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Zinc in PDB 7elb: Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)

Enzymatic activity of Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)

All present enzymatic activity of Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form):
2.7.7.48;

Other elements in 7elb:

The structure of Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form) 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 (Dimeric Form) (pdb code 7elb). 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 (Dimeric Form), PDB code: 7elb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7elb

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Zinc binding site 1 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)


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 (Dimeric Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2302

b:205.6
occ:1.00
 ND1 A:HIS472 2.1 147.2 1.0
SG A:CYS284 2.4 145.2 1.0
SG A:CYS470 2.4 171.0 1.0
SG A:CYS287 2.4 148.9 1.0
CE1 A:HIS472 2.7 147.2 1.0
CB A:CYS284 2.9 145.2 1.0
CG A:HIS472 3.2 147.2 1.0
CB A:CYS287 3.3 148.9 1.0
CB A:CYS470 3.7 171.0 1.0
N A:CYS287 3.8 148.9 1.0
CB A:HIS472 3.8 147.2 1.0
NE2 A:HIS472 3.9 147.2 1.0
CA A:CYS287 4.2 148.9 1.0
CD2 A:HIS472 4.2 147.2 1.0
CA A:CYS284 4.3 145.2 1.0
CA A:CYS470 4.4 171.0 1.0
O A:CYS284 4.4 145.2 1.0
C A:CYS284 4.5 145.2 1.0
CB A:PHE286 4.7 141.9 1.0
C A:PHE286 4.8 141.9 1.0
C A:CYS470 4.8 171.0 1.0
N A:PHE286 4.9 141.9 1.0
N A:ARG471 4.9 157.9 1.0
N A:HIS472 4.9 147.2 1.0

Zinc binding site 2 out of 8 in 7elb

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Zinc binding site 2 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)


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 (Dimeric Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2303

b:151.7
occ:1.00
 SG A:CYS1650 2.4 119.3 1.0
SG A:CYS1664 2.4 95.8 1.0
SG A:CYS1652 2.4 126.0 1.0
SG A:CYS1655 2.4 104.8 1.0
CB A:CYS1655 2.9 104.8 1.0
OG A:SER1667 3.4 85.3 1.0
N A:CYS1652 3.5 126.0 1.0
N A:CYS1655 3.6 104.8 1.0
CB A:CYS1664 3.7 95.8 1.0
CB A:CYS1652 3.8 126.0 1.0
CA A:CYS1655 3.8 104.8 1.0
N A:THR1651 4.0 126.6 1.0
CG2 A:ILE1654 4.1 94.5 1.0
CA A:CYS1652 4.1 126.0 1.0
CB A:CYS1650 4.2 119.3 1.0
CA A:THR1651 4.4 126.6 1.0
C A:THR1651 4.4 126.6 1.0
N A:CYS1664 4.5 95.8 1.0
C A:ILE1654 4.6 94.5 1.0
C A:CYS1652 4.6 126.0 1.0
CB A:SER1667 4.6 85.3 1.0
CA A:CYS1664 4.7 95.8 1.0
OD1 A:ASN1666 4.8 88.6 1.0
C A:CYS1655 4.8 104.8 1.0
C A:CYS1650 4.8 119.3 1.0
N A:ILE1654 4.8 94.5 1.0

Zinc binding site 3 out of 8 in 7elb

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


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 (Dimeric Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:191.5
occ:1.00
 SG B:CYS61 2.4 160.0 1.0
SG B:CYS58 2.4 172.5 1.0
SG B:CYS39 2.4 150.3 1.0
SG B:CYS42 2.4 142.1 1.0
CB B:CYS39 3.3 150.3 1.0
CB B:CYS61 3.6 160.0 1.0
CB B:CYS58 3.7 172.5 1.0
CB B:CYS42 3.7 142.1 1.0
CB B:ALA45 4.3 159.1 1.0
N B:CYS42 4.3 142.1 1.0
N B:CYS61 4.5 160.0 1.0
CA B:CYS42 4.6 142.1 1.0
CA B:CYS61 4.7 160.0 1.0
N B:CYS58 4.7 172.5 1.0
CB B:CYS41 4.8 143.6 1.0
CA B:CYS39 4.8 150.3 1.0
CA B:CYS58 4.8 172.5 1.0

Zinc binding site 4 out of 8 in 7elb

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Zinc binding site 4 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)


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 (Dimeric Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:244.6
occ:1.00
 NE2 B:HIS55 2.1 182.5 1.0
CE1 B:HIS55 2.3 182.5 1.0
SG B:CYS52 2.4 186.9 1.0
SG B:CYS75 2.4 161.3 1.0
SG B:CYS72 2.4 174.1 1.0
CB B:CYS52 3.0 186.9 1.0
CG2 B:ILE74 3.3 162.4 1.0
CD2 B:HIS55 3.4 182.5 1.0
CB B:CYS75 3.4 161.3 1.0
ND1 B:HIS55 3.6 182.5 1.0
CB B:CYS72 3.8 174.1 1.0
N B:CYS75 3.9 161.3 1.0
O B:CYS52 4.1 186.9 1.0
CG B:HIS55 4.1 182.5 1.0
CA B:CYS75 4.3 161.3 1.0
CA B:CYS52 4.4 186.9 1.0
C B:ILE74 4.6 162.4 1.0
C B:CYS52 4.7 186.9 1.0
CB B:ILE74 4.7 162.4 1.0
CD2 B:LEU79 4.9 186.3 1.0

Zinc binding site 5 out of 8 in 7elb

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Zinc binding site 5 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)


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 (Dimeric Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2302

b:211.9
occ:1.00
 ND1 C:HIS472 2.1 145.8 1.0
SG C:CYS284 2.4 146.2 1.0
SG C:CYS470 2.4 170.5 1.0
SG C:CYS287 2.4 147.6 1.0
CE1 C:HIS472 2.7 145.8 1.0
CB C:CYS284 2.9 146.2 1.0
CG C:HIS472 3.2 145.8 1.0
CB C:CYS287 3.3 147.6 1.0
CB C:CYS470 3.7 170.5 1.0
N C:CYS287 3.8 147.6 1.0
CB C:HIS472 3.8 145.8 1.0
NE2 C:HIS472 3.9 145.8 1.0
CA C:CYS287 4.2 147.6 1.0
CD2 C:HIS472 4.2 145.8 1.0
CA C:CYS284 4.3 146.2 1.0
CA C:CYS470 4.4 170.5 1.0
O C:CYS284 4.4 146.2 1.0
C C:CYS284 4.5 146.2 1.0
CB C:PHE286 4.7 140.4 1.0
C C:PHE286 4.8 140.4 1.0
C C:CYS470 4.8 170.5 1.0
N C:PHE286 4.9 140.4 1.0
N C:ARG471 4.9 156.0 1.0
N C:HIS472 4.9 145.8 1.0

Zinc binding site 6 out of 8 in 7elb

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Zinc binding site 6 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)


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 (Dimeric Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2303

b:154.1
occ:1.00
 SG C:CYS1650 2.4 117.5 1.0
SG C:CYS1664 2.4 94.4 1.0
SG C:CYS1652 2.4 123.4 1.0
SG C:CYS1655 2.4 104.9 1.0
CB C:CYS1655 2.9 104.9 1.0
OG C:SER1667 3.4 86.2 1.0
N C:CYS1652 3.5 123.4 1.0
N C:CYS1655 3.6 104.9 1.0
CB C:CYS1664 3.7 94.4 1.0
CB C:CYS1652 3.8 123.4 1.0
CA C:CYS1655 3.8 104.9 1.0
N C:THR1651 4.0 124.3 1.0
CG2 C:ILE1654 4.1 93.3 1.0
CA C:CYS1652 4.1 123.4 1.0
CB C:CYS1650 4.2 117.5 1.0
CA C:THR1651 4.4 124.3 1.0
C C:THR1651 4.4 124.3 1.0
N C:CYS1664 4.5 94.4 1.0
C C:ILE1654 4.6 93.3 1.0
C C:CYS1652 4.6 123.4 1.0
CB C:SER1667 4.6 86.2 1.0
CA C:CYS1664 4.7 94.4 1.0
OD1 C:ASN1666 4.8 88.5 1.0
C C:CYS1655 4.8 104.9 1.0
C C:CYS1650 4.8 117.5 1.0
N C:ILE1654 4.8 93.3 1.0

Zinc binding site 7 out of 8 in 7elb

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Zinc binding site 7 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)


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 (Dimeric Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:186.3
occ:1.00
 SG D:CYS61 2.4 160.3 1.0
SG D:CYS58 2.4 172.2 1.0
SG D:CYS39 2.4 150.2 1.0
SG D:CYS42 2.4 142.2 1.0
CB D:CYS39 3.3 150.2 1.0
CB D:CYS61 3.6 160.3 1.0
CB D:CYS58 3.7 172.2 1.0
CB D:CYS42 3.7 142.2 1.0
CB D:ALA45 4.3 160.2 1.0
N D:CYS42 4.3 142.2 1.0
N D:CYS61 4.5 160.3 1.0
CA D:CYS42 4.6 142.2 1.0
CA D:CYS61 4.7 160.3 1.0
N D:CYS58 4.8 172.2 1.0
CB D:CYS41 4.8 143.6 1.0
CA D:CYS39 4.8 150.2 1.0
CA D:CYS58 4.8 172.2 1.0

Zinc binding site 8 out of 8 in 7elb

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Zinc binding site 8 out of 8 in the Structure of Machupo Virus L Polymerase in Complex with Z Protein (Dimeric Form)


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 (Dimeric Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn102

b:246.2
occ:1.00
 NE2 D:HIS55 2.1 181.4 1.0
CE1 D:HIS55 2.3 181.4 1.0
SG D:CYS52 2.4 186.6 1.0
SG D:CYS75 2.4 162.9 1.0
SG D:CYS72 2.4 172.9 1.0
CB D:CYS52 3.0 186.6 1.0
CG2 D:ILE74 3.3 159.9 1.0
CB D:CYS75 3.4 162.9 1.0
CD2 D:HIS55 3.4 181.4 1.0
ND1 D:HIS55 3.6 181.4 1.0
CB D:CYS72 3.8 172.9 1.0
N D:CYS75 3.9 162.9 1.0
O D:CYS52 4.1 186.6 1.0
CG D:HIS55 4.1 181.4 1.0
CA D:CYS75 4.3 162.9 1.0
CA D:CYS52 4.4 186.6 1.0
C D:ILE74 4.6 159.9 1.0
C D:CYS52 4.7 186.6 1.0
CB D:ILE74 4.7 159.9 1.0
CD2 D:LEU79 4.9 184.7 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: Tue Oct 29 19:55:37 2024

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