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Zinc in PDB 4mtp: Rdrp From Japanesese Encephalitis Virus

Enzymatic activity of Rdrp From Japanesese Encephalitis Virus

All present enzymatic activity of Rdrp From Japanesese Encephalitis Virus:
2.7.7.48;

Protein crystallography data

The structure of Rdrp From Japanesese Encephalitis Virus, PDB code: 4mtp was solved by P.Surana, D.T.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.78 / 3.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.470, 174.010, 182.690, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Rdrp From Japanesese Encephalitis Virus (pdb code 4mtp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rdrp From Japanesese Encephalitis Virus, PDB code: 4mtp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4mtp

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Zinc binding site 1 out of 8 in the Rdrp From Japanesese Encephalitis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rdrp From Japanesese Encephalitis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:43.0
occ:1.00
 NE2 A:HIS444 2.1 18.3 1.0
OE2 A:GLU440 2.1 66.8 1.0
SG A:CYS452 2.4 17.5 1.0
SG A:CYS449 2.5 80.2 1.0
CD2 A:HIS444 3.0 38.7 1.0
CE1 A:HIS444 3.1 16.4 1.0
CD A:GLU440 3.2 67.4 1.0
CB A:CYS449 3.4 76.1 1.0
CB A:CYS452 3.5 52.1 1.0
CA A:CYS449 3.5 68.1 1.0
CG A:GLU440 3.7 59.1 1.0
N A:HIS450 3.8 78.4 1.0
N A:CYS452 4.0 58.3 1.0
C A:CYS449 4.1 73.5 1.0
ND1 A:HIS444 4.2 15.9 1.0
CG A:HIS444 4.2 35.7 1.0
OE1 A:GLU440 4.3 64.3 1.0
CG2 A:THR574 4.3 49.1 1.0
CA A:CYS452 4.4 56.1 1.0
N A:THR451 4.5 74.1 1.0
O A:GLU448 4.6 85.4 1.0
N A:CYS449 4.8 57.6 1.0

Zinc binding site 2 out of 8 in 4mtp

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Zinc binding site 2 out of 8 in the Rdrp From Japanesese Encephalitis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rdrp From Japanesese Encephalitis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:2.0
occ:1.00
 NE2 A:HIS717 1.9 2.0 1.0
SG A:CYS733 2.2 2.0 1.0
SG A:CYS852 2.2 2.0 1.0
CD2 A:HIS717 2.8 2.5 1.0
CE1 A:HIS717 3.0 0.8 1.0
CB A:CYS852 3.1 2.0 1.0
CB A:CYS733 3.6 2.4 1.0
NH2 B:ARG859 3.8 29.0 1.0
N A:ARG734 3.9 0.1 1.0
C A:CYS733 4.0 2.0 1.0
CG A:HIS717 4.0 3.3 1.0
ND1 A:HIS717 4.0 0.5 1.0
CA A:ARG734 4.2 0.1 1.0
CA A:CYS852 4.3 2.0 1.0
C A:ARG734 4.3 0.1 1.0
O A:CYS733 4.4 3.3 1.0
CA A:CYS733 4.4 2.0 1.0
O A:ARG734 4.5 0.1 1.0
NH1 A:ARG774 4.8 4.0 1.0
N A:GLY735 4.8 11.3 1.0

Zinc binding site 3 out of 8 in 4mtp

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Zinc binding site 3 out of 8 in the Rdrp From Japanesese Encephalitis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rdrp From Japanesese Encephalitis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:85.3
occ:1.00
 NE2 B:HIS444 2.1 91.6 1.0
SG B:CYS449 2.5 0.9 1.0
OE2 B:GLU440 2.5 0.7 1.0
SG B:CYS452 2.5 79.4 1.0
CD2 B:HIS444 2.9 0.5 1.0
CA B:CYS449 3.2 0.6 1.0
CE1 B:HIS444 3.2 78.3 1.0
CB B:CYS449 3.2 0.2 1.0
CB B:CYS452 3.4 92.2 1.0
N B:HIS450 3.5 0.8 1.0
CD B:GLU440 3.6 0.1 1.0
C B:CYS449 3.8 0.1 1.0
N B:CYS452 3.9 0.9 1.0
CG B:HIS444 4.1 0.1 1.0
CG B:GLU440 4.1 0.1 1.0
O B:GLU448 4.2 99.2 1.0
ND1 B:HIS444 4.2 77.7 1.0
CG2 B:THR574 4.3 79.9 1.0
CA B:CYS452 4.3 0.2 1.0
N B:THR451 4.4 0.4 1.0
N B:CYS449 4.4 0.0 1.0
OE1 B:GLU440 4.7 97.0 1.0
C B:GLU448 4.8 0.8 1.0
CA B:HIS450 4.8 0.5 1.0
O B:CYS449 4.9 0.3 1.0

Zinc binding site 4 out of 8 in 4mtp

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Zinc binding site 4 out of 8 in the Rdrp From Japanesese Encephalitis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rdrp From Japanesese Encephalitis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:2.0
occ:1.00
 NE2 B:HIS717 2.1 3.6 1.0
SG B:CYS733 2.2 2.0 1.0
SG B:CYS852 2.4 2.0 1.0
CD2 B:HIS717 2.7 4.6 1.0
CB B:CYS852 3.2 1.3 1.0
CE1 B:HIS717 3.3 3.1 1.0
CB B:CYS733 3.5 2.9 1.0
NH2 A:ARG859 3.6 34.3 1.0
N B:ARG734 3.8 4.6 1.0
C B:CYS733 3.9 2.7 1.0
CG B:HIS717 4.0 3.0 1.0
CA B:ARG734 4.1 1.1 1.0
O B:CYS733 4.2 2.7 1.0
ND1 B:HIS717 4.2 2.9 1.0
CA B:CYS852 4.3 2.0 1.0
C B:ARG734 4.3 1.2 1.0
CA B:CYS733 4.3 2.2 1.0
O B:ARG734 4.5 6.1 1.0
N B:GLY735 4.8 19.1 1.0
NH1 B:ARG774 4.9 0.9 1.0
CZ A:ARG859 4.9 46.9 1.0

Zinc binding site 5 out of 8 in 4mtp

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Zinc binding site 5 out of 8 in the Rdrp From Japanesese Encephalitis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rdrp From Japanesese Encephalitis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:63.4
occ:1.00
 NE2 C:HIS444 2.1 37.9 1.0
SG C:CYS449 2.4 71.6 1.0
SG C:CYS452 2.5 23.2 1.0
OE2 C:GLU440 2.5 67.5 1.0
CE1 C:HIS444 3.0 42.9 1.0
CD2 C:HIS444 3.1 45.5 1.0
CB C:CYS449 3.2 80.5 1.0
CA C:CYS449 3.3 88.7 1.0
CB C:CYS452 3.3 33.2 1.0
CD C:GLU440 3.6 65.0 1.0
N C:HIS450 3.6 0.0 1.0
C C:CYS449 3.9 93.4 1.0
N C:CYS452 3.9 71.0 1.0
CG C:GLU440 4.0 68.0 1.0
ND1 C:HIS444 4.1 47.5 1.0
CG C:HIS444 4.2 47.8 1.0
CA C:CYS452 4.3 49.0 1.0
N C:THR451 4.4 0.3 1.0
O C:GLU448 4.4 91.3 1.0
CG2 C:THR574 4.4 61.9 1.0
N C:CYS449 4.5 81.7 1.0
OE1 C:GLU440 4.7 61.4 1.0
CA C:HIS450 4.8 0.6 1.0
C C:GLU448 4.9 97.7 1.0
O C:CYS449 5.0 80.5 1.0

Zinc binding site 6 out of 8 in 4mtp

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Zinc binding site 6 out of 8 in the Rdrp From Japanesese Encephalitis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rdrp From Japanesese Encephalitis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:2.0
occ:1.00
 NE2 C:HIS717 2.0 1.6 1.0
SG C:CYS852 2.2 2.5 1.0
SG C:CYS733 2.2 2.0 1.0
CD2 C:HIS717 2.9 0.4 1.0
CB C:CYS852 3.0 2.9 1.0
CE1 C:HIS717 3.1 1.9 1.0
CB C:CYS733 3.6 0.2 1.0
N C:ARG734 3.8 2.6 1.0
C C:CYS733 3.9 2.6 1.0
CA C:ARG734 4.1 2.3 1.0
CG C:HIS717 4.1 0.3 1.0
ND1 C:HIS717 4.1 2.0 1.0
CA C:CYS852 4.1 2.7 1.0
C C:ARG734 4.2 5.3 1.0
O C:CYS733 4.3 1.3 1.0
CA C:CYS733 4.4 2.8 1.0
O C:ARG734 4.4 5.8 1.0
N C:GLY735 4.7 14.4 1.0
NH1 C:ARG774 4.7 2.0 1.0

Zinc binding site 7 out of 8 in 4mtp

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Zinc binding site 7 out of 8 in the Rdrp From Japanesese Encephalitis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rdrp From Japanesese Encephalitis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:0.0
occ:1.00
 OE2 D:GLU440 2.6 0.1 1.0
NE2 D:HIS444 2.8 0.3 1.0
CD2 D:HIS444 3.7 0.8 1.0
CD D:GLU440 3.8 0.3 1.0
CE1 D:HIS444 3.8 0.7 1.0
CG D:GLU440 4.3 0.4 1.0
CG2 D:THR574 4.5 89.6 1.0
OE1 D:GLU440 4.8 0.1 1.0
CG D:HIS444 4.9 0.8 1.0
ND1 D:HIS444 4.9 0.6 1.0

Zinc binding site 8 out of 8 in 4mtp

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Zinc binding site 8 out of 8 in the Rdrp From Japanesese Encephalitis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rdrp From Japanesese Encephalitis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:0.5
occ:1.00
 NE2 D:HIS717 1.9 3.7 1.0
SG D:CYS733 2.3 0.3 1.0
SG D:CYS852 2.4 2.5 1.0
CD2 D:HIS717 2.8 1.9 1.0
CB D:CYS852 3.0 2.0 1.0
CE1 D:HIS717 3.0 0.0 1.0
CB D:CYS733 3.6 4.3 1.0
N D:ARG734 3.7 10.3 1.0
C D:CYS733 3.9 4.1 1.0
CA D:ARG734 4.0 18.2 1.0
CG D:HIS717 4.0 0.1 1.0
ND1 D:HIS717 4.1 2.9 1.0
C D:ARG734 4.1 15.3 1.0
CA D:CYS852 4.1 2.9 1.0
O D:CYS733 4.2 0.1 1.0
O D:ARG734 4.3 9.6 1.0
CA D:CYS733 4.4 2.6 1.0
NH1 D:ARG774 4.5 1.4 1.0
N D:GLY735 4.6 37.1 1.0
O D:CYS852 4.9 3.5 1.0

Reference:

P.Surana, V.Satchidanandam, D.T.Nair. Rna-Dependent Rna Polymerase of Japanese Encephalitis Virus Binds the Initiator Nucleotide Gtp to Form A Mechanistically Important Pre-Initiation State. Nucleic Acids Res. V. 42 2758 2014.
ISSN: ISSN 0305-1048
PubMed: 24293643
DOI: 10.1093/NAR/GKT1106
Page generated: Sun Oct 27 02:47:04 2024

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