Magnesium in PDB 7c8x: Blasnase-T13A with L-Asn

The structure of Blasnase-T13A with L-Asn, PDB code: 7c8x 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)	49.29 / 1.99
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.256, 92.256, 232.931, 90, 90, 90
R / Rfree (%)	17.5 / 19.1

The binding sites of Magnesium atom in the Blasnase-T13A with L-Asn (pdb code 7c8x). 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-Asn, PDB code: 7c8x:
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-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 L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:41.1 occ:1.00 O A:HOH523 2.4 37.1 1.0 OD2 A:ASP218 2.4 35.5 1.0 O A:HOH602 2.5 34.3 1.0 OE2 B:GLU207 2.5 40.2 1.0 O A:HOH501 2.5 38.7 1.0 O B:HOH703 2.6 37.6 1.0 HZ2 A:LYS220 3.3 32.1 1.0 CG A:ASP218 3.3 33.6 1.0 CD B:GLU207 3.4 42.7 1.0 HB3 A:ASP218 3.4 31.1 1.0 O1 A:FMT408 3.5 42.7 1.0 MG B:MG402 3.6 47.3 1.0 CB A:ASP218 3.9 31.1 1.0 HG3 B:GLU207 3.9 37.2 1.0 O A:HOH617 4.0 40.7 1.0 OE1 B:GLU207 4.0 44.2 1.0 HZ1 A:LYS220 4.1 32.1 1.0 NZ A:LYS220 4.1 32.1 1.0 CG B:GLU207 4.2 37.2 1.0 OD1 A:ASP218 4.2 32.1 1.0 O B:HOH570 4.3 35.4 1.0 HB2 A:ASP218 4.3 31.1 1.0 O A:HOH596 4.4 41.7 1.0 O A:HOH565 4.4 31.1 1.0 O A:HOH575 4.4 50.5 1.0 O1 B:FMT406 4.5 40.8 1.0 C A:FMT408 4.6 53.2 1.0 HZ3 A:LYS220 4.6 32.1 1.0 HE3 A:LYS220 4.8 31.5 1.0 HB2 B:GLU207 4.9 38.6 1.0 C B:FMT406 4.9 43.0 1.0 HG2 B:GLU207 4.9 37.2 1.0 O A:HOH506 4.9 41.5 1.0 O2 A:FMT408 5.0 54.2 1.0 H A:FMT407 5.0 42.3 1.0

Magnesium binding site 2 out of 7 in the Blasnase-T13A with L-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 L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:70.8 occ:1.00 O A:SER79 2.9 56.0 1.0 OD2 A:ASP81 3.1 56.5 1.0 HA A:LYS3 3.6 62.2 1.0 O A:LYS2 3.6 68.8 1.0 HB3 A:LYS4 3.7 55.5 1.0 H A:LYS4 3.7 53.5 1.0 CG A:ASP81 3.8 54.3 1.0 OD1 A:ASP81 3.9 53.0 1.0 C A:SER79 4.0 55.9 1.0 HB2 A:SER79 4.1 54.7 1.0 HA A:SER79 4.2 59.2 1.0 HB2 A:LYS4 4.2 55.5 1.0 N A:LYS4 4.3 53.5 1.0 CB A:LYS4 4.4 55.5 1.0 CA A:LYS3 4.5 62.2 1.0 CA A:SER79 4.6 59.2 1.0 HE2 A:LYS4 4.7 58.8 1.0 HG3 A:LYS3 4.7 58.9 1.0 H A:ASP81 4.7 48.4 1.0 C A:LYS3 4.7 56.9 1.0 C A:LYS2 4.7 69.8 1.0 CB A:SER79 4.8 54.7 1.0 HA A:TYR80 4.9 52.4 1.0 N A:ASP81 4.9 48.4 1.0 CA A:LYS4 5.0 56.8 1.0

Magnesium binding site 3 out of 7 in the Blasnase-T13A with L-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 L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:42.4 occ:1.00 O A:HOH671 2.2 42.3 1.0 O1 A:FMT407 2.2 45.1 1.0 O A:ASN246 2.3 34.3 1.0 O A:HOH677 2.4 45.0 1.0 OD2 A:ASP250 2.4 36.0 1.0 O A:HOH563 2.6 39.0 1.0 C A:FMT407 3.2 42.3 1.0 HH12 A:ARG223 3.3 31.6 1.0 H A:FMT407 3.4 42.3 1.0 H A:GLY219 3.4 28.5 1.0 CG A:ASP250 3.4 37.4 1.0 C A:ASN246 3.5 37.0 1.0 HA3 A:GLY219 3.6 32.0 1.0 HB3 A:ASN246 3.7 29.8 1.0 HH11 A:ARG223 3.7 31.6 1.0 OD1 A:ASP250 3.8 35.7 1.0 HA A:MET247 3.8 32.6 1.0 NH1 A:ARG223 3.8 31.6 1.0 H A:ASP250 4.0 29.5 1.0 N A:GLY219 4.1 28.5 1.0 HA A:ASN246 4.2 31.9 1.0 O2 A:FMT407 4.2 35.1 1.0 HB2 A:ASP218 4.3 31.1 1.0 CA A:ASN246 4.3 31.9 1.0 CA A:GLY219 4.4 32.0 1.0 N A:MET247 4.4 30.5 1.0 O A:HOH587 4.5 36.5 1.0 CB A:ASN246 4.5 29.8 1.0 CA A:MET247 4.5 32.6 1.0 O A:HOH663 4.6 44.8 1.0 H A:GLY249 4.7 34.9 1.0 CB A:ASP250 4.7 29.9 1.0 HB2 A:ASP250 4.7 29.9 1.0 O A:HOH685 4.7 46.9 1.0 N A:ASP250 4.8 29.5 1.0 C A:MET247 4.9 32.6 1.0

Magnesium binding site 4 out of 7 in the Blasnase-T13A with L-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 L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:52.1 occ:1.00 O A:ASP295 2.3 27.6 1.0 O A:HOH597 2.5 42.5 1.0 O A:HOH591 3.2 29.8 1.0 O A:HOH686 3.3 41.3 1.0 H A:ASP297 3.3 27.6 1.0 O A:HOH559 3.3 36.3 1.0 C A:ASP295 3.5 28.8 1.0 O A:GLU268 3.5 26.3 1.0 HD1 A:TYR159 3.6 33.6 1.0 HB2 A:ASP295 3.6 29.3 1.0 N A:ASP297 3.7 27.6 1.0 HB2 A:ASP297 3.7 29.2 1.0 HE1 A:TYR159 4.0 31.2 1.0 HA A:TYR296 4.0 28.2 1.0 C A:TYR296 4.0 31.6 1.0 HA A:ASP297 4.2 30.4 1.0 O A:HOH549 4.2 34.9 1.0 CA A:ASP297 4.3 30.4 1.0 O A:HOH623 4.3 37.3 1.0 CD1 A:TYR159 4.4 33.6 1.0 CA A:TYR296 4.4 28.2 1.0 N A:TYR296 4.4 27.5 1.0 CB A:ASP295 4.4 29.3 1.0 C A:GLU268 4.5 28.9 1.0 CA A:ASP295 4.5 28.3 1.0 CB A:ASP297 4.5 29.2 1.0 HA A:GLU269 4.5 25.5 1.0 HA A:ASP295 4.5 28.3 1.0 CE1 A:TYR159 4.5 31.2 1.0 O A:TYR296 4.7 30.7 1.0 O A:ALA267 4.7 28.8 1.0 HA A:GLU268 4.7 26.0 1.0 O A:HOH553 4.8 30.1 1.0 HB3 A:ASP297 4.9 29.2 1.0

Magnesium binding site 5 out of 7 in the Blasnase-T13A with L-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 L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:47.3 occ:1.00 O B:HOH703 2.5 37.6 1.0 O A:HOH617 2.5 40.7 1.0 OE1 B:GLU207 2.5 44.2 1.0 O B:GLU228 2.6 44.7 1.0 OE2 B:GLU207 2.7 40.2 1.0 CD B:GLU207 3.0 42.7 1.0 HB3 B:GLU228 3.3 39.4 1.0 HZ2 A:LYS220 3.5 32.1 1.0 MG A:MG402 3.6 41.1 1.0 HE3 A:LYS220 3.7 31.5 1.0 C B:GLU228 3.7 38.0 1.0 HE2 A:LYS220 3.8 31.5 1.0 OD2 A:ASP218 4.1 35.5 1.0 CB B:GLU228 4.1 39.4 1.0 CE A:LYS220 4.1 31.5 1.0 HB2 B:GLU228 4.2 39.4 1.0 O A:HOH596 4.2 41.7 1.0 NZ A:LYS220 4.2 32.1 1.0 HA3 B:GLY229 4.3 37.2 1.0 O B:HOH503 4.3 51.3 1.0 O A:HOH501 4.5 38.7 1.0 CG B:GLU207 4.5 37.2 1.0 CA B:GLU228 4.5 37.9 1.0 N B:GLY229 4.7 37.0 1.0 HZ1 A:LYS220 4.7 32.1 1.0 HA B:GLU228 4.8 37.9 1.0 CA B:GLY229 4.8 37.2 1.0 HZ3 A:LYS220 4.8 32.1 1.0 HG2 B:GLU207 4.9 37.2 1.0 HG3 B:GLU207 4.9 37.2 1.0 HB2 B:GLU207 5.0 38.6 1.0 O A:HOH575 5.0 50.5 1.0

Magnesium binding site 6 out of 7 in the Blasnase-T13A with L-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 L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:55.0 occ:1.00 O B:HOH630 2.6 43.6 1.0 O B:ASP295 2.6 30.3 1.0 O B:HOH607 3.1 32.2 1.0 O B:HOH552 3.1 36.4 1.0 O B:HOH660 3.2 36.4 1.0 O B:HOH690 3.2 44.3 1.0 H B:ASP297 3.2 30.4 1.0 O B:GLU268 3.4 28.3 1.0 HB2 B:ASP297 3.5 30.3 1.0 N B:ASP297 3.6 30.4 1.0 HD1 B:TYR159 3.7 33.3 1.0 C B:ASP295 3.8 33.5 1.0 O B:HOH541 3.8 42.0 1.0 HB2 B:ASP295 3.9 33.2 1.0 HA B:ASP297 4.0 29.9 1.0 C B:TYR296 4.2 34.0 1.0 CA B:ASP297 4.2 29.9 1.0 O B:HOH619 4.2 37.7 1.0 CB B:ASP297 4.3 30.3 1.0 HE1 B:TYR159 4.3 31.5 1.0 HA B:TYR296 4.3 32.7 1.0 C B:GLU268 4.3 29.9 1.0 HA B:GLU268 4.5 27.8 1.0 O B:ALA267 4.5 30.8 1.0 CD1 B:TYR159 4.5 33.3 1.0 HA B:GLU269 4.6 32.9 1.0 CA B:TYR296 4.6 32.7 1.0 N B:TYR296 4.7 29.9 1.0 CB B:ASP295 4.7 33.2 1.0 O B:HOH621 4.7 39.2 1.0 CA B:ASP295 4.7 31.1 1.0 HA B:ASP295 4.7 31.1 1.0 HB3 B:ASP297 4.8 30.3 1.0 O B:HOH613 4.8 30.1 1.0 O B:TYR296 4.8 33.8 1.0 CE1 B:TYR159 4.8 31.5 1.0 O B:HOH661 5.0 26.8 1.0

Magnesium binding site 7 out of 7 in the Blasnase-T13A with L-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 L-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:44.4 occ:1.00 O1 B:FMT407 2.1 51.0 1.0 O B:HOH667 2.3 52.2 1.0 O B:ASN246 2.3 37.8 1.0 O B:HOH688 2.3 46.5 1.0 OD2 B:ASP250 2.4 37.5 1.0 O B:HOH659 2.5 43.0 1.0 C B:FMT407 3.0 45.0 1.0 H B:FMT407 3.3 45.0 1.0 HH12 B:ARG223 3.3 36.8 1.0 CG B:ASP250 3.4 38.7 1.0 H B:GLY219 3.5 34.0 1.0 C B:ASN246 3.5 37.0 1.0 HA3 B:GLY219 3.6 31.0 1.0 OD1 B:ASP250 3.7 36.8 1.0 HB3 B:ASN246 3.8 34.9 1.0 HH11 B:ARG223 3.9 36.8 1.0 HA B:MET247 3.9 34.5 1.0 H B:ASP250 3.9 35.5 1.0 NH1 B:ARG223 3.9 36.8 1.0 O2 B:FMT407 4.1 40.0 1.0 HA B:ASN246 4.1 36.9 1.0 N B:GLY219 4.2 34.0 1.0 CA B:ASN246 4.3 36.9 1.0 O B:HOH600 4.3 38.4 1.0 CA B:GLY219 4.4 31.0 1.0 HB2 B:ASP218 4.4 35.0 1.0 N B:MET247 4.5 33.6 1.0 CB B:ASN246 4.6 34.9 1.0 CA B:MET247 4.6 34.5 1.0 O B:HOH731 4.6 56.3 1.0 CB B:ASP250 4.7 35.1 1.0 O B:HOH704 4.7 53.0 1.0 N B:ASP250 4.7 35.5 1.0 O B:HOH701 4.7 48.6 1.0 HB2 B:ASP250 4.7 35.1 1.0 H B:GLY249 4.8 37.1 1.0 C B:MET247 4.9 34.2 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