Magnesium in PDB 7c91: Blasnase-T13A with D-Asn

The structure of Blasnase-T13A with D-Asn, PDB code: 7c91 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)	72.25 / 1.98
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.26, 92.26, 231.46, 90, 90, 90
R / Rfree (%)	18.3 / 21.1

The binding sites of Magnesium atom in the Blasnase-T13A with D-Asn (pdb code 7c91). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Blasnase-T13A with D-Asn, PDB code: 7c91:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 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 B:Mg402 b:53.8 occ:1.00 OE1 B:GLU207 2.5 55.5 1.0 O A:HOH571 2.5 47.6 1.0 O A:HOH645 2.5 46.7 1.0 OE2 B:GLU207 2.5 48.2 1.0 O B:HOH669 2.7 59.7 1.0 O B:GLU228 2.7 49.2 1.0 CD B:GLU207 2.9 49.8 1.0 HB3 B:GLU228 3.3 41.8 1.0 O B:HOH505 3.3 44.7 1.0 HZ2 A:LYS220 3.6 42.6 1.0 HE3 A:LYS220 3.6 41.3 1.0 HE2 A:LYS220 3.7 41.3 1.0 C B:GLU228 3.8 42.7 1.0 OD2 A:ASP218 3.9 43.2 1.0 HB2 B:GLU228 3.9 41.8 1.0 CB B:GLU228 4.0 41.8 1.0 CE A:LYS220 4.1 41.3 1.0 O A:HOH586 4.1 55.7 1.0 NZ A:LYS220 4.3 42.6 1.0 O B:HOH662 4.3 49.8 1.0 CG B:GLU207 4.4 47.0 1.0 O B:HOH612 4.4 52.6 1.0 O B:HOH653 4.5 65.6 1.0 CA B:GLU228 4.5 41.7 1.0 HA3 B:GLY229 4.5 45.0 1.0 HA B:GLU228 4.8 41.7 1.0 HZ1 A:LYS220 4.8 42.6 1.0 HG2 B:GLU207 4.8 47.0 1.0 HG3 B:GLU207 4.8 47.0 1.0 N B:GLY229 4.8 41.8 1.0 HZ3 A:LYS220 4.9 42.6 1.0 HB2 B:GLU207 4.9 44.2 1.0

Magnesium binding site 2 out of 5 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 B:Mg403 b:57.0 occ:1.00 O B:HOH658 2.2 48.4 1.0 O B:HOH562 2.2 38.1 1.0 O B:ASP295 2.3 32.7 1.0 O B:HOH637 2.5 48.1 1.0 O B:HOH589 2.7 46.0 1.0 HB2 B:ASP295 3.2 36.6 1.0 O B:GLU268 3.2 33.5 1.0 C B:ASP295 3.4 34.3 1.0 O B:HOH573 3.5 44.3 1.0 H B:ASP297 3.8 31.1 1.0 HA B:GLU269 3.9 38.4 1.0 C B:GLU268 4.0 36.3 1.0 CB B:ASP295 4.0 36.6 1.0 HA B:ASP295 4.0 36.1 1.0 N B:ASP297 4.0 31.1 1.0 HD1 B:TYR159 4.1 36.0 1.0 CA B:ASP295 4.1 36.1 1.0 O B:ALA267 4.1 33.1 1.0 HE1 B:TYR159 4.1 33.6 1.0 O B:HOH619 4.2 39.0 1.0 HB2 B:ASP297 4.2 34.4 1.0 C B:TYR296 4.3 35.4 1.0 O B:HOH591 4.3 44.6 1.0 O B:HOH534 4.4 53.1 1.0 HA B:GLU268 4.4 37.0 1.0 HA B:ASP297 4.4 34.4 1.0 N B:TYR296 4.5 33.2 1.0 HA B:TYR296 4.5 35.7 1.0 O B:GLY270 4.6 35.8 1.0 N B:GLU269 4.6 34.7 1.0 CA B:GLU269 4.6 38.4 1.0 HB3 B:ASP295 4.7 36.6 1.0 O B:TYR296 4.7 36.3 1.0 CA B:TYR296 4.7 35.7 1.0 CA B:ASP297 4.7 34.4 1.0 CD1 B:TYR159 4.8 36.0 1.0 CA B:GLU268 4.8 37.0 1.0 CE1 B:TYR159 4.8 33.6 1.0 CG B:ASP295 4.8 37.9 1.0 H B:GLY270 4.9 34.6 1.0 CB B:ASP297 5.0 34.4 1.0

Magnesium binding site 3 out of 5 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 B:Mg404 b:50.5 occ:1.00 O B:HOH638 2.0 59.6 1.0 O B:HOH660 2.1 54.0 1.0 O B:ASN246 2.3 40.6 1.0 OD2 B:ASP250 2.4 45.0 1.0 O B:HOH633 2.6 49.4 1.0 O B:HOH657 2.6 42.8 1.0 HH22 B:ARG223 3.3 39.7 1.0 H B:GLY219 3.3 39.8 1.0 CG B:ASP250 3.5 44.2 1.0 C B:ASN246 3.5 42.1 1.0 HA3 B:GLY219 3.7 34.8 1.0 HB3 B:ASN246 3.7 39.7 1.0 HH21 B:ARG223 3.9 39.7 1.0 NH2 B:ARG223 3.9 39.7 1.0 OD1 B:ASP250 3.9 43.6 1.0 HA B:MET247 4.0 40.8 1.0 N B:GLY219 4.1 39.8 1.0 HB2 B:ASP218 4.1 42.0 1.0 H B:ASP250 4.1 39.1 1.0 HA B:ASN246 4.1 39.4 1.0 CA B:ASN246 4.3 39.4 1.0 CA B:GLY219 4.4 34.8 1.0 CB B:ASN246 4.5 39.7 1.0 N B:MET247 4.5 40.5 1.0 O B:HOH605 4.6 43.7 1.0 CA B:MET247 4.7 40.8 1.0 O B:HOH680 4.7 64.9 1.0 CB B:ASP250 4.8 39.2 1.0 HB2 B:ASP250 4.8 39.2 1.0 N B:ASP250 4.9 39.1 1.0 H B:GLY249 5.0 40.9 1.0

Magnesium binding site 4 out of 5 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:Mg403 b:49.1 occ:1.00 O A:HOH631 2.1 53.8 1.0 OD2 A:ASP250 2.3 40.0 1.0 O1 A:FMT402 2.3 39.4 1.0 O A:ASN246 2.5 38.7 1.0 O A:HOH517 2.6 47.8 1.0 C A:FMT402 3.2 47.2 1.0 HH22 A:ARG223 3.2 35.8 1.0 H A:FMT402 3.3 47.2 1.0 CG A:ASP250 3.3 43.0 1.0 H A:GLY219 3.4 34.2 1.0 HA3 A:GLY219 3.6 37.2 1.0 OD1 A:ASP250 3.6 41.6 1.0 C A:ASN246 3.6 41.1 1.0 HH21 A:ARG223 3.7 35.8 1.0 NH2 A:ARG223 3.8 35.8 1.0 O A:HOH653 3.8 58.0 1.0 HB3 A:ASN246 3.9 36.0 1.0 HA A:MET247 4.0 36.3 1.0 H A:ASP250 4.0 36.1 1.0 N A:GLY219 4.1 34.2 1.0 O2 A:FMT402 4.3 47.3 1.0 HA A:ASN246 4.3 38.3 1.0 HB2 A:ASP218 4.3 36.6 1.0 CA A:GLY219 4.3 37.2 1.0 O A:HOH576 4.4 40.0 1.0 HO2 A:FMT402 4.4 47.3 0.0 CA A:ASN246 4.4 38.3 1.0 N A:MET247 4.6 33.1 1.0 CB A:ASN246 4.6 36.0 1.0 O A:HOH646 4.6 55.0 1.0 CB A:ASP250 4.7 35.6 1.0 CA A:MET247 4.7 36.3 1.0 N A:ASP250 4.7 36.1 1.0 HB2 A:ASP250 4.8 35.6 1.0 H A:GLY249 4.8 37.0 1.0 HA2 A:GLY219 5.0 37.2 1.0 HA3 A:GLY249 5.0 37.8 1.0 C A:MET247 5.0 36.4 1.0

Magnesium binding site 5 out of 5 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 A:Mg404 b:59.5 occ:1.00 O A:ASP295 2.6 33.0 1.0 O A:HOH641 3.1 46.1 1.0 H A:ASP297 3.2 33.4 1.0 HD1 A:TYR159 3.3 35.7 1.0 O A:HOH594 3.3 40.9 1.0 O A:HOH601 3.3 44.0 1.0 O A:HOH603 3.4 39.0 1.0 HB2 A:ASP297 3.6 34.3 1.0 O A:GLU268 3.6 34.3 1.0 N A:ASP297 3.6 33.4 1.0 O A:HOH574 3.6 33.8 1.0 C A:ASP295 3.8 31.5 1.0 HE1 A:TYR159 3.8 37.8 1.0 O A:HOH542 3.9 41.9 1.0 HB2 A:ASP295 4.0 32.9 1.0 HA A:TYR296 4.1 36.4 1.0 C A:TYR296 4.1 38.0 1.0 CD1 A:TYR159 4.1 35.7 1.0 HA A:ASP297 4.1 35.1 1.0 CA A:ASP297 4.3 35.1 1.0 CB A:ASP297 4.3 34.3 1.0 CE1 A:TYR159 4.4 37.8 1.0 CA A:TYR296 4.5 36.4 1.0 C A:GLU268 4.6 32.8 1.0 N A:TYR296 4.6 31.3 1.0 O A:HOH546 4.6 32.8 1.0 HA A:GLU269 4.7 30.3 1.0 O A:TYR296 4.7 33.9 1.0 HB3 A:ASP297 4.7 34.3 1.0 CB A:ASP295 4.7 32.9 1.0 O A:HOH608 4.7 33.5 1.0 CA A:ASP295 4.8 33.2 1.0 HA A:GLU268 4.8 32.9 1.0 HA A:TYR159 4.9 31.1 1.0 HA A:ASP295 4.9 33.2 1.0 O A:HOH638 4.9 57.8 1.0 O A:ALA267 5.0 32.4 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