11.3 1.0 NE2 C:HIS63 3.8 6.2 1.0 O C:HOH356 3.8 16.9 1.0 CA C:GLY173 4.0 10.3 1.0 CD2 C:HIS63 4.1 5.0 1.0 NE2 C:HIS97 4.2 16.8 1.0 ND1 C:HIS215 4.3 12.5 1.0 N C:GLY174 4.3 12.0 1.0 ND1 C:HIS64 4.4 11.7 1.0 CG C:HIS215 4.5 10.1 1.0 CG C:GLU219 4.6 10.1 1.0 CD2 C:HIS97 4.7 13.7 1.0 CG C:HIS64 4.7 11.7 1.0 C C:GLY173 4.7 10.5 1.0 CE1 C:HIS63 4.8 4.0 1.0 OD1 C:ASP101 4.9 16.6 1.0

Magnesium binding site 5 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:27.0 occ:1.00 OE1 C:GLU219 2.1 8.7 1.0 O C:HOH356 2.3 16.9 1.0 OD2 C:ASP101 2.3 16.2 1.0 OD1 C:ASP101 2.3 16.6 1.0 NE2 C:HIS63 2.4 6.2 1.0 CG C:ASP101 2.7 13.7 1.0 MG C:MG301 2.8 58.4 1.0 CD C:GLU219 3.0 8.3 1.0 CE1 C:HIS63 3.2 4.0 1.0 OE2 C:GLU219 3.3 9.5 1.0 CD2 C:HIS63 3.5 5.0 1.0 ND2 C:ASN108 4.0 4.3 1.0 OG1 C:THR172 4.1 9.6 1.0 CB C:ASP101 4.2 12.0 1.0 O C:THR172 4.2 7.5 1.0 NE2 C:HIS97 4.3 16.8 1.0 CG C:GLU219 4.3 10.1 1.0 ND1 C:HIS63 4.4 3.2 1.0 CD2 C:HIS97 4.5 13.7 1.0 NE2 C:HIS64 4.5 15.8 1.0 CG C:HIS63 4.6 6.4 1.0 CA C:GLY173 4.7 10.3 1.0 C C:THR172 4.7 9.3 1.0 NE2 C:HIS215 5.0 13.3 1.0

Magnesium binding site 6 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:48.1 occ:1.00 OE2 D:GLU219 2.5 10.9 1.0 MG D:MG302 2.6 15.1 1.0 NE2 D:HIS64 2.7 11.6 1.0 NE2 D:HIS215 3.0 8.4 1.0 OE1 D:GLU219 3.1 11.2 1.0 CD D:GLU219 3.1 9.1 1.0 CE1 D:HIS64 3.4 11.2 1.0 O D:HOH338 3.6 11.4 1.0 NE2 D:HIS63 3.6 4.7 1.0 CE1 D:HIS215 3.6 4.7 1.0 CD2 D:HIS63 3.8 4.7 1.0 NE2 D:HIS97 3.8 16.9 1.0 CD2 D:HIS64 3.8 9.2 1.0 CD2 D:HIS215 4.1 7.1 1.0 CA D:GLY173 4.2 11.4 1.0 CD2 D:HIS97 4.4 13.6 1.0 OD1 D:ASP101 4.4 16.8 1.0 N D:GLY174 4.5 12.5 1.0 CG D:GLU219 4.6 9.5 1.0 ND1 D:HIS64 4.6 11.6 1.0 CE1 D:HIS63 4.8 6.2 1.0 ND1 D:HIS215 4.8 7.8 1.0 OD2 D:ASP101 4.8 17.6 1.0 CG D:HIS64 4.9 10.0 1.0 C D:GLY173 4.9 11.7 1.0 CE1 D:HIS97 4.9 13.8 1.0 O D:THR172 4.9 10.3 1.0

Magnesium binding site 7 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:15.1 occ:1.00 OD1 D:ASP101 2.0 16.8 1.0 OE1 D:GLU219 2.2 11.2 1.0 NE2 D:HIS63 2.2 4.7 1.0 O D:HOH338 2.3 11.4 1.0 OD2 D:ASP101 2.4 17.6 1.0 CG D:ASP101 2.6 14.4 1.0 MG D:MG301 2.6 48.1 1.0 CD D:GLU219 3.0 9.1 1.0 CE1 D:HIS63 3.1 6.2 1.0 CD2 D:HIS63 3.2 4.7 1.0 OE2 D:GLU219 3.3 10.9 1.0 O D:HOH356 3.8 26.4 1.0 ND2 D:ASN108 4.0 8.0 1.0 NE2 D:HIS97 4.0 16.9 1.0 CB D:ASP101 4.1 11.9 1.0 OG1 D:THR172 4.2 9.9 1.0 CD2 D:HIS97 4.2 13.6 1.0 ND1 D:HIS63 4.3 7.7 1.0 CG D:GLU219 4.3 9.5 1.0 CG D:HIS63 4.4 7.3 1.0 NE2 D:HIS64 4.4 11.6 1.0 O D:THR172 4.5 10.3 1.0 CE1 D:HIS97 4.9 13.8 1.0

Magnesium binding site 8 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg301 b:49.4 occ:1.00 MG E:MG302 2.4 30.2 1.0 OE2 E:GLU219 2.4 13.5 1.0 NE2 E:HIS64 2.6 12.3 1.0 NE2 E:HIS215 2.8 9.6 1.0 CD E:GLU219 3.2 12.2 1.0 OE1 E:GLU219 3.2 13.0 1.0 NE2 E:HIS63 3.3 3.0 1.0 CE1 E:HIS64 3.4 8.9 1.0 CE1 E:HIS215 3.5 5.4 1.0 CD2 E:HIS63 3.6 4.2 1.0 CD2 E:HIS64 3.6 8.1 1.0 O E:HOH357 3.8 15.9 1.0 CD2 E:HIS215 3.8 8.2 1.0 NE2 E:HIS97 4.0 14.3 1.0 CA E:GLY173 4.4 11.4 1.0 CD2 E:HIS97 4.4 11.7 1.0 ND1 E:HIS64 4.5 9.2 1.0 CE1 E:HIS63 4.5 4.1 1.0 CG E:GLU219 4.6 12.2 1.0 O F:HOH378 4.6 21.5 1.0 CG E:HIS64 4.7 10.0 1.0 ND1 E:HIS215 4.7 7.7 1.0 OD2 E:ASP101 4.7 11.3 1.0 N E:GLY174 4.8 12.2 1.0 CG E:HIS215 4.9 7.4 1.0 CG E:HIS63 4.9 6.3 1.0 OD1 E:ASP101 4.9 12.3 1.0

Magnesium binding site 9 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:30.2 occ:1.00 OE1 E:GLU219 2.2 13.0 1.0 MG E:MG301 2.4 49.4 1.0 O E:HOH357 2.4 15.9 1.0 OD2 E:ASP101 2.4 11.3 1.0 NE2 E:HIS63 2.4 3.0 1.0 OD1 E:ASP101 2.8 12.3 1.0 CG E:ASP101 3.0 9.7 1.0 CD E:GLU219 3.0 12.2 1.0 OE2 E:GLU219 3.2 13.5 1.0 CE1 E:HIS63 3.3 4.1 1.0 CD2 E:HIS63 3.5 4.2 1.0 ND2 E:ASN108 4.0 7.0 1.0 NE2 E:HIS97 4.0 14.3 1.0 O E:HOH351 4.1 36.0 1.0 CD2 E:HIS97 4.2 11.7 1.0 OG1 E:THR172 4.3 7.6 1.0 CG E:GLU219 4.3 12.2 1.0 O E:THR172 4.4 9.1 1.0 CB E:ASP101 4.4 7.3 1.0 ND1 E:HIS63 4.5 5.8 1.0 NE2 E:HIS64 4.6 12.3 1.0 CG E:HIS63 4.6 6.3 1.0 CA E:GLY173 4.8 11.4 1.0 C E:THR172 4.8 9.4 1.0 NE2 E:HIS215 4.9 9.6 1.0

Magnesium binding site 10 out of 11 in the Structural Genomics, Ybgi Protein, Unknown Function


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structural Genomics, Ybgi Protein, Unknown Function within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg301 b:55.4 occ:1.00 MG F:MG302 2.4 23.0 1.0 OE2 F:GLU219 2.5 11.7 1.0 O F:HOH499 2.7 12.2 1.0 NE2 F:HIS64 2.7 10.8 1.0 NE2 F:HIS215 2.9 11.1 1.0 CD F:GLU219 3.3 10.9 1.0 OE1 F:GLU219 3.3 7.5 1.0 NE2 F:HIS63 3.5 5.2 1.0 CE1 F:HIS64 3.6 8.7 1.0 O F:HOH335 3.6 18.5 1.0 CE1 F:HIS215 3.7 9.8 1.0 CD2 F:HIS64 3.7 8.3 1.0 CD2 F:HIS63 3.8 5.1 1.0 NE2 F:HIS97 3.8 11.4 1.0 CD2 F:HIS215 3.9 8.1 1.0 CD2 F:HIS97 4.3 9.6 1.0 CA F:GLY173 4.3 9.5 1.0 OD1 F:ASP101 4.4 13.0 1.0 O E:HOH416 4.6 29.0 1.0 CE1 F:HIS63 4.6 3.9 1.0 N F:GLY174 4.7 9.1 1.0 CG F:GLU219 4.8 10.8 1.0 ND1 F:HIS64 4.8 10.0 1.0 OD2 F:ASP101 4.8 11.9 1.0 ND1 F:HIS215 4.9 11.4 1.0 CG F:HIS64 4.9 8.3 1.0 CE1 F:HIS97 5.0 10.6 1.0

J.E.Ladner, G.Obmolova, A.Teplyakov, A.J.Howard, P.P.Khil, R.D.Camerini-Otero, G.L.Gilliland. Crystal Structure of Escherichia Coli Protein Ybgi, A Toroidal Structure with A Dinuclear Metal Site Bmc Struct.Biol. V. 3 7 2003.
ISSN: ESSN 1472-6807
PubMed: 14519207
DOI: 10.1186/1472-6807-3-7