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Zinc in PDB 7cyq: Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis

Enzymatic activity of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis

All present enzymatic activity of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis:
3.4.19.12; 3.6.4.13;

Other elements in 7cyq:

The structure of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis (pdb code 7cyq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis, PDB code: 7cyq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7cyq

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:70.2
occ:1.00
 ND1 A:HIS295 2.1 49.1 1.0
SG A:CYS310 2.3 48.1 1.0
SG A:CYS301 2.3 54.4 1.0
SG A:CYS306 2.3 50.2 1.0
CE1 A:HIS295 2.9 49.1 1.0
CG A:HIS295 3.2 49.1 1.0
O A:CYS306 3.2 50.2 1.0
CB A:CYS301 3.4 54.4 1.0
CB A:CYS310 3.5 48.1 1.0
CB A:CYS306 3.6 50.2 1.0
CB A:HIS295 3.7 49.1 1.0
CA A:CYS301 3.7 54.4 1.0
C A:CYS306 3.8 50.2 1.0
NE2 A:HIS295 4.1 49.1 1.0
CA A:CYS306 4.2 50.2 1.0
N A:HIS295 4.2 49.1 1.0
CD2 A:HIS295 4.2 49.1 1.0
N A:CYS301 4.5 54.4 1.0
CA A:HIS295 4.6 49.1 1.0
N A:ILE307 4.6 47.1 1.0
O A:THR293 4.7 51.5 1.0
N A:CYS310 4.7 48.1 1.0
CA A:CYS310 4.7 48.1 1.0
O A:HIS295 4.9 49.1 1.0
N A:LEU302 4.9 57.6 1.0
C A:CYS301 4.9 54.4 1.0

Zinc binding site 2 out of 8 in 7cyq

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:71.7
occ:1.00
 ND1 A:HIS642 2.0 52.5 1.0
SG A:CYS487 2.3 54.9 1.0
SG A:CYS645 2.3 57.5 1.0
SG A:CYS646 2.3 60.1 1.0
CE1 A:HIS642 2.9 52.5 1.0
CG A:HIS642 3.2 52.5 1.0
CB A:CYS646 3.4 60.1 1.0
CB A:CYS487 3.6 54.9 1.0
CB A:CYS645 3.6 57.5 1.0
CB A:HIS642 3.6 52.5 1.0
CE1 A:PHE571 3.8 48.9 1.0
N A:CYS646 3.8 60.1 1.0
N A:CYS487 3.9 54.9 1.0
NE2 A:HIS642 4.0 52.5 1.0
CA A:CYS646 4.1 60.1 1.0
C A:CYS645 4.2 57.5 1.0
CD2 A:HIS642 4.2 52.5 1.0
CD1 A:PHE571 4.2 48.9 1.0
CA A:CYS487 4.2 54.9 1.0
NZ A:LYS532 4.5 47.9 1.0
CA A:CYS645 4.5 57.5 1.0
C A:GLY486 4.6 56.6 1.0
CA A:HIS642 4.6 52.5 1.0
O A:CYS645 4.7 57.5 1.0
CZ A:PHE571 4.8 48.9 1.0
CA A:GLY486 4.9 56.6 1.0
CE A:LYS532 5.0 47.9 1.0

Zinc binding site 3 out of 8 in 7cyq

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn701

b:0.5
occ:1.00
 ND1 F:HIS39 2.0 0.9 1.0
NE2 F:HIS33 2.1 0.6 1.0
SG F:CYS16 2.3 0.3 1.0
SG F:CYS19 2.3 0.9 1.0
CB F:CYS19 2.3 0.9 1.0
CE1 F:HIS33 2.8 0.6 1.0
CE1 F:HIS39 2.9 0.9 1.0
CG F:HIS39 3.1 0.9 1.0
CD2 F:HIS33 3.2 0.6 1.0
CB F:CYS16 3.3 0.3 1.0
CA F:CYS19 3.4 0.9 1.0
CB F:HIS39 3.5 0.9 1.0
N F:CYS19 3.9 0.9 1.0
ND1 F:HIS33 3.9 0.6 1.0
CB F:ALA110 4.0 0.4 1.0
NE2 F:HIS39 4.0 0.9 1.0
CD2 F:HIS39 4.1 0.9 1.0
CG F:HIS33 4.2 0.6 1.0
CE2 F:PHE106 4.6 0.7 1.0
C F:CYS19 4.7 0.9 1.0
CA F:CYS16 4.8 0.3 1.0
C F:ALA18 4.9 0.7 1.0
CA F:HIS39 4.9 0.9 1.0
O F:CYS16 5.0 0.3 1.0

Zinc binding site 4 out of 8 in 7cyq

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn702

b:0.4
occ:1.00
 CB F:CYS26 1.4 0.1 1.0
SG F:CYS8 2.3 0.2 1.0
SG F:CYS5 2.4 0.6 1.0
SG F:CYS26 2.4 0.1 1.0
SG F:CYS29 2.4 0.2 1.0
CB F:CYS8 2.5 0.2 1.0
CB F:CYS29 2.7 0.2 1.0
CA F:CYS26 2.8 0.1 1.0
N F:CYS26 3.1 0.1 1.0
CB F:CYS5 3.4 0.6 1.0
C F:CYS26 3.6 0.1 1.0
CA F:CYS8 3.8 0.2 1.0
O F:CYS26 3.8 0.1 1.0
N F:CYS8 3.9 0.2 1.0
CA F:CYS29 4.0 0.2 1.0
N F:CYS29 4.2 0.2 1.0
OG F:SER10 4.3 0.4 1.0
C F:LEU25 4.4 0.9 1.0
N F:CYS27 4.5 0.1 1.0
C F:LEU7 4.6 0.2 1.0
C F:CYS29 4.8 0.2 1.0
C F:CYS8 4.8 0.2 1.0
N F:GLY99 4.8 0.9 1.0
CA F:CYS5 4.9 0.6 1.0
N F:CYS30 4.9 0.6 1.0

Zinc binding site 5 out of 8 in 7cyq

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn703

b:0.0
occ:1.00
 ND1 F:HIS75 2.1 0.1 1.0
SG F:CYS55 2.3 0.2 1.0
SG F:CYS50 2.3 0.0 1.0
SG F:CYS72 2.3 0.2 1.0
CE1 F:HIS75 2.4 0.1 1.0
CG2 F:VAL57 2.7 1.0 1.0
CB F:CYS50 2.8 0.0 1.0
CB F:CYS72 3.1 0.2 1.0
CB F:CYS55 3.3 0.2 1.0
CG F:HIS75 3.5 0.1 1.0
N F:CYS72 3.6 0.2 1.0
NE2 F:HIS75 3.7 0.1 1.0
CA F:CYS72 4.0 0.2 1.0
CB F:VAL57 4.0 1.0 1.0
CG1 F:VAL57 4.2 1.0 1.0
CD2 F:HIS75 4.2 0.1 1.0
CA F:CYS50 4.3 0.0 1.0
CB F:HIS75 4.3 0.1 1.0
OG F:SER74 4.5 0.8 1.0
N F:VAL57 4.5 1.0 1.0
O F:CYS50 4.7 0.0 1.0
CA F:CYS55 4.8 0.2 1.0
C F:TYR71 4.8 0.1 1.0
C F:CYS50 4.8 0.0 1.0
N F:ASP56 4.8 0.6 1.0
CA F:VAL57 4.9 1.0 1.0
C F:CYS72 4.9 0.2 1.0

Zinc binding site 6 out of 8 in 7cyq

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:0.1
occ:1.00
 ND1 E:HIS39 2.0 0.9 1.0
NE2 E:HIS33 2.1 0.6 1.0
SG E:CYS16 2.3 0.5 1.0
SG E:CYS19 2.3 0.9 1.0
CB E:CYS19 2.3 0.9 1.0
CE1 E:HIS33 2.8 0.6 1.0
CE1 E:HIS39 2.9 0.9 1.0
CG E:HIS39 3.1 0.9 1.0
CD2 E:HIS33 3.2 0.6 1.0
CB E:CYS16 3.3 0.5 1.0
CA E:CYS19 3.4 0.9 1.0
CB E:HIS39 3.5 0.9 1.0
N E:CYS19 3.9 0.9 1.0
ND1 E:HIS33 3.9 0.6 1.0
CB E:ALA110 4.0 0.5 1.0
NE2 E:HIS39 4.0 0.9 1.0
CD2 E:HIS39 4.1 0.9 1.0
CG E:HIS33 4.2 0.6 1.0
CE2 E:PHE106 4.6 0.7 1.0
C E:CYS19 4.7 0.9 1.0
CA E:CYS16 4.8 0.5 1.0
C E:ALA18 4.9 0.1 1.0
CA E:HIS39 4.9 0.9 1.0
O E:CYS16 5.0 0.5 1.0

Zinc binding site 7 out of 8 in 7cyq

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:0.9
occ:1.00
 CB E:CYS26 1.4 0.5 1.0
SG E:CYS8 2.3 0.7 1.0
SG E:CYS5 2.4 0.8 1.0
SG E:CYS26 2.4 0.5 1.0
SG E:CYS29 2.4 0.0 1.0
CB E:CYS8 2.5 0.7 1.0
CB E:CYS29 2.7 0.0 1.0
CA E:CYS26 2.8 0.5 1.0
N E:CYS26 3.1 0.5 1.0
CB E:CYS5 3.4 0.8 1.0
C E:CYS26 3.6 0.5 1.0
CA E:CYS8 3.8 0.7 1.0
O E:CYS26 3.8 0.5 1.0
N E:CYS8 3.9 0.7 1.0
CA E:CYS29 4.0 0.0 1.0
N E:CYS29 4.2 0.0 1.0
OG E:SER10 4.3 0.1 1.0
C E:LEU25 4.4 0.2 1.0
N E:CYS27 4.5 0.2 1.0
C E:LEU7 4.6 1.0 1.0
C E:CYS29 4.8 0.0 1.0
C E:CYS8 4.8 0.7 1.0
N E:GLY99 4.8 0.9 1.0
N E:CYS30 4.9 0.2 1.0
CA E:CYS5 4.9 0.8 1.0

Zinc binding site 8 out of 8 in 7cyq

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:0.0
occ:1.00
 ND1 E:HIS75 2.1 0.9 1.0
SG E:CYS55 2.3 0.1 1.0
SG E:CYS72 2.3 0.9 1.0
SG E:CYS50 2.3 0.0 1.0
CE1 E:HIS75 2.4 0.9 1.0
CG2 E:VAL57 2.7 0.6 1.0
CB E:CYS50 2.8 0.0 1.0
CB E:CYS72 3.1 0.9 1.0
CB E:CYS55 3.3 0.1 1.0
CG E:HIS75 3.5 0.9 1.0
N E:CYS72 3.6 0.9 1.0
NE2 E:HIS75 3.7 0.9 1.0
CA E:CYS72 4.0 0.9 1.0
CB E:VAL57 4.0 0.6 1.0
CG1 E:VAL57 4.2 0.6 1.0
CD2 E:HIS75 4.2 0.9 1.0
CA E:CYS50 4.3 0.0 1.0
CB E:HIS75 4.3 0.9 1.0
OG E:SER74 4.5 0.7 1.0
N E:VAL57 4.5 0.6 1.0
O E:CYS50 4.7 0.0 1.0
CA E:CYS55 4.8 0.1 1.0
C E:TYR71 4.8 0.7 1.0
C E:CYS50 4.8 0.0 1.0
N E:ASP56 4.8 0.9 1.0
CA E:VAL57 4.9 0.6 1.0
C E:CYS72 4.9 0.9 1.0

Reference:

L.Yan, J.Ge, L.Zheng, Y.Zhang, Y.Gao, T.Wang, Y.Huang, Y.Yang, S.Gao, M.Li, Z.Liu, H.Wang, Y.Li, Y.Chen, L.W.Guddat, Q.Wang, Z.Rao, Z.Lou. Cryo-Em Structure of An Extended Sars-Cov-2 Replication and Transcription Complex Reveals An Intermediate State in Cap Synthesis. Cell 2020.
ISSN: ISSN 1097-4172
PubMed: 33232691
DOI: 10.1016/J.CELL.2020.11.016
Page generated: Tue Oct 29 18:30:33 2024

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