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

The structure of Blasnase-T13A with D-Asn, PDB code: 7cbr 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)	19.95 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.311, 92.311, 232.11, 90, 90, 90
R / Rfree (%)	16.9 / 18.2

The binding sites of Magnesium atom in the Blasnase-T13A with D-Asn (pdb code 7cbr). 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: 7cbr:
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:26.9 occ:1.00 O A:ASP295 2.4 22.1 1.0 O A:HOH536 2.5 24.3 1.0 O A:HOH702 2.7 35.4 1.0 O A:HOH628 2.9 36.6 1.0 O A:GLU268 3.0 22.0 1.0 HB2 A:ASP295 3.1 25.0 1.0 HO2 A:FMT406 3.2 24.8 0.0 C A:ASP295 3.5 24.1 1.0 HA A:GLU269 3.6 18.4 1.0 O A:HOH618 3.7 30.4 1.0 O2 A:FMT406 3.8 24.8 1.0 HD1 A:TYR159 3.8 25.5 1.0 C A:GLU268 3.9 23.8 1.0 CB A:ASP295 4.0 25.0 1.0 HE1 A:TYR159 4.0 26.9 1.0 H A:ASP297 4.1 23.5 1.0 CA A:ASP295 4.2 21.3 1.0 HA A:ASP295 4.2 21.3 1.0 O A:HOH521 4.2 32.3 1.0 O A:ALA267 4.3 21.9 1.0 N A:ASP297 4.3 23.5 1.0 CA A:GLU269 4.4 18.4 1.0 C A:TYR296 4.5 25.7 1.0 N A:GLU269 4.5 20.6 1.0 CD1 A:TYR159 4.5 25.5 1.0 HA A:TYR296 4.5 23.3 1.0 HA A:GLU268 4.6 22.3 1.0 N A:TYR296 4.6 22.6 1.0 HB2 A:ASP297 4.6 22.9 1.0 CE1 A:TYR159 4.6 26.9 1.0 HB3 A:ASP295 4.7 25.0 1.0 CG A:ASP295 4.7 26.9 1.0 O A:GLY270 4.7 22.5 1.0 O A:HOH550 4.7 35.1 1.0 H A:GLY270 4.7 22.0 1.0 C A:FMT406 4.7 24.6 1.0 CA A:TYR296 4.8 23.3 1.0 HA A:ASP297 4.8 21.9 1.0 C A:GLU269 4.9 19.6 1.0 CA A:GLU268 4.9 22.3 1.0 O A:TYR296 5.0 26.2 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:30.5 occ:1.00 O A:HOH683 2.3 39.1 1.0 O1 A:FMT407 2.3 29.3 1.0 O A:ASN246 2.3 27.4 1.0 O A:HOH695 2.4 36.4 1.0 OD2 A:ASP250 2.4 31.4 1.0 O A:HOH570 2.5 26.8 1.0 C A:FMT407 3.1 29.6 1.0 HH12 A:ARG223 3.2 27.8 1.0 H A:FMT407 3.2 29.6 1.0 H A:GLY219 3.4 23.4 1.0 CG A:ASP250 3.4 32.4 1.0 C A:ASN246 3.5 30.5 1.0 HA3 A:GLY219 3.7 26.9 1.0 HH11 A:ARG223 3.7 27.8 1.0 HB3 A:ASN246 3.8 24.1 1.0 NH1 A:ARG223 3.8 27.8 1.0 OD1 A:ASP250 3.8 31.1 1.0 HA A:MET247 3.9 22.5 1.0 H A:ASP250 4.1 26.2 1.0 N A:GLY219 4.1 23.4 1.0 HA A:ASN246 4.2 25.6 1.0 O2 A:FMT407 4.2 30.9 1.0 O A:HOH723 4.3 47.3 1.0 HB2 A:ASP218 4.3 26.8 1.0 CA A:ASN246 4.3 25.6 1.0 HO2 A:FMT407 4.3 30.9 0.0 CA A:GLY219 4.4 26.9 1.0 O A:HOH594 4.4 28.1 1.0 N A:MET247 4.5 22.9 1.0 O A:HOH641 4.5 45.1 1.0 CB A:ASN246 4.5 24.1 1.0 O A:HOH700 4.5 41.5 1.0 CA A:MET247 4.6 22.5 1.0 H A:GLY249 4.7 26.3 1.0 CB A:ASP250 4.7 25.5 1.0 HB2 A:ASP250 4.7 25.5 1.0 N A:ASP250 4.8 26.2 1.0 C A:MET247 4.9 24.5 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:31.2 occ:1.00 O B:HOH713 2.3 34.3 1.0 O A:HOH565 2.4 24.2 1.0 OE2 B:GLU207 2.4 29.3 1.0 OD2 A:ASP218 2.5 31.2 1.0 O A:HOH707 2.6 31.3 1.0 O B:HOH723 2.6 51.5 1.0 CD B:GLU207 3.2 34.5 1.0 HZ2 A:LYS220 3.3 28.0 1.0 HB3 A:ASP218 3.4 26.8 1.0 CG A:ASP218 3.4 30.0 1.0 HG3 B:GLU207 3.6 28.9 1.0 MG A:MG405 3.6 35.4 1.0 MG B:MG404 3.7 35.7 1.0 CB A:ASP218 3.9 26.8 1.0 OE1 B:GLU207 3.9 38.7 1.0 CG B:GLU207 4.0 28.9 1.0 O A:HOH588 4.0 34.7 1.0 NZ A:LYS220 4.1 28.0 1.0 HZ1 A:LYS220 4.1 28.0 1.0 OD1 A:ASP218 4.3 27.5 1.0 O B:HOH593 4.3 30.1 1.0 HB2 A:ASP218 4.4 26.8 1.0 O B:HOH777 4.4 41.0 1.0 O A:HOH715 4.4 32.6 1.0 O A:HOH572 4.4 23.1 1.0 HZ3 A:LYS220 4.5 28.0 1.0 O A:HOH583 4.6 37.7 1.0 HB2 B:GLU207 4.7 28.9 1.0 HG2 B:GLU207 4.7 28.9 1.0 O A:HOH544 4.8 31.4 1.0 O A:ASP216 4.9 24.8 1.0 HE3 A:LYS220 4.9 27.6 1.0 O B:HOH712 4.9 46.2 1.0 CB B:GLU207 5.0 28.9 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:35.4 occ:1.00 O A:HOH724 2.3 42.3 1.0 O B:HOH777 2.4 41.0 1.0 O B:HOH713 2.4 34.3 1.0 O A:HOH544 2.5 31.4 1.0 O B:HOH776 2.6 44.4 1.0 O A:HOH707 2.6 31.3 1.0 MG A:MG404 3.6 31.2 1.0 O B:HOH747 4.0 34.7 1.0 O B:HOH723 4.0 51.5 1.0 O A:HOH715 4.0 32.6 1.0 O A:HOH566 4.1 29.8 1.0 O B:HOH712 4.2 46.2 1.0 O A:HOH572 4.4 23.1 1.0 O B:HOH633 4.4 31.7 1.0 O A:HOH565 4.5 24.2 1.0 OD2 A:ASP216 4.8 24.5 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:33.6 occ:1.00 O B:ASP295 2.3 25.4 1.0 O B:HOH581 2.6 27.3 1.0 O B:HOH611 2.7 38.7 1.0 O B:HOH731 2.8 37.3 1.0 O B:GLU268 3.1 22.9 1.0 HB2 B:ASP295 3.2 26.7 1.0 C B:ASP295 3.5 28.2 1.0 O B:HOH585 3.6 32.4 1.0 H B:FMT405 3.7 25.7 1.0 HA B:GLU269 3.8 22.8 1.0 HD1 B:TYR159 3.8 27.8 1.0 H B:ASP297 3.9 23.9 1.0 C B:GLU268 4.0 26.0 1.0 CB B:ASP295 4.0 26.7 1.0 HE1 B:TYR159 4.1 29.4 1.0 O1 B:FMT405 4.1 24.8 1.0 N B:ASP297 4.1 23.9 1.0 O B:HOH603 4.1 34.4 1.0 CA B:ASP295 4.2 24.2 1.0 HA B:ASP295 4.2 24.2 1.0 O B:ALA267 4.3 23.6 1.0 C B:FMT405 4.3 25.7 1.0 O B:HOH547 4.3 35.3 1.0 HB2 B:ASP297 4.3 22.3 1.0 C B:TYR296 4.3 29.8 1.0 HA B:TYR296 4.5 26.9 1.0 N B:TYR296 4.5 25.9 1.0 HA B:GLU268 4.5 23.7 1.0 CD1 B:TYR159 4.6 27.8 1.0 HA B:ASP297 4.6 22.6 1.0 CA B:GLU269 4.6 22.8 1.0 N B:GLU269 4.6 22.4 1.0 CE1 B:TYR159 4.7 29.4 1.0 CA B:TYR296 4.7 26.9 1.0 CG B:ASP295 4.7 28.4 1.0 HB3 B:ASP295 4.8 26.7 1.0 O B:GLY270 4.8 22.8 1.0 CA B:ASP297 4.8 22.6 1.0 O B:TYR296 4.8 30.1 1.0 CA B:GLU268 4.9 23.7 1.0 H B:GLY270 5.0 22.4 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:Mg403 b:37.2 occ:1.00 O B:ASN246 2.3 31.6 1.0 OD2 B:ASP250 2.3 34.2 1.0 O1 B:FMT406 2.4 34.4 1.0 O B:HOH725 2.4 41.0 1.0 O B:HOH715 2.5 51.7 1.0 O B:HOH580 2.6 36.0 1.0 O B:HOH738 2.8 72.6 1.0 C B:FMT406 3.3 34.6 1.0 HH12 B:ARG223 3.3 26.1 1.0 CG B:ASP250 3.3 35.8 1.0 H B:FMT406 3.4 34.6 1.0 H B:GLY219 3.5 27.3 1.0 C B:ASN246 3.5 34.9 1.0 HA3 B:GLY219 3.6 24.2 1.0 OD1 B:ASP250 3.7 33.3 1.0 HH11 B:ARG223 3.7 26.1 1.0 HB3 B:ASN246 3.8 29.1 1.0 NH1 B:ARG223 3.8 26.1 1.0 HA B:MET247 3.9 27.8 1.0 H B:ASP250 3.9 29.4 1.0 N B:GLY219 4.1 27.3 1.0 HA B:ASN246 4.2 27.7 1.0 O2 B:FMT406 4.3 35.9 1.0 HB2 B:ASP218 4.3 30.0 1.0 CA B:GLY219 4.3 24.2 1.0 CA B:ASN246 4.4 27.7 1.0 HO2 B:FMT406 4.4 35.9 0.0 N B:MET247 4.5 29.6 1.0 O B:HOH733 4.5 43.1 1.0 O B:HOH604 4.5 31.3 1.0 CA B:MET247 4.5 27.8 1.0 CB B:ASN246 4.6 29.1 1.0 O B:HOH752 4.6 52.2 1.0 CB B:ASP250 4.6 30.0 1.0 HB2 B:ASP250 4.7 30.0 1.0 N B:ASP250 4.7 29.4 1.0 O B:HOH745 4.7 49.5 1.0 H B:GLY249 4.7 32.1 1.0 C B:MET247 4.9 28.1 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:35.7 occ:1.00 OE1 B:GLU207 2.4 38.7 1.0 O B:HOH723 2.5 51.5 1.0 OE2 B:GLU207 2.5 29.3 1.0 O B:GLU228 2.5 37.4 1.0 O A:HOH588 2.6 34.7 1.0 O B:HOH705 2.7 44.3 1.0 CD B:GLU207 2.8 34.5 1.0 HB3 B:GLU228 3.4 31.9 1.0 HZ2 A:LYS220 3.6 28.0 1.0 HE3 A:LYS220 3.7 27.6 1.0 MG A:MG404 3.7 31.2 1.0 C B:GLU228 3.7 34.6 1.0 HE2 A:LYS220 3.8 27.6 1.0 OD2 A:ASP218 4.1 31.2 1.0 HA3 B:GLY229 4.1 32.7 1.0 CE A:LYS220 4.1 27.6 1.0 CB B:GLU228 4.2 31.9 1.0 HB2 B:GLU228 4.2 31.9 1.0 O B:HOH582 4.2 43.8 1.0 O A:HOH583 4.2 37.7 1.0 NZ A:LYS220 4.3 28.0 1.0 CG B:GLU207 4.3 28.9 1.0 O B:HOH713 4.4 34.3 1.0 O B:HOH710 4.4 54.5 1.0 O B:HOH712 4.5 46.2 1.0 CA B:GLU228 4.5 30.2 1.0 N B:GLY229 4.6 29.9 1.0 O B:HOH572 4.6 46.7 1.0 CA B:GLY229 4.7 32.7 1.0 HG2 B:GLU207 4.7 28.9 1.0 HZ1 A:LYS220 4.8 28.0 1.0 HG3 B:GLU207 4.8 28.9 1.0 HA B:GLU228 4.8 30.2 1.0 HB2 B:GLU207 4.8 28.9 1.0 C B:GLY229 4.9 31.9 1.0 HZ3 A:LYS220 4.9 28.0 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