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

The structure of Blasnase-T13A with D-Asn, PDB code: 7cbw 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)	49.03 / 1.98
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.94, 91.94, 231.516, 90, 90, 90
R / Rfree (%)	16.7 / 18.7

The binding sites of Magnesium atom in the Blasnase-T13A with D-Asn (pdb code 7cbw). 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: 7cbw:
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:Mg403 b:46.2 occ:1.00 O A:HOH673 2.1 44.4 1.0 O A:ASP295 2.4 25.2 1.0 O A:HOH559 2.5 25.8 1.0 O A:HOH687 2.7 38.3 1.0 O A:HOH606 2.7 39.9 1.0 O A:GLU268 3.0 24.2 1.0 HB2 A:ASP295 3.2 28.3 1.0 C A:ASP295 3.5 28.0 1.0 O A:HOH629 3.6 32.5 1.0 HA A:GLU269 3.6 24.9 1.0 C A:GLU268 3.8 27.2 1.0 HD1 A:TYR159 3.9 28.2 1.0 H A:ASP297 4.0 26.0 1.0 CB A:ASP295 4.0 28.3 1.0 O A:HOH621 4.1 34.4 1.0 HE1 A:TYR159 4.1 27.5 1.0 HA A:ASP295 4.2 25.1 1.0 O A:ALA267 4.2 25.2 1.0 CA A:ASP295 4.2 25.1 1.0 O A:HOH528 4.2 32.5 1.0 N A:ASP297 4.2 26.0 1.0 CA A:GLU269 4.4 24.9 1.0 HA A:GLU268 4.4 23.6 1.0 C A:TYR296 4.4 28.0 1.0 HB2 A:ASP297 4.5 25.5 1.0 N A:GLU269 4.5 26.0 1.0 O A:HOH623 4.5 35.4 1.0 HA A:TYR296 4.6 27.4 1.0 N A:TYR296 4.6 25.7 1.0 CD1 A:TYR159 4.7 28.2 1.0 HA A:ASP297 4.7 27.1 1.0 O A:GLY270 4.7 23.2 1.0 HB3 A:ASP295 4.7 28.3 1.0 CE1 A:TYR159 4.8 27.5 1.0 CA A:GLU268 4.8 23.6 1.0 CG A:ASP295 4.8 29.0 1.0 CA A:TYR296 4.8 27.4 1.0 H A:GLY270 4.9 23.7 1.0 C A:GLU269 4.9 21.9 1.0 O A:TYR296 4.9 29.3 1.0 CA A:ASP297 4.9 27.1 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:Mg404 b:38.5 occ:1.00 O B:HOH669 2.3 37.9 1.0 O A:HOH589 2.4 28.9 1.0 OE2 B:GLU207 2.4 35.2 1.0 OD2 A:ASP218 2.5 31.0 1.0 O B:HOH719 2.5 35.5 1.0 O A:HOH696 2.6 34.5 1.0 CD B:GLU207 3.3 35.3 1.0 HZ2 A:LYS220 3.3 31.4 1.0 HB3 A:ASP218 3.3 28.9 1.0 CG A:ASP218 3.4 30.4 1.0 MG A:MG405 3.6 46.8 1.0 MG B:MG407 3.7 39.1 1.0 HG3 B:GLU207 3.7 31.6 1.0 H B:FMT404 3.8 43.0 1.0 CB A:ASP218 3.9 28.9 1.0 OE1 B:GLU207 3.9 41.3 1.0 O A:HOH610 4.0 36.1 1.0 NZ A:LYS220 4.1 31.4 1.0 CG B:GLU207 4.1 31.6 1.0 HZ1 A:LYS220 4.1 31.4 1.0 O B:HOH594 4.2 32.0 1.0 O B:HOH752 4.3 49.6 1.0 OD1 A:ASP218 4.3 27.9 1.0 HB2 A:ASP218 4.4 28.9 1.0 O A:HOH591 4.4 27.3 1.0 C B:FMT404 4.5 43.0 1.0 O A:HOH553 4.5 44.3 1.0 HZ3 A:LYS220 4.5 31.4 1.0 O2 B:FMT404 4.6 35.2 1.0 HB2 B:GLU207 4.7 33.4 1.0 O B:HOH528 4.7 33.6 1.0 HG2 B:GLU207 4.7 31.6 1.0 O B:HOH702 4.8 52.6 1.0 HE3 A:LYS220 4.9 28.8 1.0 O A:ASP216 4.9 26.8 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:Mg405 b:46.8 occ:1.00 O B:HOH528 2.4 33.6 1.0 O B:HOH669 2.5 37.9 1.0 O B:HOH752 2.6 49.6 1.0 O A:HOH696 2.6 34.5 1.0 O B:HOH750 2.6 51.2 1.0 MG A:MG404 3.6 38.5 1.0 O A:HOH590 3.9 32.2 1.0 O A:HOH699 3.9 41.7 1.0 O B:HOH719 4.0 35.5 1.0 O2 B:FMT404 4.1 35.2 1.0 O B:HOH702 4.1 52.6 1.0 O A:HOH591 4.3 27.3 1.0 O B:HOH616 4.5 34.7 1.0 O A:HOH589 4.5 28.9 1.0 H B:FMT404 4.7 43.0 1.0 OD2 A:ASP216 4.7 27.6 1.0 O A:HOH680 4.7 39.8 1.0 C B:FMT404 4.9 43.0 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:Mg406 b:38.0 occ:1.00 O A:HOH675 2.2 42.6 1.0 O A:ASN246 2.3 31.7 1.0 O1 A:FMT402 2.3 31.0 1.0 O A:HOH679 2.3 43.0 1.0 OD2 A:ASP250 2.3 33.1 1.0 O A:HOH560 2.6 30.7 1.0 HH12 A:ARG223 3.2 27.6 1.0 C A:FMT402 3.2 34.5 1.0 H A:FMT402 3.3 34.5 1.0 H A:GLY219 3.3 26.7 1.0 CG A:ASP250 3.3 34.0 1.0 C A:ASN246 3.5 33.8 1.0 HA3 A:GLY219 3.6 29.0 1.0 HH11 A:ARG223 3.7 27.6 1.0 OD1 A:ASP250 3.7 32.1 1.0 HB3 A:ASN246 3.7 25.4 1.0 NH1 A:ARG223 3.7 27.6 1.0 HA A:MET247 3.9 27.9 1.0 H A:ASP250 4.0 30.8 1.0 N A:GLY219 4.1 26.7 1.0 HA A:ASN246 4.2 30.2 1.0 O2 A:FMT402 4.2 41.0 1.0 HB2 A:ASP218 4.2 28.9 1.0 CA A:GLY219 4.3 29.0 1.0 CA A:ASN246 4.3 30.2 1.0 O A:HOH704 4.4 49.2 1.0 N A:MET247 4.5 27.9 1.0 CB A:ASN246 4.5 25.4 1.0 O A:HOH689 4.5 47.0 1.0 CA A:MET247 4.6 27.9 1.0 O A:HOH619 4.6 31.0 1.0 O A:HOH690 4.6 46.0 1.0 CB A:ASP250 4.7 26.6 1.0 H A:GLY249 4.7 29.1 1.0 HB2 A:ASP250 4.7 26.6 1.0 N A:ASP250 4.8 30.8 1.0 C A:MET247 4.9 29.4 1.0 HA2 A:GLY219 5.0 29.0 1.0 CZ A:ARG223 5.0 32.2 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:Mg405 b:42.0 occ:1.00 O B:ASN246 2.3 34.2 1.0 OD2 B:ASP250 2.3 34.9 1.0 O B:HOH717 2.4 47.4 1.0 O1 B:FMT402 2.4 38.0 1.0 O B:HOH633 2.6 37.9 1.0 C B:FMT402 3.3 41.8 1.0 HH12 B:ARG223 3.3 33.6 1.0 CG B:ASP250 3.3 37.9 1.0 H B:GLY219 3.4 30.7 1.0 H B:FMT402 3.5 41.8 1.0 C B:ASN246 3.5 35.3 1.0 HA3 B:GLY219 3.6 28.4 1.0 OD1 B:ASP250 3.8 35.6 1.0 HB3 B:ASN246 3.8 29.9 1.0 HH11 B:ARG223 3.8 33.6 1.0 HA B:MET247 3.9 31.6 1.0 NH1 B:ARG223 3.9 33.6 1.0 H B:ASP250 3.9 31.7 1.0 N B:GLY219 4.1 30.7 1.0 HA B:ASN246 4.2 30.6 1.0 HB2 B:ASP218 4.3 31.7 1.0 CA B:ASN246 4.3 30.6 1.0 O2 B:FMT402 4.3 46.7 1.0 CA B:GLY219 4.3 28.4 1.0 O B:HOH632 4.4 33.5 1.0 N B:MET247 4.4 32.9 1.0 CB B:ASN246 4.5 29.9 1.0 CA B:MET247 4.5 31.6 1.0 O B:HOH722 4.5 47.6 1.0 CB B:ASP250 4.6 32.8 1.0 HB2 B:ASP250 4.6 32.8 1.0 O B:HOH729 4.6 51.4 1.0 N B:ASP250 4.7 31.7 1.0 H B:GLY249 4.8 33.6 1.0 C B:MET247 4.9 31.4 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:Mg406 b:49.4 occ:1.00 O B:ASP295 2.4 27.8 1.0 O B:HOH587 2.6 40.8 1.0 O B:HOH707 2.8 38.4 1.0 O B:HOH568 3.0 29.2 1.0 O B:GLU268 3.3 25.7 1.0 O B:HOH625 3.4 32.5 1.0 O B:HOH629 3.4 33.8 1.0 H B:ASP297 3.5 26.5 1.0 HB2 B:ASP295 3.5 27.6 1.0 C B:ASP295 3.6 29.5 1.0 HD1 B:TYR159 3.7 30.8 1.0 N B:ASP297 3.8 26.5 1.0 HB2 B:ASP297 3.9 25.1 1.0 O B:HOH544 4.1 37.5 1.0 O B:HOH637 4.1 34.1 1.0 HE1 B:TYR159 4.1 29.1 1.0 C B:TYR296 4.2 31.5 1.0 C B:GLU268 4.2 26.9 1.0 HA B:GLU269 4.2 30.0 1.0 HA B:ASP297 4.2 29.0 1.0 HA B:TYR296 4.3 28.8 1.0 CB B:ASP295 4.3 27.6 1.0 O B:ALA267 4.4 25.0 1.0 CA B:ASP295 4.4 27.9 1.0 HA B:ASP295 4.4 27.9 1.0 CA B:ASP297 4.5 29.0 1.0 CD1 B:TYR159 4.5 30.8 1.0 N B:TYR296 4.5 27.9 1.0 HA B:GLU268 4.5 25.4 1.0 CA B:TYR296 4.6 28.8 1.0 CB B:ASP297 4.6 25.1 1.0 CE1 B:TYR159 4.7 29.1 1.0 O B:TYR296 4.7 31.2 1.0 O B:HOH613 4.9 38.6 1.0 O B:HOH640 4.9 26.1 1.0 N B:GLU269 4.9 26.3 1.0 CA B:GLU268 5.0 25.4 1.0 CA B:GLU269 5.0 30.0 1.0 CG B:ASP295 5.0 31.2 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:Mg407 b:39.1 occ:1.00 O A:HOH610 2.4 36.1 1.0 O B:HOH719 2.5 35.5 1.0 OE1 B:GLU207 2.5 41.3 1.0 O B:GLU228 2.5 40.9 1.0 OE2 B:GLU207 2.6 35.2 1.0 CD B:GLU207 2.9 35.3 1.0 HB3 B:GLU228 3.3 33.0 1.0 HZ2 A:LYS220 3.5 31.4 1.0 HE3 A:LYS220 3.6 28.8 1.0 C B:GLU228 3.7 35.1 1.0 MG A:MG404 3.7 38.5 1.0 HE2 A:LYS220 3.8 28.8 1.0 HB2 B:GLU228 4.0 33.0 1.0 OD2 A:ASP218 4.0 31.0 1.0 CB B:GLU228 4.0 33.0 1.0 CE A:LYS220 4.1 28.8 1.0 O A:HOH553 4.2 44.3 1.0 HA3 B:GLY229 4.2 34.9 1.0 NZ A:LYS220 4.2 31.4 1.0 O B:HOH533 4.3 42.4 1.0 O B:HOH702 4.4 52.6 1.0 O B:HOH675 4.4 51.0 1.0 CG B:GLU207 4.4 31.6 1.0 CA B:GLU228 4.4 34.1 1.0 O B:HOH669 4.4 37.9 1.0 N B:GLY229 4.6 32.6 1.0 HZ1 A:LYS220 4.7 31.4 1.0 HA B:GLU228 4.7 34.1 1.0 CA B:GLY229 4.7 34.9 1.0 HG2 B:GLU207 4.8 31.6 1.0 HZ3 A:LYS220 4.9 31.4 1.0 HG3 B:GLU207 4.9 31.6 1.0 HB2 B:GLU207 4.9 33.4 1.0 C B:GLY229 4.9 39.2 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