Zinc in PDB 6wjt: 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine

Protein crystallography data

The structure of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine, PDB code: 6wjt was solved by G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.79 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.917, 166.917, 98.099, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 19.1

Other elements in 6wjt:

The structure of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine (pdb code 6wjt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine, PDB code: 6wjt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6wjt

Go back to Zinc Binding Sites List in 6wjt
Zinc binding site 1 out of 4 in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4401

b:44.5
occ:1.00
NE2 B:HIS4336 2.1 61.5 1.0
SG B:CYS4327 2.3 45.8 1.0
SG B:CYS4343 2.3 47.9 1.0
SG B:CYS4330 2.3 47.5 1.0
CD2 B:HIS4336 3.0 61.7 1.0
CE1 B:HIS4336 3.1 61.5 1.0
CB B:CYS4327 3.3 45.0 1.0
CB B:CYS4343 3.3 54.0 1.0
CB B:CYS4330 3.4 46.8 1.0
N B:CYS4330 3.5 46.7 1.0
CA B:CYS4330 3.9 46.1 1.0
ND1 B:HIS4336 4.2 62.6 1.0
CG B:HIS4336 4.2 62.9 1.0
O B:HOH4556 4.4 35.9 0.5
CA B:CYS4343 4.5 56.9 1.0
C B:TYR4329 4.5 49.1 1.0
CB B:TYR4329 4.5 52.7 1.0
CA B:CYS4327 4.7 43.1 1.0
CB B:LYS4346 4.8 44.4 1.0
CA B:TYR4329 4.9 50.8 1.0
N B:LYS4346 5.0 41.7 1.0
O B:CYS4327 5.0 41.6 1.0

Zinc binding site 2 out of 4 in 6wjt

Go back to Zinc Binding Sites List in 6wjt
Zinc binding site 2 out of 4 in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4402

b:55.2
occ:1.00
SG B:CYS4381 2.3 50.3 1.0
SG B:CYS4370 2.3 56.5 1.0
SG B:CYS4373 2.3 57.4 1.0
SG B:CYS4383 2.3 61.3 1.0
CB B:CYS4370 3.2 55.1 1.0
CB B:CYS4373 3.3 58.7 1.0
CB B:CYS4383 3.4 67.7 1.0
CB B:CYS4381 3.5 52.7 1.0
N B:CYS4373 3.6 58.8 1.0
CA B:CYS4373 4.0 57.8 1.0
O B:HOH4520 4.1 36.3 0.5
CA B:CYS4381 4.1 53.4 1.0
N B:CYS4383 4.1 66.1 1.0
CA B:CYS4383 4.3 68.5 1.0
CB B:VAL4372 4.4 64.8 1.0
N B:SER4382 4.5 61.1 1.0
NZ B:LYS4377 4.5 80.1 1.0
CA B:CYS4370 4.6 53.2 1.0
C B:CYS4381 4.6 57.0 1.0
C B:VAL4372 4.6 62.0 1.0
CA B:VAL4372 4.9 62.4 1.0
C B:CYS4373 4.9 55.2 1.0
CG1 B:VAL4372 4.9 65.7 1.0
N B:VAL4372 4.9 61.3 1.0
N B:GLY4374 5.0 52.9 1.0

Zinc binding site 3 out of 4 in 6wjt

Go back to Zinc Binding Sites List in 6wjt
Zinc binding site 3 out of 4 in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4401

b:41.5
occ:1.00
NE2 D:HIS4336 2.1 57.1 1.0
SG D:CYS4327 2.3 45.5 1.0
SG D:CYS4343 2.3 46.2 1.0
SG D:CYS4330 2.3 45.7 1.0
CD2 D:HIS4336 3.1 58.2 1.0
CE1 D:HIS4336 3.1 58.0 1.0
CB D:CYS4327 3.3 44.2 1.0
CB D:CYS4343 3.3 51.5 1.0
CB D:CYS4330 3.4 44.4 1.0
N D:CYS4330 3.6 45.3 1.0
CA D:CYS4330 3.9 44.3 1.0
ND1 D:HIS4336 4.2 60.1 1.0
CG D:HIS4336 4.2 60.9 1.0
CA D:CYS4343 4.5 54.2 1.0
O D:HOH4556 4.5 41.3 0.5
C D:TYR4329 4.5 47.4 1.0
CB D:TYR4329 4.5 52.2 1.0
CA D:CYS4327 4.7 42.6 1.0
CB D:LYS4346 4.7 43.5 1.0
CA D:TYR4329 4.9 49.6 1.0
N D:LYS4346 5.0 40.6 1.0

Zinc binding site 4 out of 4 in 6wjt

Go back to Zinc Binding Sites List in 6wjt
Zinc binding site 4 out of 4 in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4402

b:57.4
occ:1.00
SG D:CYS4381 2.3 56.3 1.0
SG D:CYS4370 2.3 69.0 1.0
SG D:CYS4373 2.3 67.5 1.0
SG D:CYS4383 2.3 74.3 1.0
CB D:CYS4370 3.2 66.4 1.0
CB D:CYS4373 3.4 66.7 1.0
CB D:CYS4383 3.4 80.7 1.0
CB D:CYS4381 3.5 59.1 1.0
O D:HOH4509 3.7 64.1 1.0
N D:CYS4373 3.7 65.3 1.0
CA D:CYS4381 4.0 57.5 1.0
N D:CYS4383 4.1 79.3 1.0
CA D:CYS4373 4.1 63.6 1.0
CA D:CYS4383 4.3 83.0 1.0
N D:SER4382 4.4 67.8 1.0
C D:CYS4381 4.5 62.2 1.0
CB D:VAL4372 4.5 73.1 1.0
CA D:CYS4370 4.7 64.0 1.0
C D:VAL4372 4.7 66.9 1.0
C D:CYS4373 4.9 58.3 1.0

Reference:

G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine To Be Published.
Page generated: Wed Dec 16 13:05:01 2020

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