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Zinc in PDB 7d6n: Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase

Enzymatic activity of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase

All present enzymatic activity of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase:
2.7.7.49;

Protein crystallography data

The structure of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase, PDB code: 7d6n was solved by J.Yang, X.Jing, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.99 / 3.17
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 175.988, 235.181, 327.433, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.3

Other elements in 7d6n:

The structure of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase (pdb code 7d6n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase, PDB code: 7d6n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in 7d6n

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Zinc binding site 1 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


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 Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:68.5
occ:0.60
 SG A:CYS729 2.1 47.3 1.0
SG A:CYS848 2.5 83.0 1.0
CB A:CYS729 2.8 35.6 1.0
NE2 A:HIS715 3.0 71.0 1.0
CD2 A:HIS715 3.4 57.8 1.0
CB A:CYS848 3.9 87.2 1.0
CE1 A:HIS715 4.1 74.6 1.0
CA A:CYS729 4.1 40.7 1.0
C A:CYS729 4.4 41.8 1.0
N A:ARG730 4.4 48.7 1.0
CG A:HIS715 4.6 57.6 1.0
CB A:HIS713 4.7 39.0 1.0
NH1 A:ARG770 4.9 62.5 1.0
ND1 A:HIS715 5.0 67.4 1.0

Zinc binding site 2 out of 20 in 7d6n

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Zinc binding site 2 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


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 Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:50.3
occ:0.98
 NE2 A:HIS443 1.9 59.1 1.0
SG A:CYS451 2.2 63.2 1.0
SG A:CYS448 2.3 37.1 1.0
CB A:CYS448 2.3 62.9 1.0
CE1 A:HIS443 2.7 58.7 1.0
OE1 A:GLU439 2.7 62.7 1.0
CD2 A:HIS443 3.0 59.6 1.0
CD A:GLU439 3.1 56.5 1.0
CB A:CYS451 3.2 51.5 1.0
CG A:GLU439 3.3 47.1 1.0
CA A:CYS448 3.8 57.2 1.0
ND1 A:HIS443 3.8 55.2 1.0
CG A:HIS443 4.0 59.5 1.0
N A:CYS451 4.1 59.7 1.0
OE2 A:GLU439 4.2 74.2 1.0
CA A:CYS451 4.2 57.5 1.0
N A:HIS450 4.3 60.0 1.0
N A:ALA449 4.3 56.8 1.0
C A:CYS448 4.3 55.5 1.0
C A:HIS450 4.6 54.7 1.0
CB A:GLU439 4.8 51.9 1.0
CD1 A:LEU485 4.8 42.9 1.0
CA A:HIS450 4.8 53.4 1.0
N A:CYS448 4.9 52.5 1.0
CB A:HIS450 5.0 55.5 1.0

Zinc binding site 3 out of 20 in 7d6n

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Zinc binding site 3 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:94.4
occ:0.61
 SG B:CYS729 2.3 48.5 1.0
SG B:CYS848 2.6 0.8 1.0
NE2 B:HIS715 2.7 70.0 1.0
CB B:CYS729 3.3 36.3 1.0
CD2 B:HIS715 3.4 61.7 1.0
CE1 B:HIS715 3.8 69.8 1.0
CB B:CYS848 4.0 90.1 1.0
CD1 B:LEU840 4.5 60.0 1.0
CA B:CYS729 4.6 35.8 1.0
CG B:HIS715 4.6 58.4 1.0
C B:CYS729 4.8 40.1 1.0
CB B:HIS713 4.8 37.6 1.0
ND1 B:HIS715 4.8 62.2 1.0
O B:CYS729 5.0 45.1 1.0

Zinc binding site 4 out of 20 in 7d6n

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Zinc binding site 4 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:58.5
occ:0.88
 OE2 B:GLU439 1.7 64.4 1.0
NE2 B:HIS443 2.0 52.8 1.0
SG B:CYS448 2.0 46.3 1.0
SG B:CYS451 2.0 55.9 1.0
CD B:GLU439 2.9 67.4 1.0
CD2 B:HIS443 2.9 57.1 1.0
CE1 B:HIS443 3.0 54.9 1.0
CB B:CYS451 3.3 55.3 1.0
CB B:CYS448 3.3 59.9 1.0
CG B:GLU439 3.6 61.8 1.0
N B:CYS451 3.7 72.1 1.0
CA B:CYS448 3.7 61.1 1.0
OE1 B:GLU439 3.9 67.4 1.0
N B:ALA449 4.0 59.6 1.0
ND1 B:HIS443 4.1 56.8 1.0
CG B:HIS443 4.1 62.2 1.0
CA B:CYS451 4.1 64.8 1.0
N B:HIS450 4.1 67.5 1.0
C B:CYS448 4.3 61.5 1.0
C B:HIS450 4.6 71.8 1.0
CA B:HIS450 4.8 67.7 1.0
O B:ARG447 4.9 60.1 1.0
CD1 B:LEU485 4.9 56.6 1.0
N B:CYS448 5.0 60.6 1.0

Zinc binding site 5 out of 20 in 7d6n

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Zinc binding site 5 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:91.2
occ:0.70
 SG E:CYS729 2.1 52.6 1.0
SG E:CYS848 2.4 95.6 1.0
CB E:CYS729 2.8 38.5 1.0
NE2 E:HIS715 2.9 75.8 1.0
CD2 E:HIS715 3.3 61.5 1.0
CB E:CYS848 3.6 96.8 1.0
CE1 E:HIS715 4.1 69.6 1.0
CA E:CYS729 4.1 38.6 1.0
NH1 E:ARG770 4.2 69.9 1.0
C E:CYS729 4.3 40.1 1.0
N E:ARG730 4.4 46.8 1.0
CD2 E:LEU840 4.4 62.7 1.0
CG E:HIS715 4.6 61.4 1.0
CB E:HIS713 4.8 39.1 1.0
CA E:CYS848 5.0 0.1 1.0
O E:CYS729 5.0 41.4 1.0
ND1 E:HIS715 5.0 64.6 1.0

Zinc binding site 6 out of 20 in 7d6n

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Zinc binding site 6 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:69.6
occ:0.93
 OE1 E:GLU439 1.9 78.0 1.0
SG E:CYS448 2.1 48.8 1.0
NE2 E:HIS443 2.2 68.7 1.0
OE2 E:GLU439 2.3 88.0 1.0
CD E:GLU439 2.3 77.5 1.0
SG E:CYS451 2.3 72.5 1.0
CE1 E:HIS443 3.1 73.7 1.0
CD2 E:HIS443 3.3 67.1 1.0
CB E:CYS451 3.3 66.4 1.0
CB E:CYS448 3.5 66.5 1.0
N E:CYS451 3.6 71.3 1.0
CA E:CYS448 3.6 73.2 1.0
CG E:GLU439 3.7 67.3 1.0
N E:ALA449 3.8 70.0 1.0
N E:HIS450 3.9 74.7 1.0
CA E:CYS451 4.0 64.7 1.0
C E:CYS448 4.2 72.7 1.0
ND1 E:HIS443 4.2 72.5 1.0
CG E:HIS443 4.3 75.3 1.0
C E:HIS450 4.4 73.2 1.0
CA E:HIS450 4.7 74.2 1.0
OG E:SER482 4.7 74.6 1.0
C E:ALA449 4.8 69.7 1.0
CA E:ALA449 4.9 68.8 1.0
CB E:GLU439 4.9 71.6 1.0
N E:CYS448 4.9 83.3 1.0

Zinc binding site 7 out of 20 in 7d6n

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Zinc binding site 7 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:79.4
occ:0.67
 SG D:CYS729 2.1 64.1 1.0
SG D:CYS848 2.8 90.5 1.0
NE2 D:HIS715 3.0 72.4 1.0
CB D:CYS729 3.1 48.6 1.0
CD2 D:HIS715 3.2 57.5 1.0
CD1 D:LEU840 4.3 63.1 1.0
CE1 D:HIS715 4.3 69.7 1.0
CB D:CYS848 4.3 99.3 1.0
CA D:CYS729 4.3 44.7 1.0
C D:CYS729 4.4 43.8 1.0
CG D:HIS715 4.5 56.2 1.0
N D:ARG730 4.6 46.2 1.0
CB D:HIS713 4.7 44.3 1.0
O D:CYS729 4.8 42.3 1.0

Zinc binding site 8 out of 20 in 7d6n

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Zinc binding site 8 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:57.4
occ:0.89
 NE2 D:HIS443 1.8 55.1 1.0
OE2 D:GLU439 1.8 61.5 1.0
SG D:CYS448 2.1 43.8 1.0
SG D:CYS451 2.2 66.1 1.0
CE1 D:HIS443 2.7 58.6 1.0
CD2 D:HIS443 2.9 58.6 1.0
CD D:GLU439 2.9 60.2 1.0
CB D:CYS448 3.3 62.0 1.0
CB D:CYS451 3.4 65.5 1.0
CG D:GLU439 3.5 56.2 1.0
CA D:CYS448 3.7 64.0 1.0
ND1 D:HIS443 3.8 57.5 1.0
N D:CYS451 3.9 71.6 1.0
CG D:HIS443 3.9 61.8 1.0
OE1 D:GLU439 4.0 56.9 1.0
N D:ALA449 4.2 65.6 1.0
CA D:CYS451 4.3 66.4 1.0
N D:HIS450 4.3 61.5 1.0
C D:CYS448 4.4 67.2 1.0
C D:HIS450 4.7 71.6 1.0
CD1 D:LEU485 4.7 61.9 1.0
O D:ARG447 4.8 59.2 1.0
CA D:HIS450 4.9 63.2 1.0
N D:CYS448 4.9 66.0 1.0
CB D:GLU439 5.0 57.1 1.0

Zinc binding site 9 out of 20 in 7d6n

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Zinc binding site 9 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:80.3
occ:0.61
 SG C:CYS729 2.0 59.8 1.0
SG C:CYS848 2.5 0.9 1.0
CB C:CYS729 2.7 50.1 1.0
NE2 C:HIS715 2.9 79.6 1.0
CD2 C:HIS715 3.4 66.1 1.0
CB C:CYS848 4.0 88.2 1.0
CA C:CYS729 4.0 50.5 1.0
CE1 C:HIS715 4.1 76.9 1.0
C C:CYS729 4.1 53.1 1.0
CB C:HIS713 4.1 52.4 1.0
O C:CYS729 4.3 51.2 1.0
N C:ARG730 4.6 51.6 1.0
CG C:HIS715 4.7 64.8 1.0
CD1 C:LEU840 4.8 57.8 1.0
CG C:HIS713 4.9 61.6 1.0
NH1 C:ARG770 4.9 67.9 1.0
N C:CYS729 5.0 49.6 1.0
ND1 C:HIS715 5.0 67.0 1.0

Zinc binding site 10 out of 20 in 7d6n

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Zinc binding site 10 out of 20 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:69.2
occ:0.85
 SG C:CYS448 2.0 58.3 1.0
NE2 C:HIS443 2.2 90.8 1.0
OE1 C:GLU439 2.2 80.7 1.0
SG C:CYS451 2.3 77.0 1.0
OE2 C:GLU439 2.5 87.5 1.0
CD C:GLU439 2.6 86.1 1.0
CD2 C:HIS443 3.1 94.7 1.0
CE1 C:HIS443 3.1 86.2 1.0
CB C:CYS451 3.3 73.4 1.0
CB C:CYS448 3.5 84.4 1.0
CA C:CYS448 3.6 88.0 1.0
N C:ALA449 3.7 85.2 1.0
N C:CYS451 3.8 80.5 1.0
N C:HIS450 3.9 86.4 1.0
CG C:GLU439 4.0 84.8 1.0
C C:CYS448 4.1 89.0 1.0
CA C:CYS451 4.2 74.5 1.0
ND1 C:HIS443 4.2 85.2 1.0
CG C:HIS443 4.2 93.8 1.0
C C:HIS450 4.5 77.0 1.0
C C:ALA449 4.6 88.5 1.0
CA C:ALA449 4.7 82.2 1.0
CA C:HIS450 4.7 86.0 1.0
O C:ARG447 4.8 91.4 1.0
OG C:SER482 4.9 89.0 1.0
N C:CYS448 4.9 92.2 1.0

Reference:

J.Yang, X.Jing, B.Zhang, Z.Zheng, P.Gong. Crystal Structure of Tick-Borne Encephalitis Virus Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
Page generated: Tue Oct 29 18:44:45 2024

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