Magnesium in PDB 7bf5: Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp)

Enzymatic activity of Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp)

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp):
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp), PDB code: 7bf5 was solved by X.Ni, S.Knapp, A.Chaikuad, Structural Genomics Consortium, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.80 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.617, 111.339, 195.184, 90, 90, 90
R / Rfree (%) 17.7 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp) (pdb code 7bf5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp), PDB code: 7bf5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7bf5

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Magnesium binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:32.8
occ:1.00
 OP1 A:A2R202 2.0 32.1 1.0
O A:HOH369 2.0 36.4 1.0
OD2 A:ASP157 2.1 35.9 1.0
O A:HOH337 2.1 26.0 1.0
O E:HOH329 2.2 31.5 1.0
O A:HOH367 2.3 21.1 1.0
CG A:ASP157 2.8 30.9 1.0
OD1 A:ASP157 3.0 36.3 1.0
P2' A:A2R202 3.3 27.6 1.0
O A:HOH387 3.7 35.2 1.0
OP3 A:A2R202 3.9 28.9 1.0
ND1 E:HIS86 4.1 19.1 1.0
OP2 A:A2R202 4.1 27.0 1.0
CB A:ASP157 4.1 27.5 1.0
O2' A:A2R202 4.4 27.1 1.0
CE1 E:HIS86 4.6 19.8 1.0
OG E:SER84 4.8 21.0 1.0

Magnesium binding site 2 out of 3 in 7bf5

Go back to Magnesium Binding Sites List in 7bf5
Magnesium binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:8.8
occ:1.00
 O C:HOH304 1.8 24.6 1.0
N C:GLY0 1.9 27.3 1.0
ND1 C:HIS1 1.9 27.6 1.0
N C:HIS1 1.9 29.8 1.0
O C:HOH328 2.1 28.9 1.0
C C:GLY0 2.7 29.9 1.0
CA C:GLY0 2.8 27.7 1.0
CG C:HIS1 2.9 29.8 1.0
CE1 C:HIS1 3.0 28.3 1.0
CA C:HIS1 3.0 32.3 1.0
CB C:HIS1 3.2 31.8 1.0
N C:MET2 3.8 35.4 1.0
C C:HIS1 3.9 34.9 1.0
O C:GLY0 3.9 33.3 1.0
CD2 C:HIS1 4.0 29.0 1.0
NE2 C:HIS1 4.1 28.9 1.0
O C:HOH359 4.4 29.5 1.0
O C:HOH372 4.6 57.1 1.0

Magnesium binding site 3 out of 3 in 7bf5

Go back to Magnesium Binding Sites List in 7bf5
Magnesium binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp- Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:14.0
occ:1.00
 ND1 E:HIS1 2.0 31.8 1.0
N E:HIS1 2.0 33.1 1.0
N E:GLY0 2.1 31.4 1.0
OE2 E:GLU120 2.1 29.4 1.0
OE1 E:GLU120 2.2 30.8 1.0
CD E:GLU120 2.4 29.9 1.0
C E:GLY0 2.9 35.6 1.0
CG E:HIS1 3.0 32.4 1.0
CA E:GLY0 3.0 32.0 1.0
CE1 E:HIS1 3.0 32.3 1.0
CA E:HIS1 3.1 35.5 1.0
CB E:HIS1 3.2 35.5 1.0
N E:MET2 3.7 41.8 1.0
CG E:GLU120 3.9 29.3 1.0
C E:HIS1 3.9 37.3 1.0
O E:GLY0 4.1 38.2 1.0
CD2 E:HIS1 4.1 32.3 1.0
NE2 E:HIS1 4.1 31.3 1.0
O E:HOH303 4.1 49.8 1.0
O E:HOH351 5.0 40.9 1.0

Reference:

X.Ni, S.Knapp, A.Chaikuad, Structural Genomics Consortium. Crystal Structure of Sars-Cov-2 Macrodomain in Complex with Adp-Ribose-Phosphate (Adp-Ribose-2'-Phosphate, Adprp) To Be Published.
Page generated: Mon Jan 25 15:23:31 2021

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