Magnesium in PDB 7c8q: Blasnase-T13A with D-Asn

The structure of Blasnase-T13A with D-Asn, PDB code: 7c8q 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)	19.89 / 1.89
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.963, 91.963, 232.666, 90, 90, 90
R / Rfree (%)	15.9 / 17.5

The binding sites of Magnesium atom in the Blasnase-T13A with D-Asn (pdb code 7c8q). 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 D-Asn, PDB code: 7c8q:
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 D-Asn


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 D-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:47.3 occ:1.00 O A:ASP295 2.4 24.0 1.0 O A:HOH562 2.8 25.7 1.0 O A:HOH659 2.8 35.3 1.0 O A:HOH716 3.1 36.0 1.0 O A:GLU268 3.2 20.0 1.0 HB2 A:ASP295 3.5 23.0 1.0 O A:HOH601 3.5 29.4 1.0 C A:ASP295 3.5 23.7 1.0 H A:ASP297 3.7 23.1 1.0 HD1 A:TYR159 3.7 26.6 1.0 O A:HOH644 3.8 31.6 1.0 N A:ASP297 3.9 23.1 1.0 HB2 A:ASP297 4.0 23.7 1.0 HA A:GLU269 4.0 20.2 1.0 HE1 A:TYR159 4.1 30.7 1.0 C A:GLU268 4.1 22.9 1.0 O A:HOH523 4.2 32.2 1.0 C A:TYR296 4.2 27.0 1.0 O A:HOH591 4.3 35.4 1.0 CB A:ASP295 4.3 23.0 1.0 HA A:TYR296 4.3 25.5 1.0 CA A:ASP295 4.3 22.6 1.0 HA A:ASP295 4.4 22.6 1.0 O A:ALA267 4.4 21.7 1.0 HA A:ASP297 4.4 21.3 1.0 N A:TYR296 4.5 22.6 1.0 CD1 A:TYR159 4.5 26.6 1.0 HA A:GLU268 4.6 22.7 1.0 CA A:TYR296 4.6 25.5 1.0 CA A:ASP297 4.6 21.3 1.0 CE1 A:TYR159 4.7 30.7 1.0 O A:TYR296 4.8 25.6 1.0 CB A:ASP297 4.8 23.7 1.0 CA A:GLU269 4.8 20.2 1.0 N A:GLU269 4.8 21.7 1.0 O A:HOH594 4.9 23.9 1.0 CA A:GLU268 5.0 22.7 1.0 CG A:ASP295 5.0 27.3 1.0

Magnesium binding site 2 out of 7 in the Blasnase-T13A with D-Asn


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 D-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:30.0 occ:1.00 O A:HOH723 2.4 31.8 1.0 O A:HOH573 2.4 25.8 1.0 OD2 A:ASP218 2.4 29.3 1.0 O B:HOH675 2.4 33.4 1.0 O B:HOH740 2.5 32.5 1.0 OE2 B:GLU207 2.5 28.3 1.0 HB3 A:ASP218 3.2 25.4 1.0 HZ2 A:LYS220 3.3 28.0 1.0 CG A:ASP218 3.3 28.5 1.0 CD B:GLU207 3.3 33.7 1.0 MG A:MG404 3.7 30.0 1.0 HG3 B:GLU207 3.7 26.9 1.0 MG B:MG404 3.8 30.0 1.0 CB A:ASP218 3.8 25.4 1.0 O A:HOH570 3.9 32.0 1.0 OE1 B:GLU207 4.0 35.8 1.0 NZ A:LYS220 4.1 28.0 1.0 HZ1 A:LYS220 4.1 28.0 1.0 CG B:GLU207 4.1 26.9 1.0 OD1 A:ASP218 4.2 26.9 1.0 HB2 A:ASP218 4.2 25.4 1.0 O B:HOH793 4.2 40.1 1.0 O B:HOH600 4.4 28.8 1.0 O A:HOH726 4.4 41.4 1.0 O A:HOH537 4.4 41.5 1.0 O A:HOH564 4.4 24.9 1.0 O1 B:FMT407 4.5 20.0 1.0 HZ3 A:LYS220 4.6 28.0 1.0 HG2 B:GLU207 4.8 26.9 1.0 O B:HOH727 4.8 45.5 1.0 O B:HOH510 4.8 31.5 1.0 HB2 B:GLU207 4.8 29.6 1.0 HE3 A:LYS220 4.9 27.2 1.0 C B:FMT407 4.9 20.0 1.0 O A:ASP216 4.9 23.8 1.0

Magnesium binding site 3 out of 7 in the Blasnase-T13A with D-Asn


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 D-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:30.0 occ:1.00 O A:HOH744 2.1 39.7 1.0 O B:HOH793 2.5 40.1 1.0 O A:HOH723 2.5 31.8 1.0 O B:HOH675 2.5 33.4 1.0 O B:HOH510 2.5 31.5 1.0 O B:HOH790 2.6 46.5 1.0 MG A:MG403 3.7 30.0 1.0 O A:HOH729 3.8 34.7 1.0 O A:HOH547 3.9 28.3 1.0 O B:HOH740 4.1 32.5 1.0 O1 B:FMT407 4.1 20.0 1.0 O B:HOH727 4.2 45.5 1.0 O B:HOH611 4.3 50.8 1.0 O A:HOH564 4.3 24.9 1.0 O A:HOH726 4.4 41.4 1.0 O A:HOH573 4.5 25.8 1.0 O B:HOH632 4.5 31.7 1.0 OD2 A:ASP216 4.6 22.7 1.0 O B:HOH714 4.8 33.4 1.0 O B:HOH770 4.9 47.9 1.0 OD1 A:ASP216 4.9 24.4 1.0

Magnesium binding site 4 out of 7 in the Blasnase-T13A with D-Asn


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 D-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:30.0 occ:1.00 O A:HOH699 2.2 36.1 1.0 O A:ASN246 2.3 27.0 1.0 O A:HOH710 2.3 37.6 1.0 OD2 A:ASP250 2.4 28.4 1.0 O1 A:FMT406 2.5 20.0 1.0 O A:HOH550 2.6 27.7 1.0 H A:FMT406 3.0 20.0 1.0 C A:FMT406 3.1 20.0 1.0 HH12 A:ARG223 3.3 25.6 1.0 C A:ASN246 3.5 27.5 1.0 H A:GLY219 3.5 21.5 1.0 CG A:ASP250 3.5 29.8 1.0 HH11 A:ARG223 3.7 25.6 1.0 HB3 A:ASN246 3.7 22.5 1.0 HA3 A:GLY219 3.7 23.9 1.0 OD1 A:ASP250 3.8 30.4 1.0 NH1 A:ARG223 3.8 25.6 1.0 HA A:MET247 3.9 21.3 1.0 O A:HOH738 4.0 43.8 1.0 H A:ASP250 4.0 24.0 1.0 HA A:ASN246 4.1 24.5 1.0 N A:GLY219 4.2 21.5 1.0 CA A:ASN246 4.3 24.5 1.0 O2 A:FMT406 4.4 20.0 1.0 O A:HOH675 4.4 45.1 1.0 O A:HOH739 4.4 53.6 1.0 HB2 A:ASP218 4.4 25.4 1.0 N A:MET247 4.4 22.6 1.0 O A:HOH611 4.4 29.2 1.0 CA A:GLY219 4.4 23.9 1.0 CB A:ASN246 4.5 22.5 1.0 CA A:MET247 4.5 21.3 1.0 O A:HOH718 4.6 41.9 1.0 H A:GLY249 4.6 26.2 1.0 O A:HOH714 4.7 48.2 1.0 HO2 A:FMT406 4.7 20.0 0.0 CB A:ASP250 4.8 23.2 1.0 HB2 A:ASP250 4.8 23.2 1.0 N A:ASP250 4.8 24.0 1.0 C A:MET247 4.9 24.1 1.0

Magnesium binding site 5 out of 7 in the Blasnase-T13A with D-Asn


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 D-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:30.0 occ:1.00 O B:HOH738 2.2 41.0 1.0 O B:ASN246 2.3 29.6 1.0 OD2 B:ASP250 2.3 30.5 1.0 O1 B:FMT405 2.4 20.0 1.0 O B:HOH726 2.5 38.4 1.0 O B:HOH559 2.5 32.0 1.0 C B:FMT405 3.2 20.0 1.0 H B:FMT405 3.2 20.0 1.0 HH12 B:ARG223 3.3 25.3 1.0 CG B:ASP250 3.4 35.4 1.0 C B:ASN246 3.5 31.7 1.0 H B:GLY219 3.5 25.4 1.0 HA3 B:GLY219 3.6 23.2 1.0 HB3 B:ASN246 3.7 28.2 1.0 OD1 B:ASP250 3.8 34.4 1.0 HH11 B:ARG223 3.8 25.3 1.0 HA B:MET247 3.9 25.9 1.0 NH1 B:ARG223 3.9 25.3 1.0 H B:ASP250 4.0 28.0 1.0 HA B:ASN246 4.1 28.2 1.0 N B:GLY219 4.1 25.4 1.0 CA B:ASN246 4.3 28.2 1.0 O2 B:FMT405 4.3 20.0 1.0 HB2 B:ASP218 4.3 29.1 1.0 CA B:GLY219 4.3 23.2 1.0 O B:HOH651 4.4 32.6 1.0 N B:MET247 4.4 29.0 1.0 CB B:ASN246 4.5 28.2 1.0 CA B:MET247 4.5 25.9 1.0 HO2 B:FMT405 4.5 20.0 0.0 O B:HOH741 4.5 45.7 1.0 O B:HOH754 4.6 46.4 1.0 CB B:ASP250 4.7 30.5 1.0 HB2 B:ASP250 4.7 30.5 1.0 O B:HOH761 4.7 48.1 1.0 H B:GLY249 4.7 28.7 1.0 N B:ASP250 4.7 28.0 1.0 C B:MET247 5.0 25.7 1.0 O B:HOH762 5.0 55.3 1.0 HA2 B:GLY219 5.0 23.2 1.0

Magnesium binding site 6 out of 7 in the Blasnase-T13A with D-Asn


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 D-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:30.0 occ:1.00 O B:HOH732 2.2 30.0 1.0 O B:HOH717 2.2 30.0 1.0 O B:HOH579 2.4 30.0 1.0 O B:ASP295 2.7 26.7 1.0 O B:GLU268 2.9 22.2 1.0 O B:HOH689 3.0 30.0 1.0 HB2 B:ASP295 3.1 26.0 1.0 HA B:GLU269 3.4 23.1 1.0 O B:HOH618 3.7 30.9 1.0 C B:GLU268 3.7 24.7 1.0 C B:ASP295 3.8 27.6 1.0 HD1 B:TYR159 4.0 27.2 1.0 O B:HOH608 4.0 31.4 1.0 CB B:ASP295 4.0 26.0 1.0 O B:ALA267 4.2 24.6 1.0 HA B:ASP295 4.2 26.0 1.0 CA B:GLU269 4.2 23.1 1.0 HE1 B:TYR159 4.2 26.5 1.0 H B:ASP297 4.2 23.8 1.0 CA B:ASP295 4.3 26.0 1.0 N B:GLU269 4.3 22.8 1.0 O B:HOH648 4.4 31.0 1.0 HA B:GLU268 4.4 20.9 1.0 N B:ASP297 4.5 23.8 1.0 H B:GLY270 4.5 24.0 1.0 O B:HOH514 4.5 36.3 1.0 O B:GLY270 4.5 23.7 1.0 HB2 B:ASP297 4.7 21.1 1.0 HB3 B:ASP295 4.7 26.0 1.0 C B:GLU269 4.7 22.4 1.0 CA B:GLU268 4.7 20.9 1.0 CD1 B:TYR159 4.7 27.2 1.0 C B:TYR296 4.8 29.2 1.0 N B:GLY270 4.8 24.0 1.0 CG B:ASP295 4.8 28.8 1.0 N B:TYR296 4.8 24.3 1.0 CE1 B:TYR159 4.8 26.5 1.0 HA B:TYR296 4.9 26.9 1.0 HA B:ASP297 4.9 22.9 1.0

Magnesium binding site 7 out of 7 in the Blasnase-T13A with D-Asn


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 D-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:30.0 occ:1.00 O B:GLU228 2.4 36.5 1.0 O A:HOH570 2.4 32.0 1.0 O B:HOH701 2.5 47.2 1.0 O B:HOH740 2.5 32.5 1.0 OE1 B:GLU207 2.6 35.8 1.0 OE2 B:GLU207 2.7 28.3 1.0 CD B:GLU207 3.0 33.7 1.0 HB3 B:GLU228 3.3 32.4 1.0 C B:GLU228 3.6 34.0 1.0 HE3 A:LYS220 3.6 27.2 1.0 HZ2 A:LYS220 3.7 28.0 1.0 MG A:MG403 3.8 30.0 1.0 HE2 A:LYS220 3.9 27.2 1.0 CB B:GLU228 4.0 32.4 1.0 OD2 A:ASP218 4.0 29.3 1.0 HB2 B:GLU228 4.1 32.4 1.0 HA3 B:GLY229 4.1 33.8 1.0 CE A:LYS220 4.1 27.2 1.0 O B:HOH700 4.2 43.0 1.0 O A:HOH537 4.2 41.5 1.0 NZ A:LYS220 4.3 28.0 1.0 CA B:GLU228 4.4 31.0 1.0 O B:HOH541 4.4 41.4 1.0 O B:HOH727 4.4 45.5 1.0 O B:HOH763 4.5 50.3 1.0 O B:HOH675 4.5 33.4 1.0 N B:GLY229 4.5 29.4 1.0 CG B:GLU207 4.5 26.9 1.0 HA B:GLU228 4.6 31.0 1.0 CA B:GLY229 4.6 33.8 1.0 HZ1 A:LYS220 4.8 28.0 1.0 HG2 B:GLU207 4.9 26.9 1.0 HG3 B:GLU207 5.0 26.9 1.0 HZ3 A:LYS220 5.0 28.0 1.0 C B:GLY229 5.0 31.4 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