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Sodium in PDB 6z6i: Sars-Cov-2 Macrodomain in Complex with Adp-Hpd

Enzymatic activity of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd

All present enzymatic activity of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd:
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 Sars-Cov-2 Macrodomain in Complex with Adp-Hpd, PDB code: 6z6i was solved by V.Zorzini, J.Rack, I.Ahel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.63 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.816, 83.096, 84.363, 90.00, 94.51, 90.00
R / Rfree (%) 22.9 / 27.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd (pdb code 6z6i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd, PDB code: 6z6i:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6z6i

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Sodium binding site 1 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:25.1
occ:1.00
 ND2 A:ASN363 2.7 31.4 1.0
O A:HOH603 2.9 28.8 1.0
OD2 A:ASP366 3.0 33.9 1.0
O A:HOH642 3.1 55.5 1.0
CA A:ASN363 3.4 29.6 1.0
CB A:ASP366 3.5 30.4 1.0
CG A:ASP366 3.7 30.4 1.0
CG A:ASN363 3.7 33.8 1.0
CB A:ASN363 3.9 30.2 1.0
CE A:LYS362 4.0 39.8 1.0
CD A:LYS362 4.1 38.6 1.0
O A:ASN363 4.1 29.4 1.0
O A:LYS362 4.1 28.8 1.0
N A:ASN363 4.2 29.1 1.0
O A:HOH632 4.2 35.6 1.0
C A:ASN363 4.3 36.2 1.0
C A:LYS362 4.4 33.0 1.0
O A:HOH611 4.7 30.9 1.0
OD1 A:ASN363 4.8 35.3 1.0
CA A:ASP366 4.9 29.8 1.0
OD1 A:ASP366 4.9 30.1 1.0

Sodium binding site 2 out of 9 in 6z6i

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Sodium binding site 2 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:47.7
occ:1.00
 OD2 A:ASP339 3.0 41.3 1.0
CD1 A:ILE341 3.7 31.9 1.0
CG A:ASP339 4.0 37.1 1.0
OD1 A:ASP339 4.3 36.0 1.0
CB A:ILE341 4.6 31.1 1.0
CG1 A:ILE341 4.6 33.4 1.0
CG2 A:ILE341 5.0 31.6 1.0

Sodium binding site 3 out of 9 in 6z6i

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Sodium binding site 3 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:25.2
occ:1.00
 O B:HOH570 2.4 49.8 1.0
O B:HOH622 2.9 37.3 1.0
ND2 B:ASN263 3.3 39.4 1.0
CG B:GLN266 3.3 35.7 1.0
O B:HOH512 3.8 38.4 1.0
CB B:GLN266 4.0 35.0 1.0
CG B:ASN263 4.2 40.7 1.0
OD1 B:ASN263 4.2 36.8 1.0
OD2 B:ASP270 4.4 40.0 1.0
O B:HOH641 4.5 30.3 1.0
CD B:GLN266 4.6 36.9 1.0
CG2 B:VAL267 4.8 40.4 1.0
C B:GLN266 4.9 35.6 1.0

Sodium binding site 4 out of 9 in 6z6i

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Sodium binding site 4 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na408

b:26.8
occ:1.00
 ND2 C:ASN263 2.7 17.1 1.0
O C:HOH504 3.2 26.5 1.0
CG C:ASN263 3.8 11.0 1.0
CG C:GLN266 4.0 11.2 1.0
OD1 C:ASN263 4.1 16.4 1.0
CG2 C:VAL267 4.2 11.4 1.0
CB C:GLN266 4.4 11.1 1.0
O C:HOH557 4.4 25.4 1.0
O C:HOH596 4.5 49.1 1.0
O C:HOH671 4.9 26.6 1.0
OD2 C:ASP270 4.9 19.5 1.0
O C:HOH599 4.9 30.6 1.0
N C:VAL267 5.0 11.4 1.0

Sodium binding site 5 out of 9 in 6z6i

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Sodium binding site 5 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na409

b:21.3
occ:1.00
 N C:LYS280 3.1 19.3 1.0
CD2 C:LEU279 3.6 24.8 1.0
CA C:LEU279 3.7 12.3 1.0
CB C:LEU279 3.7 12.8 1.0
O C:HOH608 3.7 31.6 1.0
CA C:GLY283 3.7 15.1 1.0
C C:LEU279 3.9 14.7 1.0
CB C:LYS280 4.0 21.3 1.0
N C:SER284 4.0 12.1 1.0
CA C:LYS280 4.1 15.1 1.0
O C:LYS280 4.2 24.9 1.0
CG C:LEU279 4.2 17.8 1.0
C C:GLY283 4.3 16.7 1.0
CG C:LYS280 4.3 21.6 1.0
O C:SER284 4.3 12.4 1.0
C C:LYS280 4.6 17.3 1.0
O C:HOH649 4.7 33.0 1.0
N C:GLY283 4.7 23.0 1.0
CD1 C:LEU279 4.9 17.3 1.0

Sodium binding site 6 out of 9 in 6z6i

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Sodium binding site 6 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na410

b:33.9
occ:1.00
 O C:HOH528 2.3 38.5 1.0
ND1 C:HIS342 3.0 23.4 1.0
NE C:ARG345 3.1 29.0 1.0
CA C:HIS342 3.4 14.8 1.0
CB C:HIS342 3.4 16.0 1.0
CG C:HIS342 3.7 21.8 1.0
CD C:ARG345 3.8 21.9 1.0
N C:HIS342 3.9 15.6 1.0
CZ C:ARG345 4.1 32.1 1.0
CE1 C:HIS342 4.2 23.1 1.0
NH1 C:ARG345 4.2 35.6 1.0
CB C:ARG345 4.2 16.2 1.0
C C:ILE341 4.4 13.9 1.0
O C:ILE341 4.5 14.2 1.0
CG C:ARG345 4.6 20.8 1.0
CG2 C:ILE341 4.6 13.1 1.0
C C:HIS342 4.7 14.6 1.0
CE C:MET375 4.8 23.7 1.0
O C:HIS342 4.9 22.0 1.0
CD2 C:HIS342 5.0 23.1 1.0

Sodium binding site 7 out of 9 in 6z6i

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Sodium binding site 7 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na411

b:26.4
occ:1.00
 O C:HOH714 3.1 51.0 1.0
O C:HOH590 3.2 8.4 1.0
CD1 C:ILE335 3.6 39.6 1.0
N C:GLY251 3.6 10.8 1.0
CG2 C:ILE335 4.2 26.8 1.0
CA C:GLY250 4.4 26.7 1.0
C1N C:A1R401 4.5 13.3 1.0
CA C:GLY251 4.5 10.8 1.0
CG1 C:ILE335 4.5 35.9 1.0
C C:GLY250 4.5 29.4 1.0
CB C:ILE335 4.9 27.0 1.0

Sodium binding site 8 out of 9 in 6z6i

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Sodium binding site 8 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na409

b:14.9
occ:1.00
 O D:VAL325 2.9 13.6 1.0
O D:HOH604 3.1 32.8 1.0
N D:VAL325 3.2 16.1 1.0
CG1 D:VAL325 3.4 12.0 1.0
CB D:THR237 3.6 14.0 1.0
CG2 D:THR237 3.7 14.8 1.0
C D:VAL325 3.8 12.1 1.0
N D:GLU324 3.8 14.6 1.0
CG2 D:VAL238 3.8 13.7 1.0
CA D:VAL325 3.9 12.3 1.0
CB D:GLU324 3.9 16.1 1.0
C D:GLU324 4.2 18.6 1.0
CA D:GLU324 4.2 17.2 1.0
CB D:VAL325 4.2 12.0 1.0
O D:HOH586 4.3 12.4 1.0
OG1 D:THR237 4.3 18.4 1.0
C D:HIS323 4.6 18.1 1.0
CB D:HIS323 4.6 12.2 1.0
CB D:VAL238 4.6 12.0 1.0
N D:VAL238 4.6 11.9 1.0
CA D:THR237 4.8 11.8 1.0
CA D:HIS323 4.9 12.2 1.0
C D:THR237 4.9 11.8 1.0

Sodium binding site 9 out of 9 in 6z6i

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Sodium binding site 9 out of 9 in the Sars-Cov-2 Macrodomain in Complex with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Sars-Cov-2 Macrodomain in Complex with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na410

b:45.1
occ:1.00
 O D:HOH510 2.3 29.2 1.0
C1 D:EDO404 2.7 13.2 1.0
O1 D:EDO404 3.2 27.1 1.0
C2 D:EDO404 3.3 15.1 1.0
O2 D:EDO404 3.6 15.4 1.0
CD1 D:ILE335 4.2 34.3 1.0
CG2 D:ILE335 4.3 31.2 1.0
N D:GLY251 4.7 18.2 1.0
CG1 D:ILE335 4.9 34.5 1.0
C1N D:A1R401 5.0 12.8 1.0
CA D:GLY250 5.0 27.6 1.0

Reference:

J.G.M.Rack, V.Zorzini, Z.Zhu, M.Schuller, D.Ahel, I.Ahel. Viral Macrodomains: A Structural and Evolutionary Assessment of the Pharmacological Potential. Open Biology V. 10 00237 2020.
ISSN: ESSN 2046-2441
PubMed: 33202171
DOI: 10.1098/RSOB.200237
Page generated: Tue Oct 8 15:20:30 2024

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