Magnesium in PDB 7cbu: Blasnase-T13A with L-Asp

The structure of Blasnase-T13A with L-Asp, PDB code: 7cbu was solved by F.Lu, T.Ran, L.Jiao, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.651, 92.651, 234.096, 90, 90, 90
R / Rfree (%)	19.6 / 21.7

The binding sites of Magnesium atom in the Blasnase-T13A with L-Asp (pdb code 7cbu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Blasnase-T13A with L-Asp, PDB code: 7cbu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Blasnase-T13A with L-Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Blasnase-T13A with L-Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:46.5 occ:1.00 OE2 B:GLU207 2.1 47.6 1.0 OD2 A:ASP218 2.2 47.1 1.0 O B:HOH563 2.2 48.2 1.0 O A:HOH621 2.3 43.8 1.0 O A:HOH536 2.6 41.0 1.0 O B:HOH629 2.6 44.1 1.0 CD B:GLU207 3.1 47.2 1.0 CG A:ASP218 3.2 41.6 1.0 HZ2 A:LYS220 3.2 43.5 1.0 HB3 A:ASP218 3.4 39.9 1.0 MG B:MG401 3.6 48.7 1.0 HG3 B:GLU207 3.8 48.5 1.0 OE1 B:GLU207 3.8 51.7 1.0 MG A:MG404 3.8 30.0 1.0 CB A:ASP218 3.9 39.9 1.0 O A:HOH591 3.9 66.9 1.0 NZ A:LYS220 4.0 43.5 1.0 CG B:GLU207 4.1 48.5 1.0 HZ1 A:LYS220 4.1 43.5 1.0 OD1 A:ASP218 4.1 41.6 1.0 HB2 A:ASP218 4.4 39.9 1.0 O B:HOH638 4.4 61.6 1.0 O B:HOH562 4.4 42.5 1.0 O2 B:FMT405 4.4 20.0 1.0 HZ3 A:LYS220 4.5 43.5 1.0 O A:HOH524 4.6 38.9 1.0 HG2 B:GLU207 4.7 48.5 1.0 HE3 A:LYS220 4.7 43.2 1.0 HB2 B:GLU207 4.8 43.9 1.0 CE A:LYS220 5.0 43.2 1.0

Magnesium binding site 2 out of 7 in the Blasnase-T13A with L-Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Blasnase-T13A with L-Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:30.0 occ:1.00 O1 A:FMT405 1.9 20.0 1.0 O A:ASN246 2.3 44.0 1.0 OD2 A:ASP250 2.3 45.8 1.0 O A:HOH602 2.4 41.0 1.0 O A:HOH569 2.8 43.9 1.0 C A:FMT405 3.0 20.0 1.0 HH12 A:ARG223 3.1 35.3 1.0 H A:FMT405 3.2 20.0 1.0 CG A:ASP250 3.4 43.0 1.0 H A:GLY219 3.4 34.8 1.0 C A:ASN246 3.4 43.0 1.0 HB3 A:ASN246 3.6 39.2 1.0 HH11 A:ARG223 3.7 35.3 1.0 HA3 A:GLY219 3.7 36.8 1.0 NH1 A:ARG223 3.7 35.3 1.0 OD1 A:ASP250 3.7 45.4 1.0 HA A:MET247 3.8 40.9 1.0 H A:ASP250 4.0 41.8 1.0 O2 A:FMT405 4.1 20.0 1.0 HA A:ASN246 4.1 40.9 1.0 N A:GLY219 4.2 34.8 1.0 CA A:ASN246 4.2 40.9 1.0 HB2 A:ASP218 4.3 39.9 1.0 N A:MET247 4.4 39.2 1.0 CB A:ASN246 4.4 39.2 1.0 CA A:GLY219 4.4 36.8 1.0 CA A:MET247 4.5 40.9 1.0 H A:GLY249 4.6 42.1 1.0 O A:HOH578 4.6 41.8 1.0 CB A:ASP250 4.7 39.8 1.0 HB2 A:ASP250 4.7 39.8 1.0 N A:ASP250 4.8 41.8 1.0 C A:MET247 4.9 41.0 1.0 HB2 A:ASN246 5.0 39.2 1.0 CZ A:ARG223 5.0 39.4 1.0

Magnesium binding site 3 out of 7 in the Blasnase-T13A with L-Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Blasnase-T13A with L-Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:30.0 occ:1.00 O B:HOH632 2.2 51.8 1.0 O B:HOH589 2.4 48.6 1.0 OE2 A:GLU207 2.4 50.4 1.0 O A:HOH620 2.5 52.9 1.0 OD2 B:ASP218 2.6 42.9 1.0 O A:HOH619 2.7 53.8 1.0 CD A:GLU207 3.3 51.5 1.0 HZ2 B:LYS220 3.4 36.2 1.0 HB3 B:ASP218 3.4 42.0 1.0 CG B:ASP218 3.5 43.4 1.0 HG3 A:GLU207 3.5 44.5 1.0 CG A:GLU207 4.0 44.5 1.0 CB B:ASP218 4.0 42.0 1.0 OE1 A:GLU207 4.1 51.9 1.0 HZ1 B:LYS220 4.1 36.2 1.0 NZ B:LYS220 4.1 36.2 1.0 O B:HOH570 4.3 47.2 1.0 O A:HOH576 4.4 45.4 1.0 O A:HOH624 4.4 46.6 1.0 OD1 B:ASP218 4.5 42.0 1.0 HB2 B:ASP218 4.5 42.0 1.0 HZ3 B:LYS220 4.5 36.2 1.0 HG2 A:GLU207 4.6 44.5 1.0 HB2 A:GLU207 4.7 43.6 1.0 CB A:GLU207 5.0 43.6 1.0

Magnesium binding site 4 out of 7 in the Blasnase-T13A with L-Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Blasnase-T13A with L-Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:30.0 occ:1.00 O A:HOH621 2.4 43.8 1.0 O B:HOH638 2.7 61.6 1.0 O B:HOH563 2.7 48.2 1.0 O B:HOH523 2.7 43.6 1.0 O B:HOH635 2.9 55.2 1.0 O A:HOH531 3.7 52.1 1.0 MG A:MG401 3.8 46.5 1.0 O B:HOH629 4.0 44.1 1.0 O2 B:FMT405 4.3 20.0 1.0 O A:HOH524 4.4 38.9 1.0 O A:HOH536 4.7 41.0 1.0 O B:HOH628 4.8 49.9 1.0 O B:HOH560 4.8 47.2 1.0 OD2 A:ASP216 4.9 37.3 1.0 OD1 A:ASP216 5.0 35.0 1.0

Magnesium binding site 5 out of 7 in the Blasnase-T13A with L-Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Blasnase-T13A with L-Asp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:48.7 occ:1.00 O A:HOH591 2.2 66.9 1.0 OE1 B:GLU207 2.3 51.7 1.0 O B:HOH629 2.6 44.1 1.0 O B:GLU228 2.6 49.3 1.0 OE2 B:GLU207 2.8 47.6 1.0 CD B:GLU207 2.9 47.2 1.0 HB3 B:GLU228 3.4 44.8 1.0 MG A:MG401 3.6 46.5 1.0 HZ2 A:LYS220 3.6 43.5 1.0 HE3 A:LYS220 3.7 43.2 1.0 C B:GLU228 3.7 47.2 1.0 HE2 A:LYS220 3.8 43.2 1.0 OD2 A:ASP218 3.9 47.1 1.0 CB B:GLU228 4.1 44.8 1.0 HB2 B:GLU228 4.1 44.8 1.0 CE A:LYS220 4.1 43.2 1.0 NZ A:LYS220 4.3 43.5 1.0 HA3 B:GLY229 4.3 45.2 1.0 CG B:GLU207 4.4 48.5 1.0 O B:HOH563 4.4 48.2 1.0 CA B:GLU228 4.5 45.9 1.0 N B:GLY229 4.7 49.1 1.0 HA B:GLU228 4.8 45.9 1.0 HG2 B:GLU207 4.8 48.5 1.0 HZ1 A:LYS220 4.8 43.5 1.0 CA B:GLY229 4.8 45.2 1.0 HZ3 A:LYS220 4.9 43.5 1.0 OE2 B:GLU228 4.9 66.7 1.0 HG3 B:GLU207 4.9 48.5 1.0 HB2 B:GLU207 4.9 43.9 1.0 O B:HOH638 5.0 61.6 1.0

Magnesium binding site 6 out of 7 in the Blasnase-T13A with L-Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Blasnase-T13A with L-Asp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:30.0 occ:1.00 O B:HOH601 2.1 59.9 1.0 O B:ASN246 2.2 45.4 1.0 OD2 B:ASP250 2.2 41.4 1.0 O1 B:FMT406 2.4 20.0 1.0 O B:HOH622 2.4 53.3 1.0 O B:HOH539 2.6 48.3 1.0 CG B:ASP250 3.3 44.9 1.0 HH12 B:ARG223 3.3 42.8 1.0 C B:FMT406 3.4 20.0 1.0 C B:ASN246 3.4 46.9 1.0 H B:FMT406 3.6 20.0 1.0 OD1 B:ASP250 3.6 46.0 1.0 H B:GLY219 3.6 46.2 1.0 HA3 B:GLY219 3.7 38.5 1.0 HA B:MET247 3.8 46.4 1.0 H B:ASP250 3.8 44.2 1.0 HB3 B:ASN246 3.8 44.5 1.0 HH11 B:ARG223 3.9 42.8 1.0 NH1 B:ARG223 3.9 42.8 1.0 O B:HOH588 4.1 47.9 1.0 HA B:ASN246 4.1 41.8 1.0 N B:GLY219 4.2 46.2 1.0 CA B:ASN246 4.3 41.8 1.0 HB2 B:ASP218 4.3 42.0 1.0 N B:MET247 4.3 45.3 1.0 O2 B:FMT406 4.4 20.0 1.0 CA B:GLY219 4.4 38.5 1.0 CA B:MET247 4.4 46.4 1.0 CB B:ASN246 4.5 44.5 1.0 H B:GLY249 4.6 44.8 1.0 CB B:ASP250 4.6 44.6 1.0 N B:ASP250 4.6 44.2 1.0 HB2 B:ASP250 4.6 44.6 1.0 C B:MET247 4.7 43.0 1.0 HA3 B:GLY249 4.9 47.9 1.0 O B:MET247 5.0 42.9 1.0

Magnesium binding site 7 out of 7 in the Blasnase-T13A with L-Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Blasnase-T13A with L-Asp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:30.0 occ:1.00 O B:ASP295 2.6 40.9 1.0 O B:HOH579 3.0 51.4 1.0 H B:ASP297 3.2 37.3 1.0 O B:HOH585 3.2 41.9 1.0 O B:HOH603 3.3 44.2 1.0 O B:HOH545 3.3 51.9 1.0 HB2 B:ASP297 3.4 37.0 1.0 O B:HOH627 3.4 46.5 1.0 N B:ASP297 3.5 37.3 1.0 O B:GLU268 3.6 39.8 1.0 HD1 B:TYR159 3.7 41.0 1.0 C B:ASP295 3.8 40.7 1.0 HB2 B:ASP295 3.9 42.1 1.0 HA B:ASP297 4.0 37.8 1.0 C B:TYR296 4.1 42.8 1.0 O B:HOH577 4.1 43.4 1.0 CA B:ASP297 4.1 37.8 1.0 CB B:ASP297 4.2 37.0 1.0 HA B:TYR296 4.2 39.8 1.0 HE1 B:TYR159 4.2 42.7 1.0 C B:GLU268 4.5 40.7 1.0 HA B:GLU268 4.5 37.5 1.0 CA B:TYR296 4.5 39.8 1.0 CD1 B:TYR159 4.5 41.0 1.0 O B:ALA267 4.6 38.0 1.0 N B:TYR296 4.6 38.9 1.0 HB3 B:ASP297 4.6 37.0 1.0 CB B:ASP295 4.7 42.1 1.0 O B:HOH600 4.7 36.9 1.0 CA B:ASP295 4.7 40.6 1.0 O B:TYR296 4.7 44.9 1.0 HA B:ASP295 4.7 40.6 1.0 HA B:GLU269 4.8 40.4 1.0 CE1 B:TYR159 4.8 42.7 1.0

T.Ran, L.Jiao, W.Wang, J.Chen, H.Chi, Z.Lu, C.Zhang, D.Xu, F.Lu. Structures of L-Asparaginase From Bacillus Licheniformis Reveal An Essential Residue For Its Substrate Stereoselectivity. J.Agric.Food Chem. V. 69 223 2021.
ISSN: ESSN 1520-5118
PubMed: 33371681
DOI: 10.1021/ACS.JAFC.0C06609