Zinc in PDB 7el9: Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)

Enzymatic activity of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)

All present enzymatic activity of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex):
2.7.7.48;

Other elements in 7el9:

The structure of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) (pdb code 7el9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex), PDB code: 7el9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7el9

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Zinc binding site 1 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2302

b:78.3
occ:1.00
 ND1 A:HIS472 2.1 59.1 1.0
SG A:CYS284 2.4 61.9 1.0
SG A:CYS287 2.4 59.2 1.0
SG A:CYS470 2.4 73.8 1.0
CE1 A:HIS472 2.6 59.1 1.0
CB A:CYS284 3.0 61.9 1.0
CG A:HIS472 3.1 59.1 1.0
CB A:CYS470 3.6 73.8 1.0
CB A:CYS287 3.6 59.2 1.0
NE2 A:HIS472 3.6 59.1 1.0
CA A:CYS470 3.7 73.8 1.0
CB A:HIS472 3.7 59.1 1.0
CD2 A:HIS472 3.9 59.1 1.0
N A:CYS287 4.0 59.2 1.0
C A:CYS470 4.0 73.8 1.0
O A:CYS470 4.1 73.8 1.0
CA A:CYS287 4.3 59.2 1.0
CA A:CYS284 4.5 61.9 1.0
OG A:SER282 4.8 59.0 1.0
N A:HIS472 4.9 59.1 1.0
N A:ARG471 4.9 68.5 1.0
O A:ILE469 4.9 76.0 1.0
C A:PHE286 4.9 48.7 1.0
CA A:HIS472 4.9 59.1 1.0
CB A:PHE286 4.9 48.7 1.0
N A:CYS470 5.0 73.8 1.0
C A:CYS284 5.0 61.9 1.0

Zinc binding site 2 out of 8 in 7el9

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Zinc binding site 2 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2303

b:99.5
occ:1.00
 SG A:CYS1650 2.4 91.3 1.0
SG A:CYS1664 2.4 68.7 1.0
SG A:CYS1652 2.4 90.0 1.0
SG A:CYS1655 2.4 72.7 1.0
CB A:CYS1650 3.1 91.3 1.0
CB A:CYS1655 3.2 72.7 1.0
N A:CYS1655 3.2 72.7 1.0
CB A:CYS1664 3.4 68.7 1.0
CB A:CYS1652 3.8 90.0 1.0
CA A:CYS1655 3.8 72.7 1.0
N A:CYS1652 3.8 90.0 1.0
CB A:ILE1654 4.0 74.9 1.0
C A:ILE1654 4.0 74.9 1.0
N A:ILE1654 4.2 74.9 1.0
C A:CYS1650 4.2 91.3 1.0
CA A:CYS1650 4.2 91.3 1.0
CA A:CYS1652 4.2 90.0 1.0
CA A:ILE1654 4.3 74.9 1.0
N A:THR1651 4.3 94.1 1.0
CA A:CYS1664 4.4 68.7 1.0
N A:CYS1664 4.5 68.7 1.0
C A:CYS1652 4.6 90.0 1.0
CG2 A:ILE1654 4.6 74.9 1.0
O A:CYS1650 4.7 91.3 1.0
C A:THR1651 4.9 94.1 1.0
O A:CYS1652 4.9 90.0 1.0
CA A:THR1651 5.0 94.1 1.0

Zinc binding site 3 out of 8 in 7el9

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Zinc binding site 3 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:111.3
occ:1.00
 SG B:CYS61 2.4 99.7 1.0
SG B:CYS58 2.4 94.5 1.0
SG B:CYS39 2.4 81.5 1.0
SG B:CYS42 2.4 71.4 1.0
CB B:CYS39 3.2 81.5 1.0
CB B:CYS42 3.4 71.4 1.0
CB B:CYS61 3.5 99.7 1.0
CB B:CYS58 3.5 94.5 1.0
N B:CYS42 4.0 71.4 1.0
CB B:ALA45 4.1 75.8 1.0
CA B:CYS42 4.3 71.4 1.0
N B:CYS58 4.5 94.5 1.0
N B:CYS61 4.5 99.7 1.0
CA B:CYS61 4.6 99.7 1.0
CA B:CYS58 4.6 94.5 1.0
CB B:CYS41 4.7 72.8 1.0
CA B:CYS39 4.7 81.5 1.0
CG B:ARG60 4.7 98.2 1.0
CD B:ARG60 4.8 98.2 1.0
C B:CYS41 5.0 72.8 1.0

Zinc binding site 4 out of 8 in 7el9

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Zinc binding site 4 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:108.7
occ:1.00
 NE2 B:HIS55 2.1 95.5 1.0
CE1 B:HIS55 2.3 95.5 1.0
SG B:CYS75 2.4 88.6 1.0
SG B:CYS72 2.4 92.6 1.0
SG B:CYS52 2.4 104.9 1.0
CB B:CYS52 2.7 104.9 1.0
CD2 B:HIS55 3.3 95.5 1.0
ND1 B:HIS55 3.5 95.5 1.0
CB B:CYS75 3.5 88.6 1.0
CB B:CYS72 3.6 92.6 1.0
N B:CYS75 4.0 88.6 1.0
CG B:HIS55 4.0 95.5 1.0
CA B:CYS52 4.2 104.9 1.0
N B:ASN53 4.3 104.8 1.0
CA B:CYS75 4.4 88.6 1.0
CB B:ILE74 4.5 84.0 1.0
C B:CYS52 4.6 104.9 1.0
CG2 B:ILE74 4.8 84.0 1.0
N B:CYS52 4.9 104.9 1.0
CD2 B:LEU79 5.0 104.6 1.0
C B:ILE74 5.0 84.0 1.0

Zinc binding site 5 out of 8 in 7el9

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Zinc binding site 5 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2302

b:79.2
occ:1.00
 ND1 D:HIS472 2.1 59.2 1.0
SG D:CYS284 2.4 61.7 1.0
SG D:CYS287 2.4 59.1 1.0
SG D:CYS470 2.4 74.1 1.0
CE1 D:HIS472 2.6 59.2 1.0
CB D:CYS284 3.0 61.7 1.0
CG D:HIS472 3.0 59.2 1.0
CB D:CYS470 3.6 74.1 1.0
CB D:CYS287 3.6 59.1 1.0
NE2 D:HIS472 3.6 59.2 1.0
CA D:CYS470 3.7 74.1 1.0
CB D:HIS472 3.7 59.2 1.0
CD2 D:HIS472 3.9 59.2 1.0
N D:CYS287 4.0 59.1 1.0
C D:CYS470 4.0 74.1 1.0
O D:CYS470 4.1 74.1 1.0
CA D:CYS287 4.3 59.1 1.0
CA D:CYS284 4.5 61.7 1.0
OG D:SER282 4.8 58.9 1.0
N D:HIS472 4.9 59.2 1.0
N D:ARG471 4.9 69.5 1.0
O D:ILE469 4.9 76.6 1.0
C D:PHE286 4.9 49.3 1.0
CA D:HIS472 4.9 59.2 1.0
CB D:PHE286 4.9 49.3 1.0
N D:CYS470 5.0 74.1 1.0
C D:CYS284 5.0 61.7 1.0

Zinc binding site 6 out of 8 in 7el9

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Zinc binding site 6 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2303

b:97.2
occ:1.00
 SG D:CYS1650 2.4 91.0 1.0
SG D:CYS1664 2.4 68.1 1.0
SG D:CYS1652 2.4 90.0 1.0
SG D:CYS1655 2.4 72.8 1.0
CB D:CYS1650 3.1 91.0 1.0
CB D:CYS1655 3.2 72.8 1.0
N D:CYS1655 3.2 72.8 1.0
CB D:CYS1664 3.4 68.1 1.0
CB D:CYS1652 3.8 90.0 1.0
CA D:CYS1655 3.8 72.8 1.0
N D:CYS1652 3.8 90.0 1.0
CB D:ILE1654 4.0 74.0 1.0
C D:ILE1654 4.0 74.0 1.0
N D:ILE1654 4.2 74.0 1.0
C D:CYS1650 4.2 91.0 1.0
CA D:CYS1650 4.2 91.0 1.0
CA D:CYS1652 4.2 90.0 1.0
CA D:ILE1654 4.3 74.0 1.0
N D:THR1651 4.3 93.9 1.0
CA D:CYS1664 4.4 68.1 1.0
N D:CYS1664 4.5 68.1 1.0
C D:CYS1652 4.6 90.0 1.0
CG2 D:ILE1654 4.6 74.0 1.0
O D:CYS1650 4.7 91.0 1.0
C D:THR1651 4.9 93.9 1.0
O D:CYS1652 4.9 90.0 1.0
CA D:THR1651 5.0 93.9 1.0

Zinc binding site 7 out of 8 in 7el9

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Zinc binding site 7 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:111.9
occ:1.00
 SG E:CYS61 2.4 99.7 1.0
SG E:CYS58 2.4 95.8 1.0
SG E:CYS39 2.4 81.8 1.0
SG E:CYS42 2.4 71.5 1.0
CB E:CYS39 3.2 81.8 1.0
CB E:CYS42 3.4 71.5 1.0
CB E:CYS61 3.5 99.7 1.0
CB E:CYS58 3.5 95.8 1.0
N E:CYS42 4.0 71.5 1.0
CB E:ALA45 4.1 75.9 1.0
CA E:CYS42 4.3 71.5 1.0
N E:CYS58 4.5 95.8 1.0
N E:CYS61 4.5 99.7 1.0
CA E:CYS61 4.6 99.7 1.0
CA E:CYS58 4.6 95.8 1.0
CB E:CYS41 4.7 73.0 1.0
CA E:CYS39 4.7 81.8 1.0
CG E:ARG60 4.7 97.8 1.0
CD E:ARG60 4.8 97.8 1.0
C E:CYS41 5.0 73.0 1.0

Zinc binding site 8 out of 8 in 7el9

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Zinc binding site 8 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Machupo Virus L Polymerase in Complex with Z Protein and 3'-Vrna (Dimeric Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn102

b:111.2
occ:1.00
 NE2 E:HIS55 2.1 95.5 1.0
CE1 E:HIS55 2.3 95.5 1.0
SG E:CYS75 2.4 88.8 1.0
SG E:CYS72 2.4 92.7 1.0
SG E:CYS52 2.4 105.4 1.0
CB E:CYS52 2.7 105.4 1.0
CD2 E:HIS55 3.3 95.5 1.0
ND1 E:HIS55 3.5 95.5 1.0
CB E:CYS75 3.5 88.8 1.0
CB E:CYS72 3.6 92.7 1.0
N E:CYS75 4.0 88.8 1.0
CG E:HIS55 4.0 95.5 1.0
CA E:CYS52 4.2 105.4 1.0
N E:ASN53 4.3 105.5 1.0
CA E:CYS75 4.4 88.8 1.0
CB E:ILE74 4.5 83.8 1.0
C E:CYS52 4.6 105.4 1.0
CG2 E:ILE74 4.8 83.8 1.0
N E:CYS52 4.9 105.4 1.0
CD2 E:LEU79 5.0 104.2 1.0
C E:ILE74 5.0 83.8 1.0

Reference:

R.Peng, X.Xu, Q.Peng, Y.Shi. Cryo-Em Structures of Lassa and Machupo Virus Polymerases Complexed with Cognate Regulatory Z Proteins Identify Targets For Antivirals. Nat Microbiol 2021.
ISSN: ESSN 2058-5276
Page generated: Mon Jul 12 17:03:41 2021

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