Magnesium in PDB 8xrf: The Crystal Structure of Asfvtopii in Complex with G-Dna

All present enzymatic activity of The Crystal Structure of Asfvtopii in Complex with G-Dna:
5.6.2.2;

The structure of The Crystal Structure of Asfvtopii in Complex with G-Dna, PDB code: 8xrf was solved by J.Yang, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.86 / 2.94
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	135.77, 126.41, 135.69, 90, 90, 90
R / Rfree (%)	21.8 / 26.3

The binding sites of Magnesium atom in the The Crystal Structure of Asfvtopii in Complex with G-Dna (pdb code 8xrf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The Crystal Structure of Asfvtopii in Complex with G-Dna, PDB code: 8xrf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the The Crystal Structure of Asfvtopii in Complex with G-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Asfvtopii in Complex with G-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:66.1 occ:1.00 OE2 A:GLU593 2.0 98.7 1.0 OE1 A:GLU827 2.7 77.8 1.0 CD A:GLU593 2.8 100.7 1.0 OE1 A:GLU593 3.0 108.1 1.0 CD A:GLU827 3.4 75.9 1.0 OE2 A:GLU827 3.6 84.6 1.0 OD2 A:ASP597 3.9 75.7 1.0 CG A:GLU593 4.2 83.1 1.0 CG A:GLU827 4.7 69.6 1.0 CG1 A:VAL825 4.8 62.9 1.0 NH1 A:ARG716 4.9 83.5 1.0 O A:PHE826 5.0 70.3 1.0

Magnesium binding site 2 out of 5 in the The Crystal Structure of Asfvtopii in Complex with G-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Asfvtopii in Complex with G-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:49.3 occ:1.00 O C:HOH101 2.2 85.0 1.0 OP2 D:DC12 2.4 67.0 1.0 OD2 A:ASP539 2.4 71.5 1.0 OD2 A:ASP541 2.4 68.2 1.0 O A:LYS615 2.4 65.3 1.0 OE1 A:GLU438 3.1 73.7 1.0 CG A:ASP539 3.4 74.1 1.0 CG A:ASP541 3.5 70.5 1.0 CB A:ASP539 3.6 63.1 1.0 C A:LYS615 3.6 53.1 1.0 P D:DC12 3.7 48.5 1.0 OD1 A:ASP541 3.9 77.0 1.0 CD A:GLU438 3.9 62.4 1.0 C3' C:DT11 3.9 55.2 1.0 OE2 A:GLU438 4.0 65.7 1.0 O3' C:DT11 4.2 78.0 1.0 CA A:GLY616 4.2 55.3 1.0 OP1 D:DC12 4.2 65.4 1.0 N A:GLY616 4.4 49.7 1.0 OH B:TYR800 4.4 52.0 1.0 OD1 A:ASP539 4.5 80.5 1.0 C5' C:DT11 4.6 53.5 1.0 CE1 B:TYR800 4.6 62.4 1.0 CA A:LYS615 4.7 46.2 1.0 C4' C:DT11 4.7 53.6 1.0 CB A:ASP541 4.8 52.6 1.0 O5' D:DC12 4.8 54.8 1.0 OP1 C:DT11 5.0 62.7 1.0 CZ B:TYR800 5.0 52.3 1.0

Magnesium binding site 3 out of 5 in the The Crystal Structure of Asfvtopii in Complex with G-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Asfvtopii in Complex with G-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:78.0 occ:1.00 OD1 B:ASN1075 2.0 95.7 1.0 OD1 A:ASN1075 2.1 90.9 1.0 O A:ALA1072 2.4 90.7 1.0 O B:ALA1072 2.6 83.5 1.0 CG B:ASN1075 2.9 88.6 1.0 CG A:ASN1075 3.0 87.9 1.0 ND2 A:ASN1075 3.2 80.3 1.0 ND2 B:ASN1075 3.2 70.6 1.0 C A:ALA1072 3.4 92.3 1.0 C B:ALA1072 3.6 83.9 1.0 CA A:ALA1072 3.7 74.8 1.0 CA B:ALA1072 4.0 83.9 1.0 CB B:ASN1075 4.4 90.8 1.0 CB A:ALA1072 4.4 89.5 1.0 CB A:ASN1075 4.4 92.5 1.0 N A:GLU1073 4.6 99.9 1.0 CB B:ALA1072 4.6 82.6 1.0 O A:SER1071 4.7 89.6 1.0 N B:GLU1073 4.8 83.8 1.0 O B:SER1071 4.9 75.1 1.0 CA B:ASN1075 4.9 81.8 1.0

Magnesium binding site 4 out of 5 in the The Crystal Structure of Asfvtopii in Complex with G-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Asfvtopii in Complex with G-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1201 b:56.5 occ:1.00 OE2 B:GLU593 2.1 77.0 1.0 OE1 B:GLU827 2.5 72.8 1.0 CD B:GLU827 3.2 69.2 1.0 CD B:GLU593 3.3 64.0 1.0 OE2 B:GLU827 3.4 69.1 1.0 OE1 B:GLU593 3.8 60.9 1.0 OD2 B:ASP597 4.3 64.1 1.0 CG B:GLU593 4.4 56.9 1.0 CG B:GLU827 4.6 50.4 1.0 CG1 B:VAL825 4.8 42.2 1.0 NH1 B:ARG716 5.0 75.3 1.0

Magnesium binding site 5 out of 5 in the The Crystal Structure of Asfvtopii in Complex with G-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of Asfvtopii in Complex with G-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1202 b:53.1 occ:1.00 OD2 B:ASP539 2.1 66.9 1.0 O E:HOH101 2.1 50.7 1.0 O B:HOH1301 2.2 63.9 1.0 O B:LYS615 2.5 59.6 1.0 OP2 F:DC12 2.5 58.6 1.0 OD2 B:ASP541 2.6 68.4 1.0 CG B:ASP539 3.0 66.5 1.0 CB B:ASP539 3.4 66.2 1.0 CG B:ASP541 3.5 65.8 1.0 C B:LYS615 3.7 52.3 1.0 OD1 B:ASP541 3.7 65.3 1.0 P F:DC12 3.9 56.5 1.0 CA B:GLY616 4.1 55.5 1.0 OD1 B:ASP539 4.1 65.2 1.0 OE2 B:GLU438 4.3 91.7 1.0 N B:GLY616 4.3 59.2 1.0 C3' E:DC11 4.4 46.9 1.0 CE1 A:TYR800 4.5 51.9 1.0 OP1 F:DC12 4.5 51.7 1.0 C5' E:DC11 4.6 45.0 1.0 OH A:TYR800 4.6 50.0 1.0 O3' E:DC11 4.7 67.2 1.0 OP1 E:DC11 4.7 40.0 1.0 CA B:LYS615 4.8 47.3 1.0 CB B:ASP541 4.9 58.8 1.0 CA B:ASP539 4.9 65.8 1.0 C4' E:DC11 5.0 45.3 1.0

J.Yang, J.H.Gan. The Crystal Structure of Asfvtopii in Complex with G-Dna Nat Commun 2024.
ISSN: ESSN 2041-1723