Magnesium in PDB 2ggh: The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase

All present enzymatic activity of The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase:
5.1.1.10;

The structure of The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase, PDB code: 2ggh was solved by W.C.Wang, W.C.Chiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	116.188, 116.188, 120.815, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.8

The binding sites of Magnesium atom in the The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase (pdb code 2ggh). 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 Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase, PDB code: 2ggh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1377 b:31.4 occ:1.00 OE1 A:GLU220 2.7 16.3 1.0 NZ A:LYS168 2.8 21.8 1.0 OE2 A:GLU220 3.0 19.9 1.0 CD A:GLU220 3.1 17.6 1.0 OD2 A:ASP195 3.2 25.0 1.0 CE A:LYS168 3.3 19.1 1.0 CG A:ASP195 3.7 22.3 1.0 CD A:LYS168 3.8 18.0 1.0 ND2 A:ASN267 3.9 14.2 1.0 CH2 A:TRP294 4.0 15.8 1.0 CB A:ASP195 4.3 19.3 1.0 O A:HOH1471 4.3 31.9 1.0 OD1 A:ASP195 4.3 21.4 1.0 CG A:GLU220 4.6 18.3 1.0 OD2 A:ASP322 4.6 18.6 1.0 CZ2 A:TRP294 4.9 15.1 1.0 CZ3 A:TRP294 4.9 15.8 1.0 OD1 A:ASP245 5.0 21.5 1.0 CG A:LYS168 5.0 15.9 1.0

Magnesium binding site 2 out of 4 in the The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2377 b:27.9 occ:1.00 OE1 B:GLU220 2.6 18.6 1.0 CE B:LYS168 2.9 23.4 1.0 OD2 B:ASP195 3.1 23.9 1.0 OE2 B:GLU220 3.2 23.8 1.0 CD B:GLU220 3.2 21.6 1.0 CG B:ASP195 3.7 20.1 1.0 O B:HOH2543 3.7 27.7 1.0 O B:HOH2433 3.9 21.6 1.0 NZ B:LYS168 3.9 24.4 1.0 CD B:LYS168 4.0 20.8 1.0 OD1 B:ASN267 4.1 21.1 1.0 CB B:ASP195 4.2 17.5 1.0 CH2 B:TRP294 4.2 17.1 1.0 OD1 B:ASP195 4.3 19.6 1.0 O B:HOH2533 4.3 39.9 1.0 OD2 B:ASP322 4.6 23.9 1.0 CG B:GLU220 4.6 21.8 1.0 O B:HOH2570 4.7 33.3 1.0 CZ2 B:TRP294 4.9 15.4 1.0 CG B:LYS168 5.0 19.0 1.0

Magnesium binding site 3 out of 4 in the The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3377 b:50.3 occ:1.00 OD2 C:ASP195 2.3 35.9 1.0 OXT C:NLQ1376 3.1 54.8 1.0 NZ C:LYS168 3.1 26.2 1.0 OE1 C:GLU220 3.1 20.5 1.0 O C:HOH3417 3.3 32.6 1.0 O C:HOH3504 3.3 24.1 1.0 CG C:ASP195 3.4 34.9 1.0 OD2 C:ASP245 3.4 17.6 1.0 CD C:GLU220 3.8 20.6 1.0 C C:NLQ1376 3.8 53.1 1.0 O C:NLQ1376 3.9 52.9 1.0 OD1 C:ASP195 3.9 35.4 1.0 O C:HOH3444 3.9 26.6 1.0 CE C:LYS168 4.0 26.4 1.0 CE C:LYS170 4.0 38.0 1.0 OE2 C:GLU220 4.0 23.6 1.0 NZ C:LYS170 4.0 31.1 1.0 NZ C:LYS269 4.1 23.5 1.0 OD1 C:ASN267 4.4 20.2 1.0 CB C:ASP195 4.6 32.5 1.0 CG C:ASP245 4.7 16.5 1.0 CG C:GLU220 4.9 19.8 1.0 OD2 C:ASP322 5.0 29.9 1.0

Magnesium binding site 4 out of 4 in the The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Mutant A68C-D72C-Nlq of Deinococcus Radiodurans Nacylamino Acid Racemase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4377 b:42.2 occ:1.00 OD2 D:ASP195 2.7 33.1 1.0 ND2 D:ASN197 3.1 34.2 1.0 OE1 D:GLU246 3.2 27.9 1.0 CA D:ASN197 3.4 42.6 1.0 OE1 D:GLU220 3.4 19.0 1.0 OD1 D:ASP245 3.5 20.0 1.0 CG D:ASP195 3.5 33.1 1.0 CB D:GLN221 3.6 17.6 1.0 CG D:GLU220 3.6 19.4 1.0 N D:ASN197 3.6 38.5 1.0 CD D:GLU220 3.7 19.7 1.0 CG D:ASN197 3.7 38.2 1.0 OD1 D:ASP195 3.7 35.6 1.0 CB D:ASP245 3.8 18.7 1.0 OE2 D:GLU246 4.0 26.9 1.0 CD D:GLU246 4.0 26.7 1.0 CG D:ASP245 4.1 19.4 1.0 CB D:ASN197 4.1 39.4 1.0 OD1 D:ASN197 4.3 34.1 1.0 C D:ASN197 4.4 45.3 1.0 CG D:GLN221 4.4 20.7 1.0 CB D:GLU220 4.5 18.6 1.0 O D:GLU220 4.5 19.2 1.0 OE2 D:GLU220 4.5 20.6 1.0 C D:GLU220 4.6 18.6 1.0 N D:SER198 4.7 45.1 1.0 CA D:GLN221 4.7 19.6 1.0 N D:GLN221 4.8 19.5 1.0 O D:GLN221 4.9 21.6 1.0 C D:ALA196 4.9 34.6 1.0 N D:ALA196 4.9 35.4 1.0 CB D:ASP195 5.0 31.6 1.0

W.C.Chiu, J.Y.You, J.S.Liu, S.K.Hsu, W.H.Hsu, C.H.Shih, J.K.Hwang, W.C.Wang. Structure-Stability-Activity Relationship in Covalently Cross-Linked N-Carbamoyl D-Amino Acid Amidohydrolase and N-Acylamino Acid Racemase. J.Mol.Biol. V. 359 741 2006.
ISSN: ISSN 0022-2836
PubMed: 16650857
DOI: 10.1016/J.JMB.2006.03.063