Magnesium in PDB 1xs2: 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: 1xs2 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 (°)	116.669, 116.669, 120.616, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 23.8

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 1xs2). 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: 1xs2:
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:Mg1376 b:37.7 occ:1.00 OE1 A:GLU220 2.5 29.7 1.0 NZ A:LYS168 2.7 27.0 1.0 CE A:LYS168 3.2 27.7 1.0 CD A:GLU220 3.3 29.5 1.0 OE2 A:GLU220 3.3 29.1 1.0 OD2 A:ASP195 3.3 28.1 1.0 CD A:LYS168 3.7 27.4 1.0 O A:HOH1449 4.0 39.7 1.0 ND2 A:ASN267 4.0 26.6 1.0 CH2 A:TRP294 4.0 25.8 1.0 CG A:ASP195 4.0 27.7 1.0 O A:HOH1537 4.2 37.1 1.0 OD2 A:ASP322 4.3 30.0 1.0 O A:HOH1549 4.5 35.9 1.0 CB A:ASP195 4.6 26.9 1.0 OD1 A:ASP195 4.6 27.5 1.0 CG A:GLU220 4.7 28.9 1.0 CZ3 A:TRP294 4.8 25.6 1.0 CZ2 A:TRP294 4.8 25.5 1.0 CG A:LYS168 5.0 27.4 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:Mg2376 b:41.6 occ:1.00 OE1 B:GLU220 2.7 28.3 1.0 NZ B:LYS168 2.8 28.1 1.0 CE B:LYS168 3.1 28.4 1.0 OD2 B:ASP195 3.2 27.7 1.0 OE2 B:GLU220 3.3 28.4 1.0 CD B:GLU220 3.3 29.1 1.0 CD B:LYS168 3.7 27.3 1.0 O B:HOH2408 3.8 34.5 1.0 CG B:ASP195 3.8 25.8 1.0 CH2 B:TRP294 4.1 26.5 1.0 OD1 B:ASN267 4.1 24.3 1.0 O B:HOH2404 4.2 38.7 1.0 CB B:ASP195 4.4 24.9 1.0 OD1 B:ASP195 4.4 26.0 1.0 OD2 B:ASP322 4.5 28.9 1.0 CG B:GLU220 4.8 29.0 1.0 CZ2 B:TRP294 4.8 26.3 1.0 CG B:LYS168 4.9 26.6 1.0 CZ3 B:TRP294 5.0 26.1 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:Mg3376 b:77.2 occ:1.00 OD2 C:ASP195 2.5 38.5 1.0 OE1 C:GLU220 2.7 29.7 1.0 O C:HOH3475 2.9 32.3 1.0 CD C:GLU220 3.0 29.3 1.0 NZ C:LYS168 3.0 41.5 1.0 CG C:ASP195 3.2 37.6 1.0 OE2 C:GLU220 3.3 31.9 1.0 OD1 C:ASP195 3.6 38.5 1.0 OD2 C:ASP245 3.7 35.7 1.0 CG C:GLU220 4.0 27.6 1.0 CE C:LYS168 4.0 41.6 1.0 CB C:ASP195 4.3 37.2 1.0 OD1 C:ASN267 4.4 26.9 1.0 O C:HOH3492 4.5 39.6 1.0 CD C:LYS168 4.8 40.9 1.0 CG C:ASP245 4.8 34.1 1.0 CB C:GLU220 4.9 26.6 1.0 NZ C:LYS269 5.0 34.9 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:Mg4376 b:77.2 occ:1.00 OD1 D:ASP195 2.6 41.9 1.0 OE1 D:GLU220 2.8 34.1 1.0 O D:HOH4488 2.8 41.7 1.0 CG D:ASP195 3.0 41.0 1.0 OD2 D:ASP195 3.1 41.8 1.0 CD D:GLU220 3.2 32.0 1.0 OE2 D:GLU220 3.5 33.6 1.0 OD1 D:ASP245 3.8 32.4 1.0 CG D:GLU220 4.0 30.7 1.0 CB D:ASP195 4.1 40.1 1.0 CE D:LYS168 4.3 43.4 1.0 NZ D:LYS168 4.5 44.0 1.0 ND2 D:ASN267 4.6 24.8 1.0 NZ D:LYS269 4.7 33.5 1.0 CB D:GLU220 4.8 29.8 1.0 CG D:ASP245 4.9 31.6 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