Magnesium in PDB 8xri: The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- Dna

Enzymatic activity of The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- Dna

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

Protein crystallography data

The structure of The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- Dna, PDB code: 8xri 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) 25.61 / 2.92
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 129.21, 134.366, 135.926, 90, 90, 90
R / Rfree (%) 20.5 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- Dna (pdb code 8xri). 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 Both G-Dna and T- Dna, PDB code: 8xri:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8xri

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Magnesium binding site 1 out of 5 in the The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- 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 Both G-Dna and T- Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1201

b:95.2
occ:0.00
 CB B:ALA1072 3.7 92.4 1.0
CB A:ALA1072 4.0 91.2 1.0
CA B:ALA1072 4.1 94.9 1.0
CA A:ALA1072 4.2 93.9 1.0
O A:ALA1072 4.8 76.1 1.0
CB A:ASN1075 4.8 113.8 1.0
CG A:ASN1075 4.9 124.0 1.0
N B:ALA1072 4.9 97.0 1.0
OD1 A:ASN1075 5.0 115.1 1.0

Magnesium binding site 2 out of 5 in 8xri

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Magnesium binding site 2 out of 5 in the The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- 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 Both G-Dna and T- Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1202

b:46.4
occ:1.00
 OE1 A:GLU438 2.4 55.0 1.0
OD2 A:ASP539 2.6 51.9 1.0
OP1 C:DC12 2.6 58.4 1.0
O3' C:DG11 2.7 60.9 1.0
OD2 A:ASP541 3.0 54.7 1.0
OE2 A:GLU438 3.1 51.2 1.0
CD A:GLU438 3.1 52.1 1.0
P C:DC12 3.3 62.5 1.0
OD1 A:ASP541 3.3 48.8 1.0
CG A:ASP539 3.4 52.7 1.0
CB A:ASP539 3.5 46.6 1.0
CG A:ASP541 3.6 52.1 1.0
O A:LYS615 3.7 55.9 1.0
C3' C:DG11 3.8 48.3 1.0
C4' C:DG11 3.9 46.8 1.0
C5' C:DG11 4.2 47.4 1.0
O5' C:DC12 4.3 55.2 1.0
OP2 C:DC12 4.4 40.3 1.0
OD1 A:ASP539 4.5 54.7 1.0
N A:GLY544 4.6 45.1 1.0
CG A:GLU438 4.6 44.6 1.0
CA A:GLY544 4.7 43.6 1.0
CA A:ASP539 4.8 45.9 1.0
CB A:ASP543 4.8 49.4 1.0
C2' C:DG11 4.9 45.9 1.0
N A:ASP539 4.9 46.2 1.0
C A:LYS615 5.0 59.7 1.0

Magnesium binding site 3 out of 5 in 8xri

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Magnesium binding site 3 out of 5 in the The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- 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 Both G-Dna and T- Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1203

b:64.2
occ:1.00
 OE2 A:GLU593 2.2 76.4 1.0
OE1 A:GLU827 2.3 64.4 1.0
CD A:GLU827 3.1 58.6 1.0
CD A:GLU593 3.4 73.2 1.0
CG A:GLU827 3.7 55.6 1.0
OD2 A:ASP597 3.9 69.2 1.0
OE2 A:GLU827 3.9 56.8 1.0
OE1 A:GLU593 4.0 66.5 1.0
CG2 A:VAL825 4.1 58.8 1.0
O A:PHE826 4.4 66.7 1.0
CG A:GLU593 4.6 65.1 1.0
CB A:GLU827 4.6 50.9 1.0
CA A:GLU827 4.8 52.6 1.0
CG A:ASP597 4.9 75.0 1.0

Magnesium binding site 4 out of 5 in 8xri

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Magnesium binding site 4 out of 5 in the The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- 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 Both G-Dna and T- Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1201

b:51.0
occ:1.00
 OE2 B:GLU438 2.4 50.3 1.0
OD2 B:ASP539 2.7 53.3 1.0
OP1 E:DG14 2.9 50.0 1.0
O3' E:DT13 2.9 47.1 1.0
OD2 B:ASP541 3.0 56.7 1.0
CD B:GLU438 3.3 54.7 1.0
P E:DG14 3.4 50.6 1.0
OD1 B:ASP541 3.5 61.0 1.0
O B:LYS615 3.5 55.7 1.0
OE1 B:GLU438 3.6 53.2 1.0
CG B:ASP539 3.6 52.6 1.0
CG B:ASP541 3.6 57.4 1.0
CB B:ASP539 3.8 51.8 1.0
C5' E:DT13 3.8 43.0 1.0
C4' E:DT13 3.9 43.9 1.0
C3' E:DT13 4.0 45.5 1.0
OP2 E:DG14 4.2 50.6 1.0
OD1 B:ASP539 4.7 54.0 1.0
C B:LYS615 4.7 55.1 1.0
CG B:GLU438 4.7 48.6 1.0
O5' E:DG14 4.8 43.4 1.0
O5' E:DT13 4.9 44.2 1.0

Magnesium binding site 5 out of 5 in 8xri

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Magnesium binding site 5 out of 5 in the The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T- 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 Both G-Dna and T- Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1202

b:65.1
occ:1.00
 OE2 B:GLU593 2.1 80.3 1.0
OE1 B:GLU827 2.3 63.1 1.0
CD B:GLU593 3.0 72.0 1.0
CD B:GLU827 3.1 62.0 1.0
OE1 B:GLU593 3.2 64.2 1.0
OE2 B:GLU827 3.3 65.5 1.0
CG B:GLU593 4.4 65.6 1.0
CG B:GLU827 4.5 53.2 1.0
OD2 B:ASP597 4.8 76.5 1.0

Reference:

J.Yang, J.H.Gan. The Crystal Structure of Asfvtopii in Complex with Both G-Dna and T-Dna Nat Commun 2024.
ISSN: ESSN 2041-1723
Page generated: Sat Oct 5 07:48:26 2024

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