Magnesium in PDB 6lj3: Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion

Protein crystallography data

The structure of Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion, PDB code: 6lj3 was solved by R.Liang, G.Q.Peng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.24 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.040, 68.427, 117.969, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion (pdb code 6lj3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion, PDB code: 6lj3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6lj3

Go back to Magnesium Binding Sites List in 6lj3
Magnesium binding site 1 out of 3 in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:30.6
occ:1.00
O A:HOH307 2.0 17.6 1.0
O2A A:DUP202 2.1 37.5 1.0
O B:HOH400 2.2 33.6 1.0
O1B A:DUP202 2.2 40.0 1.0
O2G A:DUP202 2.3 37.6 1.0
O A:HOH327 2.4 25.4 1.0
PA A:DUP202 3.4 34.2 1.0
PB A:DUP202 3.4 35.6 1.0
PG A:DUP202 3.5 39.2 1.0
O A:HOH344 3.8 24.0 1.0
N3A A:DUP202 3.8 33.8 1.0
O1G A:DUP202 3.9 45.6 1.0
O3B A:DUP202 4.0 41.1 1.0
NE A:ARG71 4.0 21.0 1.0
OD1 A:ASP33 4.1 25.1 1.0
OE1 A:GLN120 4.1 15.3 1.0
O B:HOH355 4.2 23.4 1.0
O B:HOH327 4.2 16.4 1.0
OD2 A:ASP33 4.2 24.9 1.0
NH2 A:ARG71 4.3 23.9 1.0
O5' A:DUP202 4.3 31.6 1.0
C5' A:DUP202 4.3 26.6 1.0
O1A A:DUP202 4.5 31.6 1.0
CG A:ASP33 4.6 20.4 1.0
CZ A:ARG71 4.7 22.7 1.0
O2B A:DUP202 4.7 32.4 1.0
OD2 B:ASP91 4.7 23.9 1.0
O3G A:DUP202 4.8 40.1 1.0
CD A:GLN120 4.8 15.3 1.0
CG A:ARG71 4.9 19.3 1.0
NE2 A:GLN120 5.0 15.5 1.0
CD A:ARG71 5.0 20.7 1.0

Magnesium binding site 2 out of 3 in 6lj3

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Magnesium binding site 2 out of 3 in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:31.8
occ:1.00
O B:HOH333 2.1 28.4 1.0
O1A B:DUP202 2.1 30.0 1.0
O B:HOH318 2.1 17.5 1.0
O B:HOH394 2.1 30.1 1.0
O1B B:DUP202 2.2 32.4 1.0
O3G B:DUP202 2.3 37.0 1.0
PG B:DUP202 3.4 39.8 1.0
PB B:DUP202 3.4 34.0 1.0
O B:HOH362 3.4 44.3 1.0
PA B:DUP202 3.4 31.3 1.0
O1G B:DUP202 3.7 43.1 1.0
O B:HOH393 3.8 36.4 1.0
O3B B:DUP202 3.8 36.6 1.0
N3A B:DUP202 3.9 32.7 1.0
O B:HOH310 4.0 36.7 1.0
NE B:ARG71 4.1 18.3 1.0
C5' B:DUP202 4.2 26.4 1.0
OD1 B:ASP33 4.2 17.9 1.0
NH2 B:ARG71 4.2 21.7 1.0
OD2 B:ASP33 4.3 21.9 1.0
OE1 B:GLN120 4.3 14.3 1.0
O C:HOH319 4.4 22.2 1.0
O5' B:DUP202 4.4 29.5 1.0
O2A B:DUP202 4.5 29.7 1.0
CZ B:ARG71 4.6 19.1 1.0
O2G B:DUP202 4.7 42.1 1.0
O2B B:DUP202 4.7 36.5 1.0
CG B:ASP33 4.7 18.0 1.0
OD2 C:ASP91 4.9 29.4 1.0

Magnesium binding site 3 out of 3 in 6lj3

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Magnesium binding site 3 out of 3 in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:30.4
occ:1.00
O A:HOH347 1.8 35.2 1.0
O1A A:DUP201 1.9 28.2 1.0
O2G A:DUP201 2.0 25.9 1.0
O1B A:DUP201 2.0 22.6 1.0
O A:HOH377 2.3 20.6 1.0
O C:HOH309 2.4 17.2 1.0
PA A:DUP201 3.1 23.3 1.0
PG A:DUP201 3.1 29.5 1.0
PB A:DUP201 3.1 24.4 1.0
O3B A:DUP201 3.4 28.4 1.0
N3A A:DUP201 3.7 23.1 1.0
O1G A:DUP201 3.7 32.6 1.0
NH1 A:ARG149 3.8 34.6 1.0
O C:HOH316 4.0 22.5 1.0
O A:HOH336 4.0 27.3 1.0
C5' A:DUP201 4.1 24.3 1.0
O2A A:DUP201 4.1 28.4 1.0
O5' A:DUP201 4.2 25.5 1.0
OD1 C:ASP33 4.2 23.4 1.0
O A:HOH314 4.3 24.0 1.0
NE C:ARG71 4.3 25.9 1.0
CG2 A:THR157 4.3 44.6 1.0
NH2 C:ARG71 4.4 27.6 1.0
OE1 C:GLN120 4.4 13.4 1.0
O3G A:DUP201 4.4 31.2 1.0
OD2 C:ASP33 4.5 26.1 1.0
O2B A:DUP201 4.5 24.1 1.0
OD2 A:ASP91 4.6 27.2 1.0
CZ A:ARG149 4.8 33.0 1.0
CG C:ASP33 4.8 21.8 1.0
CZ C:ARG71 4.9 27.8 1.0
CB A:THR157 4.9 47.7 1.0

Reference:

R.Liang, G.Wang, D.Zhang, G.Ye, M.Li, Y.Shi, J.Shi, H.Chen, G.Peng. Structural Comparisons of Host and African Swine Fever Virus Dutpases Reveal New Clues For Inhibitor Development. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33139328
DOI: 10.1074/JBC.RA120.014005
Page generated: Mon Dec 14 23:13:08 2020

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