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Magnesium in PDB 8h4c: Blasnase-T13A/M57P

Protein crystallography data

The structure of Blasnase-T13A/M57P, PDB code: 8h4c 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) 19.83 / 1.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.716, 91.716, 233.017, 90, 90, 90
R / Rfree (%) 18.4 / 19.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Blasnase-T13A/M57P (pdb code 8h4c). 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: 8h4c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8h4c

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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:32.7
occ:0.00
 O A:HOH502 2.2 39.7 1.0
O A:HOH640 2.3 29.4 1.0
OE2 B:GLU207 2.3 35.8 1.0
OD2 A:ASP218 2.4 28.8 1.0
O A:HOH738 2.4 36.8 1.0
O A:HOH512 2.7 32.0 1.0
CD B:GLU207 3.1 36.2 1.0
CG A:ASP218 3.3 29.1 1.0
O1 A:FMT406 3.5 35.0 0.0
MG B:MG401 3.6 37.0 0.0
OE1 B:GLU207 3.7 39.4 1.0
NZ A:LYS220 3.8 26.1 1.0
O A:HOH612 3.9 36.6 1.0
CB A:ASP218 3.9 23.9 1.0
CG B:GLU207 4.0 32.9 1.0
OD1 A:ASP218 4.2 26.1 1.0
O B:HOH539 4.2 31.1 1.0
O A:HOH516 4.2 39.7 1.0
C A:FMT406 4.4 35.3 0.0
O A:HOH532 4.5 41.7 1.0
O2 B:FMT404 4.5 27.1 0.0
O A:HOH665 4.6 25.0 1.0
CE A:LYS220 4.8 26.3 1.0
CB B:GLU207 5.0 28.1 1.0
O A:ASP216 5.0 25.3 1.0

Magnesium binding site 2 out of 7 in 8h4c

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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:45.7
occ:0.00
 O A:SER79 3.0 43.4 1.0
OD2 A:ASP81 3.6 43.1 1.0
C A:SER79 4.0 43.2 1.0
CG A:ASP81 4.2 44.1 1.0
OD1 A:ASP81 4.3 46.4 1.0
CA A:SER79 4.3 46.8 1.0
O A:LYS2 4.4 55.7 1.0
CB A:SER79 4.6 44.6 1.0
N A:LYS4 4.7 43.0 1.0
CA A:LYS3 4.9 45.2 1.0
CB A:LYS4 4.9 43.2 1.0

Magnesium binding site 3 out of 7 in 8h4c

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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:29.8
occ:0.00
 O2 A:FMT405 2.2 29.0 0.0
O A:HOH633 2.3 35.4 1.0
O A:ASN246 2.4 25.0 1.0
O A:HOH568 2.4 33.2 1.0
OD2 A:ASP250 2.4 29.8 1.0
O A:HOH718 2.5 33.7 1.0
C A:FMT405 3.4 29.8 0.0
CG A:ASP250 3.4 27.6 1.0
C A:ASN246 3.5 25.8 1.0
OD1 A:ASP250 3.7 28.6 1.0
NH1 A:ARG223 3.8 28.1 1.0
O A:HOH753 4.2 43.7 1.0
CA A:ASN246 4.2 24.0 1.0
N A:GLY219 4.2 23.6 1.0
O1 A:FMT405 4.3 31.9 0.0
CB A:ASN246 4.3 23.5 1.0
O A:HOH725 4.3 39.1 1.0
O A:HOH666 4.3 28.4 1.0
CA A:GLY219 4.4 22.7 1.0
N A:MET247 4.6 22.7 1.0
O A:HOH696 4.6 44.2 1.0
CB A:ASP250 4.7 21.8 1.0
N A:ASP250 4.7 23.6 1.0
CA A:MET247 4.8 22.0 1.0

Magnesium binding site 4 out of 7 in 8h4c

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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
A:Mg404

b:23.8
occ:0.00
 O A:HOH715 2.2 31.1 1.0
O A:HOH596 2.4 22.8 1.0
O A:HOH551 2.4 31.9 1.0
O A:ASP295 2.5 21.8 1.0
O A:HOH736 2.6 26.5 1.0
O A:GLU268 2.7 23.5 1.0
C A:ASP295 3.5 21.8 1.0
C A:GLU268 3.6 21.5 1.0
O A:HOH634 3.8 28.2 1.0
O A:ALA267 4.1 22.0 1.0
CB A:ASP295 4.1 21.4 1.0
CA A:ASP295 4.2 20.4 1.0
O A:HOH598 4.2 27.2 1.0
N A:GLU269 4.2 20.4 1.0
CA A:GLU269 4.3 19.0 1.0
N A:ASP297 4.4 20.9 1.0
C A:TYR296 4.5 21.2 1.0
CA A:GLU268 4.5 21.3 1.0
N A:TYR296 4.6 21.3 1.0
O A:HOH581 4.7 35.3 1.0
O A:GLY270 4.7 22.1 1.0
C A:GLU269 4.7 19.2 1.0
CD1 A:TYR159 4.7 21.6 1.0
CA A:TYR296 4.8 20.5 1.0
CE1 A:TYR159 4.8 23.8 1.0
CG A:ASP295 4.8 23.5 1.0
O A:TYR296 4.9 23.1 1.0
N A:GLY270 4.9 20.7 1.0

Magnesium binding site 5 out of 7 in 8h4c

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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:Mg401

b:37.0
occ:0.00
 O A:HOH612 2.4 36.6 1.0
O A:HOH738 2.5 36.8 1.0
OE1 B:GLU207 2.6 39.4 1.0
O B:GLU228 2.6 38.5 1.0
OE2 B:GLU207 2.7 35.8 1.0
CD B:GLU207 3.1 36.2 1.0
MG A:MG401 3.6 32.7 0.0
C B:GLU228 3.8 32.8 1.0
CB B:GLU228 3.8 32.9 1.0
OD2 A:ASP218 4.0 28.8 1.0
CE A:LYS220 4.0 26.3 1.0
O B:HOH503 4.1 42.7 1.0
NZ A:LYS220 4.2 26.1 1.0
O A:HOH532 4.3 41.7 1.0
CA B:GLU228 4.3 33.0 1.0
O A:HOH502 4.4 39.7 1.0
CG B:GLU207 4.6 32.9 1.0
N B:GLY229 4.8 29.6 1.0
OE2 B:GLU228 4.9 48.4 1.0
O A:HOH516 4.9 39.7 1.0
CG B:GLU228 5.0 37.0 1.0

Magnesium binding site 6 out of 7 in 8h4c

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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:Mg402

b:26.1
occ:0.00
 O B:HOH751 2.2 33.4 1.0
O B:ASP295 2.3 21.5 1.0
O B:HOH653 2.3 25.5 1.0
O B:HOH761 2.5 29.9 1.0
O B:HOH568 2.6 34.5 1.0
O B:GLU268 2.9 26.5 1.0
C B:ASP295 3.4 24.7 1.0
C B:GLU268 3.8 23.6 1.0
O B:HOH637 3.9 29.3 1.0
CB B:ASP295 3.9 25.2 1.0
CA B:ASP295 4.0 24.6 1.0
O B:ALA267 4.2 24.6 1.0
O B:HOH586 4.2 26.3 1.0
CA B:GLU269 4.3 22.1 1.0
N B:GLU269 4.3 21.3 1.0
N B:ASP297 4.4 19.8 1.0
N B:TYR296 4.5 24.5 1.0
C B:TYR296 4.5 24.1 1.0
O B:GLY270 4.6 25.0 1.0
CG B:ASP295 4.7 26.2 1.0
CD1 B:TYR159 4.7 24.8 1.0
CA B:GLU268 4.7 24.6 1.0
CE1 B:TYR159 4.7 23.4 1.0
C B:GLU269 4.7 22.3 1.0
CA B:TYR296 4.8 22.6 1.0
O B:HOH578 4.9 34.8 1.0
O B:TYR296 4.9 26.1 1.0
N B:GLY270 4.9 24.5 1.0

Magnesium binding site 7 out of 7 in 8h4c

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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:Mg403

b:32.7
occ:0.00
 O B:HOH763 2.2 39.5 1.0
O B:HOH696 2.4 42.5 1.0
O2 B:FMT405 2.4 31.4 0.0
O B:HOH618 2.4 36.5 1.0
O B:ASN246 2.4 30.0 1.0
OD2 B:ASP250 2.4 31.1 1.0
C B:FMT405 3.3 33.2 0.0
CG B:ASP250 3.4 29.4 1.0
C B:ASN246 3.6 30.5 1.0
OD1 B:ASP250 3.8 31.8 1.0
NH1 B:ARG223 3.8 28.6 1.0
N B:GLY219 4.2 22.9 1.0
CA B:ASN246 4.3 29.0 1.0
O1 B:FMT405 4.3 33.8 0.0
CB B:ASN246 4.4 27.0 1.0
O B:HOH676 4.5 32.5 1.0
CA B:GLY219 4.5 24.5 1.0
N B:MET247 4.6 27.7 1.0
CB B:ASP250 4.7 28.0 1.0
CA B:MET247 4.8 26.5 1.0
N B:ASP250 4.8 28.4 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 04:22:07 2024

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