Magnesium in PDB 2e67: Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8

The structure of Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8, PDB code: 2e67 was solved by T.Imagawa, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.90
Space group	H 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.006, 202.006, 345.294, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 25.9

The binding sites of Magnesium atom in the Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 (pdb code 2e67). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8, PDB code: 2e67:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8


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 Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:10.6 occ:1.00 ND1 A:HIS127 2.0 25.8 1.0 OD2 A:ASP21 2.0 19.7 1.0 NE2 A:HIS60 2.1 18.6 1.0 CE1 A:HIS127 2.8 26.7 1.0 CE1 A:HIS60 3.1 19.6 1.0 CG A:ASP21 3.1 18.8 1.0 CG A:HIS127 3.1 25.1 1.0 CD2 A:HIS60 3.1 18.6 1.0 OD2 A:ASP20 3.5 30.8 1.0 OD1 A:ASP21 3.5 23.5 1.0 CB A:HIS127 3.6 25.8 1.0 CA A:HIS127 3.7 25.8 1.0 NE2 A:HIS127 4.0 24.8 1.0 CD2 A:HIS127 4.1 23.7 1.0 ND1 A:HIS60 4.2 20.3 1.0 CG A:ASP20 4.3 23.9 1.0 CG A:HIS60 4.3 16.7 1.0 CE A:MET43 4.3 2.0 1.0 CB A:ASP20 4.4 18.0 1.0 CB A:ASP21 4.4 15.9 1.0 N A:GLN128 4.5 26.8 1.0 N A:ASP21 4.6 15.6 1.0 NE2 A:HIS215 4.6 19.0 1.0 C A:HIS127 4.6 26.5 1.0 CA A:ASP21 4.7 15.8 1.0 N A:HIS127 4.7 25.1 1.0 CD2 A:HIS215 4.9 18.6 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8


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 Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:17.1 occ:1.00 OD2 B:ASP21 2.2 26.3 1.0 ND1 B:HIS127 2.2 31.9 1.0 NE2 B:HIS60 2.3 31.1 1.0 O B:HOH328 2.8 14.8 1.0 CE1 B:HIS127 3.0 30.3 1.0 CE1 B:HIS60 3.2 33.3 1.0 CG B:HIS127 3.3 30.0 1.0 CG B:ASP21 3.3 24.3 1.0 CD2 B:HIS60 3.3 29.3 1.0 OD2 B:ASP20 3.4 31.2 1.0 CB B:HIS127 3.7 28.5 1.0 OD1 B:ASP21 3.8 26.2 1.0 CA B:HIS127 3.8 28.2 1.0 O B:HOH331 4.2 37.0 1.0 NE2 B:HIS127 4.2 28.6 1.0 N B:GLN128 4.2 28.8 1.0 CG B:ASP20 4.3 27.4 1.0 ND1 B:HIS60 4.3 31.6 1.0 CD2 B:HIS127 4.4 27.9 1.0 CG B:HIS60 4.4 25.9 1.0 N B:ASP21 4.6 22.8 1.0 CB B:ASP20 4.6 24.3 1.0 C B:HIS127 4.6 28.3 1.0 CE B:MET43 4.6 5.4 1.0 NE2 B:HIS215 4.6 28.3 1.0 CB B:ASP21 4.6 22.9 1.0 CA B:ASP21 4.8 22.4 1.0 CD2 B:HIS215 4.8 25.5 1.0 N B:HIS127 5.0 27.5 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8


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 Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:21.0 occ:1.00 ND1 C:HIS127 2.1 30.3 1.0 OD2 C:ASP21 2.2 29.7 1.0 NE2 C:HIS60 2.5 31.3 1.0 CE1 C:HIS127 3.0 31.8 1.0 CG C:HIS127 3.2 30.8 1.0 CG C:ASP21 3.2 26.7 1.0 CD2 C:HIS60 3.3 31.3 1.0 CB C:HIS127 3.5 32.4 1.0 CE1 C:HIS60 3.6 32.3 1.0 OD1 C:ASP21 3.6 28.2 1.0 CA C:HIS127 3.8 32.4 1.0 OD2 C:ASP20 4.0 37.8 1.0 NE2 C:HIS127 4.2 29.0 1.0 CD2 C:HIS127 4.3 28.8 1.0 N C:GLN128 4.4 34.1 1.0 CG C:ASP20 4.4 33.1 1.0 CG C:HIS60 4.5 28.2 1.0 NE2 C:HIS215 4.5 27.9 1.0 C C:HIS127 4.6 33.5 1.0 CB C:ASP21 4.6 24.6 1.0 ND1 C:HIS60 4.6 32.4 1.0 SD C:MET43 4.8 12.8 1.0 N C:ASP21 4.8 25.2 1.0 CB C:ASP20 4.8 29.1 1.0 CA C:ASP21 4.8 24.1 1.0 CD2 C:HIS215 4.9 24.5 1.0 N C:HIS127 4.9 32.0 1.0 OD1 C:ASP20 5.0 36.7 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8


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 Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg304 b:13.1 occ:1.00 ND1 D:HIS127 2.1 31.0 1.0 OD2 D:ASP21 2.2 26.5 1.0 NE2 D:HIS60 2.3 24.3 1.0 CE1 D:HIS127 2.9 33.0 1.0 CE1 D:HIS60 3.1 24.7 1.0 CG D:HIS127 3.3 28.8 1.0 CG D:ASP21 3.3 23.1 1.0 OD2 D:ASP20 3.4 31.9 1.0 CD2 D:HIS60 3.4 24.1 1.0 OD1 D:ASP21 3.6 28.1 1.0 CA D:HIS127 3.7 26.5 1.0 CB D:HIS127 3.7 27.1 1.0 NE2 D:HIS127 4.1 32.0 1.0 CG D:ASP20 4.1 27.4 1.0 N D:GLN128 4.1 26.7 1.0 CD2 D:HIS127 4.3 29.9 1.0 ND1 D:HIS60 4.3 24.9 1.0 CG D:HIS60 4.5 21.9 1.0 C D:HIS127 4.5 26.1 1.0 CB D:ASP20 4.5 22.8 1.0 NE2 D:HIS215 4.6 24.9 1.0 CB D:ASP21 4.6 20.0 1.0 N D:ASP21 4.7 20.1 1.0 N D:HIS127 4.8 26.1 1.0 CD2 D:HIS215 4.9 23.7 1.0 CA D:ASP21 4.9 19.7 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg305 b:14.2 occ:1.00 OD2 E:ASP21 2.0 18.0 1.0 ND1 E:HIS127 2.2 44.9 1.0 NE2 E:HIS60 2.3 32.1 1.0 CE1 E:HIS127 2.9 44.9 1.0 CG E:ASP21 3.1 18.1 1.0 CD2 E:HIS60 3.1 31.3 1.0 CG E:HIS127 3.4 42.0 1.0 CE1 E:HIS60 3.4 33.1 1.0 OD1 E:ASP21 3.6 18.7 1.0 OD2 E:ASP20 3.6 30.0 1.0 CB E:HIS127 3.9 40.4 1.0 CG E:ASP20 4.0 27.4 1.0 CA E:HIS127 4.0 40.7 1.0 NE2 E:HIS127 4.1 44.4 1.0 CB E:ASP20 4.2 22.4 1.0 N E:ASP21 4.2 19.4 1.0 CB E:ASP21 4.4 17.4 1.0 CG E:HIS60 4.4 28.6 1.0 CD2 E:HIS127 4.4 41.9 1.0 NE2 E:HIS215 4.4 32.1 1.0 ND1 E:HIS60 4.4 30.9 1.0 CA E:ASP21 4.5 18.4 1.0 N E:GLN128 4.6 41.8 1.0 OD1 E:ASP20 4.6 31.6 1.0 CE E:MET43 4.6 8.8 1.0 CD2 E:HIS215 4.8 28.6 1.0 C E:HIS127 4.8 41.3 1.0 C E:ASP20 5.0 20.1 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg306 b:18.2 occ:1.00 OD2 F:ASP21 1.9 31.4 1.0 ND1 F:HIS127 2.1 41.5 1.0 NE2 F:HIS60 2.2 31.8 1.0 CE1 F:HIS127 2.9 41.4 1.0 CG F:ASP21 3.0 27.6 1.0 CE1 F:HIS60 3.1 34.7 1.0 CG F:HIS127 3.1 39.9 1.0 OD2 F:ASP20 3.2 34.9 1.0 CD2 F:HIS60 3.2 32.4 1.0 OD1 F:ASP21 3.4 32.5 1.0 CB F:HIS127 3.6 39.0 1.0 CA F:HIS127 3.6 39.2 1.0 CG F:ASP20 3.9 30.6 1.0 NE2 F:HIS127 4.1 40.7 1.0 CB F:ASP20 4.1 26.0 1.0 CD2 F:HIS127 4.2 39.1 1.0 ND1 F:HIS60 4.2 33.8 1.0 CG F:HIS60 4.3 30.3 1.0 CB F:ASP21 4.3 24.3 1.0 N F:GLN128 4.4 40.6 1.0 N F:ASP21 4.5 24.6 1.0 CE F:MET43 4.5 10.0 1.0 C F:HIS127 4.5 39.7 1.0 N F:HIS127 4.6 38.0 1.0 CA F:ASP21 4.6 23.8 1.0 NE2 F:HIS215 4.8 33.8 1.0 OD1 F:ASP20 4.9 35.7 1.0

T.Imagawa, H.Iino, M.Kanagawa, A.Ebihara, S.Kuramitsu, H.Tsuge. Crystal Structure of the Ydjc-Family Protein TTHB029 From Thermus Thermophilus HB8: Structural Relationship with Peptidoglycan N-Acetylglucosamine Deacetylase. Biochem.Biophys.Res.Commun. V. 367 535 2008.
ISSN: ISSN 0006-291X
PubMed: 18177738
DOI: 10.1016/J.BBRC.2007.12.144