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Magnesium in PDB 8h4d: Blasnase-T13A/M57N

Protein crystallography data

The structure of Blasnase-T13A/M57N, PDB code: 8h4d 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) 49.02 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.643, 91.643, 232.07, 90, 90, 90
R / Rfree (%) 18 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Blasnase-T13A/M57N (pdb code 8h4d). 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/M57N, PDB code: 8h4d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8h4d

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Magnesium binding site 1 out of 7 in the Blasnase-T13A/M57N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Blasnase-T13A/M57N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:27.2
occ:0.00
 O A:HOH538 2.4 27.2 1.0
O A:ASP295 2.5 25.5 1.0
O A:HOH695 2.5 30.1 1.0
O A:GLU268 2.7 24.4 1.0
O A:HOH534 2.8 34.8 1.0
C A:ASP295 3.6 27.1 1.0
C A:GLU268 3.6 26.4 1.0
O A:HOH657 3.8 34.1 1.0
O2 A:FMT405 3.9 20.0 1.0
CB A:ASP295 4.1 27.9 1.0
O A:HOH566 4.1 30.5 1.0
O A:ALA267 4.2 25.3 1.0
CA A:ASP295 4.2 25.1 1.0
CA A:GLU269 4.2 23.0 1.0
N A:GLU269 4.2 25.2 1.0
N A:ASP297 4.4 22.7 1.0
C A:TYR296 4.6 26.5 1.0
CA A:GLU268 4.6 23.8 1.0
N A:TYR296 4.6 26.2 1.0
O A:GLY270 4.7 25.4 1.0
C A:GLU269 4.7 24.7 1.0
CD1 A:TYR159 4.7 31.4 1.0
CG A:ASP295 4.8 30.6 1.0
CE1 A:TYR159 4.8 29.1 1.0
N A:GLY270 4.9 21.5 1.0
CA A:TYR296 4.9 24.9 1.0
O A:TYR296 5.0 25.0 1.0
C A:FMT405 5.0 20.0 1.0

Magnesium binding site 2 out of 7 in 8h4d

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Magnesium binding site 2 out of 7 in the Blasnase-T13A/M57N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Blasnase-T13A/M57N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:38.1
occ:0.00
 OD2 A:ASP218 2.1 38.9 1.0
O A:HOH704 2.3 41.9 1.0
O A:HOH553 3.0 37.2 1.0
MG B:MG403 3.0 41.1 0.0
CG A:ASP218 3.0 34.1 1.0
OE2 B:GLU207 3.2 41.7 1.0
CB A:ASP218 3.5 27.1 1.0
O A:HOH587 3.7 43.0 1.0
MG B:MG404 3.8 41.0 0.0
CD B:GLU207 3.9 44.3 1.0
OD1 A:ASP218 4.1 32.6 1.0
OE1 B:GLU207 4.3 47.4 1.0
O1 A:FMT404 4.3 34.0 0.0
O A:HOH585 4.4 36.2 1.0
NZ A:LYS220 4.5 32.9 1.0
CA A:ASP218 4.8 27.6 1.0
CG B:GLU207 4.9 43.2 1.0

Magnesium binding site 3 out of 7 in 8h4d

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Magnesium binding site 3 out of 7 in the Blasnase-T13A/M57N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Blasnase-T13A/M57N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:34.9
occ:0.00
 O A:HOH654 2.0 44.3 1.0
O2 A:FMT404 2.0 33.6 0.0
OD2 A:ASP250 2.2 39.5 1.0
O A:HOH551 2.4 36.1 1.0
O A:ASN246 2.5 30.7 1.0
O A:HOH688 2.6 41.0 1.0
C A:FMT404 2.9 34.0 0.0
CG A:ASP250 3.2 33.5 1.0
NH1 A:ARG223 3.5 31.6 1.0
OD1 A:ASP250 3.6 35.2 1.0
C A:ASN246 3.7 32.0 1.0
O1 A:FMT404 4.1 34.0 0.0
N A:GLY219 4.2 28.1 1.0
O A:HOH702 4.3 45.0 1.0
CA A:GLY219 4.3 28.2 1.0
CB A:ASP250 4.5 27.6 1.0
CA A:ASN246 4.5 30.5 1.0
O A:HOH622 4.5 30.5 1.0
CB A:ASN246 4.6 32.2 1.0
N A:ASP250 4.6 27.2 1.0
O A:HOH696 4.7 46.6 1.0
N A:MET247 4.7 28.4 1.0
CA A:MET247 4.8 26.7 1.0
CZ A:ARG223 4.8 35.9 1.0

Magnesium binding site 4 out of 7 in 8h4d

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Magnesium binding site 4 out of 7 in the Blasnase-T13A/M57N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Blasnase-T13A/M57N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:35.3
occ:0.00
 O B:ASN246 2.2 33.0 1.0
O2 B:FMT405 2.2 36.3 0.0
OD2 B:ASP250 2.4 38.4 1.0
O B:HOH616 2.8 43.2 1.0
C B:FMT405 3.3 37.4 0.0
C B:ASN246 3.4 38.0 1.0
CG B:ASP250 3.5 35.3 1.0
OD1 B:ASP250 3.9 39.8 1.0
NH1 B:ARG223 4.0 33.4 1.0
CA B:ASN246 4.1 31.6 1.0
N B:GLY219 4.2 28.7 1.0
O1 B:FMT405 4.3 38.0 0.0
CB B:ASN246 4.3 32.0 1.0
CA B:GLY219 4.4 29.9 1.0
N B:MET247 4.5 32.4 1.0
O B:HOH633 4.5 40.3 1.0
CA B:MET247 4.6 31.4 1.0
CB B:ASP250 4.7 32.2 1.0
N B:ASP250 4.7 32.4 1.0
C B:MET247 4.9 29.3 1.0

Magnesium binding site 5 out of 7 in 8h4d

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Magnesium binding site 5 out of 7 in the Blasnase-T13A/M57N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Blasnase-T13A/M57N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:31.6
occ:0.00
 O B:HOH691 2.1 41.5 1.0
O B:HOH615 2.2 31.1 1.0
O B:HOH728 2.3 34.2 1.0
O B:ASP295 2.6 26.6 1.0
O B:GLU268 2.6 27.1 1.0
O B:HOH528 2.8 41.9 1.0
C B:GLU268 3.5 29.4 1.0
C B:ASP295 3.7 31.9 1.0
O B:HOH566 3.7 35.3 1.0
CA B:GLU269 4.0 27.4 1.0
CB B:ASP295 4.0 28.0 1.0
O B:HOH564 4.0 29.9 1.0
N B:GLU269 4.1 26.7 1.0
O B:ALA267 4.1 29.8 1.0
CA B:ASP295 4.2 33.1 1.0
C B:GLU269 4.5 25.8 1.0
O B:GLY270 4.5 30.0 1.0
CA B:GLU268 4.5 28.5 1.0
N B:ASP297 4.7 24.4 1.0
N B:GLY270 4.7 29.6 1.0
CG B:ASP295 4.8 31.7 1.0
C B:TYR296 4.8 30.1 1.0
N B:TYR296 4.8 28.5 1.0
CD1 B:TYR159 4.8 30.9 1.0
CE1 B:TYR159 4.9 27.3 1.0
O B:HOH591 5.0 39.1 1.0

Magnesium binding site 6 out of 7 in 8h4d

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Magnesium binding site 6 out of 7 in the Blasnase-T13A/M57N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Blasnase-T13A/M57N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:41.1
occ:0.00
 O A:HOH704 2.1 41.9 1.0
MG A:MG402 3.0 38.1 0.0
O A:HOH675 3.2 70.2 1.0
O A:HOH553 3.9 37.2 1.0
O2 B:FMT406 4.0 33.9 0.0
O A:HOH559 4.3 37.0 1.0
O A:HOH585 4.4 36.2 1.0
O B:HOH604 4.5 35.2 1.0
CD B:GLU207 4.7 44.3 1.0
OE2 B:GLU207 4.8 41.7 1.0
OE1 B:GLU207 4.8 47.4 1.0
C B:FMT406 4.9 32.4 0.0
O B:HOH748 4.9 48.6 1.0
OD2 A:ASP216 4.9 28.3 1.0

Magnesium binding site 7 out of 7 in 8h4d

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Magnesium binding site 7 out of 7 in the Blasnase-T13A/M57N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Blasnase-T13A/M57N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:41.0
occ:0.00
 O A:HOH587 2.1 43.0 1.0
O B:GLU228 2.9 42.3 1.0
OE2 B:GLU207 3.1 41.7 1.0
OE1 B:GLU207 3.1 47.4 1.0
CD B:GLU207 3.5 44.3 1.0
CB B:GLU228 3.5 35.7 1.0
MG A:MG402 3.8 38.1 0.0
OD2 A:ASP218 3.8 38.9 1.0
C B:GLU228 3.9 39.6 1.0
CE A:LYS220 3.9 33.5 1.0
CA B:GLU228 4.2 37.7 1.0
NZ A:LYS220 4.3 32.9 1.0
OE1 B:GLU228 4.6 54.4 1.0
CG B:GLU228 4.6 41.4 1.0
CD B:GLU228 4.8 53.6 1.0
CG A:ASP218 4.9 34.1 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 04:22:20 2024

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