Magnesium in PDB 1xpy: Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans

The structure of Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans, PDB code: 1xpy was solved by W.-C.Wang, W.-C.Chiu, S.-K.Hsu, C.-L.Wu, C.-Y.Chen, J.-S.Liu, W.-H.Hsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	116.159, 116.159, 120.426, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 22.7

The binding sites of Magnesium atom in the Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans (pdb code 1xpy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans, PDB code: 1xpy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1377 b:29.5 occ:1.00 OE1 A:GLU220 2.6 20.9 1.0 CE A:LYS168 3.0 28.1 1.0 OE2 A:GLU220 3.1 22.9 1.0 CD A:GLU220 3.1 20.7 1.0 OD2 A:ASP195 3.2 22.4 1.0 CG A:ASP195 3.8 20.7 1.0 NZ A:LYS168 3.8 29.7 1.0 ND2 A:ASN267 4.1 11.8 1.0 CD A:LYS168 4.1 26.5 1.0 CH2 A:TRP294 4.1 19.4 1.0 CB A:ASP195 4.3 20.1 1.0 OD2 A:ASP322 4.5 22.9 1.0 CG A:GLU220 4.5 20.1 1.0 OD1 A:ASP195 4.5 20.9 1.0 CZ3 A:TRP294 4.9 19.5 1.0 CZ2 A:TRP294 5.0 19.3 1.0 OD1 A:ASP245 5.0 18.7 1.0

Magnesium binding site 2 out of 4 in the Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2377 b:38.3 occ:1.00 NZ B:LYS168 2.6 27.0 1.0 OE1 B:GLU220 2.8 23.0 1.0 OE2 B:GLU220 3.0 23.5 1.0 CE B:LYS168 3.1 25.4 1.0 OD2 B:ASP195 3.1 20.3 1.0 CD B:GLU220 3.2 21.9 1.0 CD B:LYS168 3.6 23.9 1.0 CG B:ASP195 3.7 20.1 1.0 O B:HOH2570 3.8 38.1 1.0 O B:HOH2564 4.0 41.9 1.0 CB B:ASP195 4.1 19.1 1.0 O B:HOH2419 4.2 37.9 1.0 CH2 B:TRP294 4.2 18.5 1.0 OD1 B:ASN267 4.3 20.3 1.0 OD2 B:ASP322 4.5 24.3 1.0 OD1 B:ASP195 4.5 19.6 1.0 CG B:GLU220 4.6 21.0 1.0 O B:HOH2474 4.7 31.5 1.0 NZ B:LYS170 4.8 31.2 1.0 CG B:LYS168 4.8 22.2 1.0

Magnesium binding site 3 out of 4 in the Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3377 b:44.9 occ:1.00 OD2 C:ASP195 2.5 32.0 1.0 O C:NLQ3376 2.6 30.5 1.0 NZ C:LYS170 3.1 42.6 1.0 C C:NLQ3376 3.2 32.2 1.0 OD2 C:ASP245 3.2 17.4 1.0 OE1 C:GLU220 3.2 22.3 1.0 OXT C:NLQ3376 3.2 32.3 1.0 O C:HOH3389 3.3 33.1 1.0 CG C:ASP195 3.5 32.2 1.0 NZ C:LYS168 3.7 30.0 1.0 OD1 C:ASP195 3.8 31.4 1.0 OD1 C:ASN197 3.8 40.1 1.0 NZ C:LYS269 3.8 16.6 1.0 CD C:GLU220 4.0 20.9 1.0 O4 C:NLQ3376 4.0 33.0 1.0 C6 C:NLQ3376 4.1 32.3 1.0 O C:HOH3378 4.2 20.5 1.0 CE C:LYS168 4.3 30.4 1.0 CG C:ASP245 4.4 18.0 1.0 OE2 C:GLU220 4.4 20.9 1.0 CA C:NLQ3376 4.5 32.4 1.0 CE C:LYS170 4.5 42.7 1.0 OD1 C:ASN267 4.7 18.9 1.0 CG C:ASN197 4.7 41.8 1.0 CE C:LYS269 4.7 16.6 1.0 N C:NLQ3376 4.8 32.7 1.0 CB C:ASP195 4.9 32.3 1.0 CG C:GLU220 4.9 21.3 1.0 CE2 C:TYR62 5.0 21.2 1.0

Magnesium binding site 4 out of 4 in the Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4377 b:45.1 occ:1.00 OD1 D:ASP195 2.4 29.0 1.0 O D:NLQ4376 2.8 30.5 1.0 NZ D:LYS170 2.9 39.9 1.0 OD1 D:ASN197 3.0 30.8 1.0 OXT D:NLQ4376 3.1 33.1 1.0 C D:NLQ4376 3.2 32.3 1.0 O D:HOH4460 3.2 27.2 1.0 CG D:ASP195 3.4 28.6 1.0 OE1 D:GLU220 3.4 21.4 1.0 OD1 D:ASP245 3.5 18.6 1.0 OD2 D:ASP195 3.5 29.1 1.0 ND2 D:ASN197 3.6 28.5 1.0 CG D:ASN197 3.6 31.6 1.0 O4 D:NLQ4376 3.8 34.6 1.0 NZ D:LYS168 3.9 31.2 1.0 NZ D:LYS269 3.9 17.0 1.0 CD D:GLU220 4.1 20.6 1.0 C6 D:NLQ4376 4.2 34.2 1.0 CE D:LYS168 4.4 31.5 1.0 O D:HOH4445 4.4 22.8 1.0 CE D:LYS170 4.4 40.4 1.0 CA D:NLQ4376 4.4 33.0 1.0 OE2 D:GLU220 4.6 21.4 1.0 CB D:ASP195 4.7 28.2 1.0 CG D:ASP245 4.8 18.9 1.0 N D:NLQ4376 4.8 34.0 1.0 ND2 D:ASN267 4.9 15.2 1.0 CE D:LYS269 5.0 17.6 1.0

W.-C.Wang, W.-C.Chiu, S.-K.Hsu, C.-L.Wu, C.-Y.Chen, J.-S.Liu, W.-H.Hsu. Structural Basis For Catalytic Racemization and Substrate Specificity of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans J.Mol.Biol. V. 342 155 2004.
ISSN: ISSN 0022-2836
PubMed: 15313614
DOI: 10.1016/J.JMB.2004.07.023