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Magnesium in PDB 8h4a: Blasnase-T13A/M57P

Protein crystallography data

The structure of Blasnase-T13A/M57P, PDB code: 8h4a was solved by F.Lu, W.Wang, H.Chi, T.Ran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.84 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.672, 91.672, 233.707, 90, 90, 90
R / Rfree (%) 17.2 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Blasnase-T13A/M57P (pdb code 8h4a). 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/M57P, PDB code: 8h4a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8h4a

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Magnesium binding site 1 out of 7 in the Blasnase-T13A/M57P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Blasnase-T13A/M57P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.9
occ:0.00
 O A:HOH728 2.3 26.4 1.0
O A:HOH544 2.4 21.6 1.0
O A:GLU268 2.6 19.2 1.0
O A:ASP295 2.6 19.8 1.0
O A:HOH537 3.0 27.5 1.0
C A:GLU268 3.5 19.2 1.0
O A:HOH640 3.7 28.1 1.0
C A:ASP295 3.8 20.8 1.0
O A:HOH565 3.9 27.2 1.0
CA A:GLU269 4.1 18.5 1.0
CB A:ASP295 4.1 17.9 1.0
N A:GLU269 4.2 18.6 1.0
O A:ALA267 4.3 19.5 1.0
CA A:ASP295 4.3 21.4 1.0
CA A:GLU268 4.6 22.9 1.0
CD1 A:TYR159 4.6 21.1 1.0
C A:GLU269 4.6 18.4 1.0
CE1 A:TYR159 4.7 22.2 1.0
N A:ASP297 4.7 19.2 1.0
O A:GLY270 4.7 20.4 1.0
N A:GLY270 4.8 17.9 1.0
CG A:ASP295 4.8 21.5 1.0
C A:TYR296 4.8 22.3 1.0
N A:TYR296 4.8 21.0 1.0
O A:HOH687 4.9 29.3 1.0

Magnesium binding site 2 out of 7 in 8h4a

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Magnesium binding site 2 out of 7 in the Blasnase-T13A/M57P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Blasnase-T13A/M57P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:31.8
occ:0.00
 O A:HOH736 2.0 33.2 1.0
OD2 A:ASP218 2.1 27.4 1.0
O A:HOH724 2.1 41.9 1.0
CG A:ASP218 3.0 27.0 1.0
O A:HOH542 3.1 28.0 1.0
CB A:ASP218 3.4 24.1 1.0
OE2 B:GLU207 3.4 34.8 1.0
MG B:MG403 3.5 31.9 0.0
O A:HOH583 3.6 35.8 1.0
MG B:MG404 3.9 34.7 0.0
O B:HOH808 4.1 49.7 1.0
OD1 A:ASP218 4.1 25.4 1.0
O A:HOH610 4.3 24.4 1.0
CD B:GLU207 4.3 36.5 1.0
O1 A:FMT404 4.4 28.1 0.0
NZ A:LYS220 4.6 25.4 1.0
C A:FMT404 4.7 27.6 0.0
OE1 B:GLU207 4.7 41.7 1.0
CA A:ASP218 4.8 25.7 1.0

Magnesium binding site 3 out of 7 in 8h4a

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Magnesium binding site 3 out of 7 in the Blasnase-T13A/M57P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Blasnase-T13A/M57P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:28.5
occ:0.00
 O2 A:FMT404 2.1 27.6 0.0
O A:HOH709 2.2 34.0 1.0
O A:HOH688 2.3 36.0 1.0
O A:HOH553 2.4 31.3 1.0
OD2 A:ASP250 2.4 29.9 1.0
O A:ASN246 2.4 25.3 1.0
C A:FMT404 3.1 27.6 0.0
CG A:ASP250 3.4 25.3 1.0
C A:ASN246 3.6 24.0 1.0
OD1 A:ASP250 3.7 27.7 1.0
NH1 A:ARG223 3.9 26.1 1.0
O A:HOH742 4.1 42.3 1.0
O1 A:FMT404 4.2 28.1 0.0
CA A:ASN246 4.3 24.8 1.0
N A:GLY219 4.3 21.2 1.0
O A:HOH612 4.4 24.0 1.0
CB A:ASN246 4.5 23.5 1.0
O A:HOH722 4.5 39.9 1.0
CA A:GLY219 4.5 26.6 1.0
O A:HOH712 4.5 43.3 1.0
N A:MET247 4.6 20.4 1.0
CB A:ASP250 4.6 21.5 1.0
N A:ASP250 4.6 19.9 1.0
CA A:MET247 4.8 18.6 1.0

Magnesium binding site 4 out of 7 in 8h4a

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Magnesium binding site 4 out of 7 in the Blasnase-T13A/M57P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Blasnase-T13A/M57P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:31.6
occ:0.00
 O B:HOH752 2.1 44.7 1.0
O1 B:FMT405 2.3 30.8 0.0
O B:HOH734 2.3 37.5 1.0
O B:ASN246 2.4 29.0 1.0
OD2 B:ASP250 2.4 29.5 1.0
O B:HOH708 2.5 40.1 1.0
C B:FMT405 3.1 32.4 0.0
CG B:ASP250 3.4 29.2 1.0
C B:ASN246 3.5 32.0 1.0
OD1 B:ASP250 3.8 32.5 1.0
NH1 B:ARG223 3.8 29.2 1.0
O2 B:FMT405 4.1 33.6 0.0
N B:GLY219 4.2 21.7 1.0
CA B:ASN246 4.3 27.2 1.0
CA B:GLY219 4.4 23.4 1.0
CB B:ASN246 4.4 22.3 1.0
O B:HOH667 4.4 30.8 1.0
N B:MET247 4.5 25.9 1.0
CB B:ASP250 4.6 27.0 1.0
CA B:MET247 4.6 24.7 1.0
N B:ASP250 4.7 26.9 1.0
O B:HOH767 4.9 39.6 1.0
C B:MET247 5.0 23.7 1.0

Magnesium binding site 5 out of 7 in 8h4a

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Magnesium binding site 5 out of 7 in the Blasnase-T13A/M57P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Blasnase-T13A/M57P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:24.9
occ:0.00
 O B:HOH627 2.1 25.9 1.0
O B:HOH721 2.2 34.6 1.0
O B:HOH763 2.5 27.9 1.0
O B:ASP295 2.5 21.5 1.0
O B:HOH582 2.7 28.5 1.0
O B:GLU268 2.7 20.9 1.0
C B:ASP295 3.6 25.6 1.0
C B:GLU268 3.6 22.0 1.0
O B:HOH623 3.9 26.9 1.0
CB B:ASP295 3.9 25.4 1.0
CA B:GLU269 4.0 20.7 1.0
CA B:ASP295 4.1 24.1 1.0
N B:GLU269 4.1 20.1 1.0
O B:HOH622 4.1 24.8 1.0
O B:ALA267 4.1 23.9 1.0
O B:GLY270 4.5 22.7 1.0
C B:GLU269 4.5 20.3 1.0
N B:ASP297 4.6 20.5 1.0
CA B:GLU268 4.6 20.9 1.0
N B:TYR296 4.7 22.0 1.0
CG B:ASP295 4.7 25.3 1.0
C B:TYR296 4.7 22.4 1.0
N B:GLY270 4.7 20.9 1.0
CD1 B:TYR159 4.8 24.5 1.0
CE1 B:TYR159 4.8 20.9 1.0
CA B:TYR296 5.0 20.4 1.0
O B:HOH719 5.0 33.8 1.0

Magnesium binding site 6 out of 7 in 8h4a

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Magnesium binding site 6 out of 7 in the Blasnase-T13A/M57P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Blasnase-T13A/M57P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:31.9
occ:0.00
 O A:HOH525 2.2 36.2 1.0
O A:HOH736 2.7 33.2 1.0
O B:HOH808 3.4 49.7 1.0
O2 B:FMT406 3.4 26.3 0.0
MG A:MG402 3.5 31.8 0.0
O A:HOH542 3.7 28.0 1.0
O B:HOH628 3.8 28.1 1.0
O A:HOH724 3.9 41.9 1.0
O B:HOH784 4.3 37.6 1.0
C B:FMT406 4.3 25.6 0.0
OD2 A:ASP216 4.5 22.8 1.0
O A:HOH622 4.5 30.4 1.0
O A:HOH610 4.6 24.4 1.0
OE2 B:GLU207 4.7 34.8 1.0
CD B:GLU207 4.7 36.5 1.0
O A:ASP216 4.8 21.9 1.0
CG B:GLU207 4.9 34.5 1.0
CG A:ASP216 5.0 20.9 1.0
CB B:GLU207 5.0 28.1 1.0

Magnesium binding site 7 out of 7 in 8h4a

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Magnesium binding site 7 out of 7 in the Blasnase-T13A/M57P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Blasnase-T13A/M57P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:34.7
occ:0.00
 O A:HOH583 2.3 35.8 1.0
O A:HOH724 2.6 41.9 1.0
OE1 B:GLU207 2.6 41.7 1.0
O B:GLU228 2.6 38.9 1.0
OE2 B:GLU207 2.8 34.8 1.0
CD B:GLU207 3.1 36.5 1.0
C B:GLU228 3.7 33.3 1.0
CB B:GLU228 3.7 26.3 1.0
MG A:MG402 3.9 31.8 0.0
OD2 A:ASP218 4.1 27.4 1.0
CE A:LYS220 4.2 25.3 1.0
CA B:GLU228 4.3 29.3 1.0
O B:HOH727 4.4 30.0 1.0
NZ A:LYS220 4.4 25.4 1.0
CG B:GLU207 4.6 34.5 1.0
N B:GLY229 4.8 28.2 1.0
O B:HOH808 5.0 49.7 1.0
CG B:GLU228 5.0 33.5 1.0

Reference:

F.Lu, W.Wang, H.Chi, T.Ran. Structure-Based Rational Design of Bacillus Licheniformis L-Asparaginase with Low/No D-Asparaginase Activity For A Safer Enzyme To Be Published.
Page generated: Fri Oct 4 04:20:08 2024

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