Zinc in PDB 7l6t: Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions.

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions., PDB code: 7l6t was solved by G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, J.S.Brunzelle, 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) 29.33 / 1.78
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.351, 169.351, 52.629, 90, 90, 120
R / Rfree (%) 14.1 / 16.2

Other elements in 7l6t:

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions. (pdb code 7l6t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions., PDB code: 7l6t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7l6t

Go back to Zinc Binding Sites List in 7l6t
Zinc binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4401

b:34.8
occ:1.00
NE2 B:HIS4336 2.1 40.1 1.0
SG B:CYS4327 2.3 34.8 1.0
SG B:CYS4343 2.3 40.8 1.0
SG B:CYS4330 2.3 35.9 1.0
CD2 B:HIS4336 3.1 45.3 1.0
CE1 B:HIS4336 3.1 42.5 1.0
CB B:CYS4327 3.2 33.9 1.0
CB B:CYS4343 3.3 45.0 1.0
CB B:CYS4330 3.4 33.2 1.0
N B:CYS4330 3.6 33.3 1.0
CA B:CYS4330 4.0 32.8 1.0
ND1 B:HIS4336 4.2 43.4 1.0
CG B:HIS4336 4.2 44.9 1.0
CA B:CYS4343 4.4 47.3 1.0
O B:HOH4526 4.4 55.1 1.0
C B:TYR4329 4.6 35.5 1.0
CB B:TYR4329 4.6 39.6 1.0
CA B:CYS4327 4.6 32.8 1.0
CB B:LYS4346 4.9 38.5 1.0
CA B:TYR4329 4.9 37.6 1.0

Zinc binding site 2 out of 2 in 7l6t

Go back to Zinc Binding Sites List in 7l6t
Zinc binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4402

b:53.5
occ:1.00
SG B:CYS4381 2.3 60.9 1.0
SG B:CYS4370 2.3 67.6 1.0
SG B:CYS4373 2.3 56.2 1.0
SG B:CYS4383 2.3 75.8 1.0
CB B:CYS4370 3.2 65.8 1.0
CB B:CYS4373 3.3 60.7 1.0
CB B:CYS4383 3.4 85.8 1.0
CB B:CYS4381 3.4 59.5 1.0
O B:HOH4535 3.7 55.8 1.0
N B:CYS4373 3.7 64.2 1.0
CA B:CYS4381 4.0 57.0 1.0
N B:CYS4383 4.0 78.0 1.0
CA B:CYS4373 4.1 59.9 1.0
CA B:CYS4383 4.3 85.8 1.0
N B:SER4382 4.4 64.0 1.0
C B:CYS4381 4.5 61.6 1.0
CB B:VAL4372 4.5 74.4 1.0
CA B:CYS4370 4.7 64.5 1.0
C B:VAL4372 4.8 67.0 1.0
C B:CYS4373 4.9 55.0 1.0

Reference:

G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, J.S.Brunzelle, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1), S-Adenosyl-L-Homocysteine (Sah) and Two Magnesium (Mg) Ions. To Be Published.
Page generated: Mon Jan 25 16:48:02 2021

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