Magnesium 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:

Zinc (Zn) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase, PDB code: 7d6n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 7d6n

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Magnesium binding site 1 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1003

b:51.3
occ:1.00
 OD2 A:ASP535 2.4 53.1 1.0
OD1 A:ASP665 2.4 43.4 1.0
O A:ALA533 3.2 43.6 1.0
O A:PRO708 3.3 44.9 1.0
CG A:ASP535 3.4 57.9 1.0
CG A:ASP665 3.4 43.4 1.0
OD2 A:ASP665 3.5 46.5 1.0
OD1 A:ASP535 3.6 62.4 1.0
O A:CYS666 3.8 42.1 1.0
CB A:ALA533 4.0 37.5 1.0
C A:ALA533 4.1 41.8 1.0
C A:PRO708 4.2 41.7 1.0
CG A:PRO708 4.3 32.1 1.0
O A:ASP534 4.4 48.6 1.0
CA A:ALA533 4.5 37.8 1.0
CB A:PRO708 4.6 35.7 1.0
CB A:ASP535 4.8 51.6 1.0
CA A:PHE709 4.8 36.4 1.0
N A:PHE709 4.8 38.3 1.0
C A:ASP534 4.8 42.0 1.0
CB A:ASP665 4.8 35.1 1.0
N A:CYS666 4.9 37.7 1.0
C A:CYS666 5.0 37.6 1.0
CA A:PRO708 5.0 33.5 1.0

Magnesium binding site 2 out of 10 in 7d6n

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Magnesium binding site 2 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg1003

b:45.5
occ:1.00
 OD2 B:ASP535 2.1 54.7 1.0
OD1 B:ASP665 2.4 45.7 1.0
CG B:ASP535 3.1 58.1 1.0
O B:ALA533 3.3 38.7 1.0
O B:CYS666 3.3 36.9 1.0
OD1 B:ASP535 3.4 58.6 1.0
CG B:ASP665 3.5 47.9 1.0
O B:PRO708 3.6 49.9 1.0
CB B:ALA533 3.7 30.6 1.0
C B:ALA533 3.8 35.3 1.0
O B:ASP534 4.0 41.1 1.0
OD2 B:ASP665 4.1 53.2 1.0
CA B:ALA533 4.1 32.8 1.0
N B:CYS666 4.2 45.6 1.0
C B:ASP534 4.4 34.2 1.0
C B:CYS666 4.4 35.3 1.0
CB B:ASP535 4.4 42.5 1.0
C B:PRO708 4.6 41.2 1.0
N B:ASP535 4.7 38.9 1.0
N B:ASP534 4.7 36.8 1.0
CA B:ASP535 4.7 46.1 1.0
CB B:ASP665 4.8 41.4 1.0
CA B:ASP665 4.8 40.9 1.0
CG B:PRO708 4.8 32.3 1.0
CA B:CYS666 5.0 38.0 1.0
C B:ASP665 5.0 40.0 1.0
CA B:PHE709 5.0 38.6 1.0

Magnesium binding site 3 out of 10 in 7d6n

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Magnesium binding site 3 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
E:Mg1003

b:58.5
occ:1.00
 OD1 E:ASP535 2.2 61.5 1.0
OD1 E:ASP665 2.4 54.8 1.0
CG E:ASP535 3.1 65.0 1.0
CG E:ASP665 3.2 50.5 1.0
OD2 E:ASP535 3.3 69.7 1.0
OD2 E:ASP665 3.4 57.2 1.0
O E:PRO708 3.5 44.5 1.0
O E:ALA533 3.6 52.4 1.0
O E:CYS666 3.7 50.8 1.0
CB E:ALA533 3.9 42.0 1.0
C E:ALA533 4.2 52.0 1.0
C E:PRO708 4.2 42.1 1.0
CA E:ALA533 4.5 44.4 1.0
CA E:PHE709 4.5 42.5 1.0
CB E:ASP535 4.5 45.5 1.0
O E:ASP534 4.6 52.5 1.0
N E:CYS666 4.6 44.9 1.0
CB E:ASP665 4.6 43.9 1.0
N E:PHE709 4.7 41.0 1.0
CG E:PRO708 4.8 35.5 1.0
C E:CYS666 4.8 42.9 1.0
CD1 E:PHE709 4.8 43.6 1.0
C E:ASP534 4.9 48.5 1.0
CB E:PRO708 4.9 35.1 1.0
CA E:ASP665 5.0 42.6 1.0

Magnesium binding site 4 out of 10 in 7d6n

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Magnesium binding site 4 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg1003

b:52.6
occ:1.00
 OD1 D:ASP535 2.0 60.4 1.0
OD1 D:ASP665 2.1 58.1 1.0
CG D:ASP535 2.9 64.8 1.0
OD2 D:ASP535 3.0 67.0 1.0
CG D:ASP665 3.1 55.8 1.0
OD2 D:ASP665 3.4 55.0 1.0
O D:ALA533 3.4 37.6 1.0
O D:PRO708 3.6 47.1 1.0
O D:CYS666 3.6 42.4 1.0
CB D:ALA533 4.1 41.9 1.0
C D:ALA533 4.3 41.0 1.0
C D:PRO708 4.3 43.8 1.0
CB D:ASP535 4.4 49.1 1.0
N D:CYS666 4.4 48.9 1.0
O D:ASP534 4.5 54.2 1.0
CA D:PHE709 4.5 47.2 1.0
CB D:ASP665 4.5 47.2 1.0
CA D:ALA533 4.6 41.8 1.0
N D:PHE709 4.7 46.5 1.0
CG D:PRO708 4.7 39.1 1.0
C D:CYS666 4.7 44.2 1.0
CA D:ASP665 4.8 45.4 1.0
CB D:PRO708 4.8 34.4 1.0
C D:ASP534 4.9 46.1 1.0
CD1 D:PHE709 4.9 44.6 1.0
CA D:ASP535 5.0 45.7 1.0

Magnesium binding site 5 out of 10 in 7d6n

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Magnesium binding site 5 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg1003

b:61.8
occ:1.00
 OD1 C:ASP665 2.1 58.3 1.0
OD1 C:ASP535 2.3 64.1 1.0
OD2 C:ASP535 3.0 73.8 1.0
CG C:ASP535 3.0 68.7 1.0
CG C:ASP665 3.2 55.0 1.0
O C:PRO708 3.3 46.7 1.0
O C:ALA533 3.4 61.5 1.0
OD2 C:ASP665 3.6 53.4 1.0
O C:CYS666 3.8 59.2 1.0
CB C:ALA533 3.8 49.5 1.0
C C:ALA533 4.2 56.8 1.0
C C:PRO708 4.3 46.6 1.0
O C:ASP534 4.4 61.9 1.0
N C:CYS666 4.4 54.4 1.0
CB C:ASP535 4.5 59.1 1.0
CA C:ALA533 4.5 53.1 1.0
CB C:ASP665 4.6 51.5 1.0
CA C:PHE709 4.7 47.6 1.0
CG C:PRO708 4.7 39.4 1.0
CA C:ASP665 4.8 52.7 1.0
C C:CYS666 4.8 55.2 1.0
C C:ASP534 4.8 58.2 1.0
N C:PHE709 4.9 50.0 1.0
CA C:ASP535 5.0 63.1 1.0

Magnesium binding site 6 out of 10 in 7d6n

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Magnesium binding site 6 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
F:Mg1003

b:47.3
occ:1.00
 OD2 F:ASP535 2.3 57.7 1.0
OD1 F:ASP665 2.4 49.3 1.0
CG F:ASP535 3.0 63.8 1.0
OD1 F:ASP535 3.1 75.2 1.0
O F:ALA533 3.3 42.5 1.0
CG F:ASP665 3.3 48.9 1.0
O F:PRO708 3.4 45.7 1.0
OD2 F:ASP665 3.5 48.8 1.0
O F:CYS666 3.8 41.6 1.0
CB F:ALA533 4.0 41.6 1.0
C F:ALA533 4.1 44.3 1.0
C F:PRO708 4.3 42.5 1.0
CB F:ASP535 4.5 46.9 1.0
CA F:ALA533 4.5 41.8 1.0
O F:ASP534 4.6 42.9 1.0
CG F:PRO708 4.6 38.3 1.0
CB F:PRO708 4.7 36.6 1.0
C F:ASP534 4.8 41.4 1.0
CB F:ASP665 4.8 41.0 1.0
N F:CYS666 4.8 45.1 1.0
CA F:PHE709 4.8 44.1 1.0
N F:PHE709 4.9 44.6 1.0
CA F:ASP535 4.9 51.0 1.0
N F:ASP535 4.9 46.6 1.0
C F:CYS666 5.0 40.6 1.0

Magnesium binding site 7 out of 10 in 7d6n

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Magnesium binding site 7 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
G:Mg1003

b:66.2
occ:1.00
 OD1 G:ASP665 2.0 68.8 1.0
OD2 G:ASP535 2.1 68.5 1.0
CG G:ASP535 2.9 72.3 1.0
OD1 G:ASP535 3.0 71.8 1.0
CG G:ASP665 3.0 61.4 1.0
OD2 G:ASP665 3.4 60.9 1.0
O G:PRO708 3.4 58.3 1.0
O G:ALA533 3.4 56.4 1.0
O G:CYS666 3.7 52.1 1.0
O G:ASP534 4.0 59.7 1.0
CB G:ALA533 4.1 45.4 1.0
C G:ALA533 4.2 57.9 1.0
CB G:ASP535 4.3 60.8 1.0
N G:CYS666 4.4 56.3 1.0
CB G:ASP665 4.4 54.9 1.0
C G:PRO708 4.4 57.6 1.0
CA G:ALA533 4.6 48.3 1.0
C G:ASP534 4.6 56.2 1.0
CA G:ASP665 4.6 55.4 1.0
C G:CYS666 4.8 50.8 1.0
CA G:ASP535 4.8 61.0 1.0
CA G:PHE709 4.8 53.1 1.0
N G:ASP535 4.9 53.2 1.0
CG G:PRO708 4.9 48.9 1.0

Magnesium binding site 8 out of 10 in 7d6n

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Magnesium binding site 8 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
J:Mg1003

b:75.4
occ:1.00
 OD2 J:ASP535 2.2 69.9 1.0
OD1 J:ASP535 2.5 72.7 1.0
OD1 J:ASP665 2.5 66.3 1.0
CG J:ASP535 2.7 79.7 1.0
O J:ALA533 3.1 53.6 1.0
CG J:ASP665 3.3 65.6 1.0
O J:PRO708 3.4 55.5 1.0
OD2 J:ASP665 3.5 66.7 1.0
O J:CYS666 3.6 54.2 1.0
CB J:ALA533 3.8 58.5 1.0
C J:ALA533 3.9 58.8 1.0
C J:PRO708 4.1 54.3 1.0
CA J:ALA533 4.2 53.6 1.0
CB J:ASP535 4.2 70.8 1.0
O J:ASP534 4.3 73.4 1.0
N J:CYS666 4.5 59.1 1.0
CA J:PHE709 4.6 50.4 1.0
N J:PHE709 4.6 51.4 1.0
CG J:PRO708 4.7 50.9 1.0
C J:CYS666 4.7 61.2 1.0
C J:ASP534 4.7 69.4 1.0
CB J:ASP665 4.7 60.9 1.0
CB J:PRO708 4.8 50.5 1.0
CA J:ASP535 4.9 67.8 1.0

Magnesium binding site 9 out of 10 in 7d6n

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Magnesium binding site 9 out of 10 in the Crystal Structure of Tick-Borne Encephalitis Virus Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
I:Mg1003

b:73.5
occ:1.00
 OD1 I:ASP665 2.3 68.5 1.0
OD1 I:ASP535 2.5 70.5 1.0
O I:ALA533 3.0 49.5 1.0
CG I:ASP535 3.0 74.1 1.0
OD2 I:ASP535 3.0 83.8 1.0
CG I:ASP665 3.1 69.5 1.0
OD2 I:ASP665 3.2 68.7 1.0
O I:PRO708 3.5 58.3 1.0
C I:ALA533 3.8 57.0 1.0
CB I:ALA533 3.9 50.5 1.0
O I:CYS666 3.9 55.7 1.0
O I:ASP534 4.3 58.0 1.0
CA I:ALA533 4.3 53.4 1.0
CB I:ASP535 4.3 69.4 1.0
C I:PRO708 4.5 56.5 1.0
C I:ASP534 4.5 53.8 1.0
CB I:ASP665 4.6 64.4 1.0
CA I:ASP535 4.6 66.7 1.0
N I:ASP535 4.7 59.3 1.0
N I:CYS666 4.7 58.0 1.0
CG I:PRO708 4.7 43.1 1.0
N I:ASP534 4.8 61.4 1.0
CA I:PHE709 4.9 52.7 1.0
C I:CYS666 5.0 57.7 1.0

Magnesium binding site 10 out of 10 in 7d6n

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
H:Mg1003

b:76.0
occ:1.00
 OD1 H:ASP665 2.2 71.7 1.0
OD1 H:ASP535 2.2 73.7 1.0
OD2 H:ASP535 2.7 87.0 1.0
OD2 H:ASP665 2.8 74.0 1.0
CG H:ASP535 2.8 85.1 1.0
CG H:ASP665 2.8 72.9 1.0
O H:PRO708 3.3 65.3 1.0
O H:ALA533 3.4 60.4 1.0
CB H:ALA533 3.8 60.5 1.0
O H:CYS666 3.9 59.4 1.0
C H:ALA533 4.0 67.4 1.0
C H:PRO708 4.2 62.0 1.0
CB H:ASP535 4.3 71.9 1.0
CA H:ALA533 4.3 62.9 1.0
CB H:ASP665 4.3 59.0 1.0
O H:ASP534 4.5 66.4 1.0
CA H:PHE709 4.6 63.7 1.0
C H:ASP534 4.7 66.9 1.0
N H:CYS666 4.7 58.7 1.0
CG H:PRO708 4.7 56.8 1.0
N H:PHE709 4.7 64.1 1.0
CA H:ASP535 4.8 71.2 1.0
N H:ASP535 4.8 70.2 1.0
CA H:ASP665 4.9 58.8 1.0
CB H:PRO708 4.9 56.9 1.0
C H:CYS666 5.0 62.1 1.0
N H:ASP534 5.0 66.3 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: Mon Jan 25 15:24:09 2021

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