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Magnesium in PDB 2nok: Crystal Structure of An Rna Domain From Hepatitis C Virus.

Protein crystallography data

The structure of Crystal Structure of An Rna Domain From Hepatitis C Virus., PDB code: 2nok was solved by S.M.Dibrov, H.Johnston-Cos, Y.H.Weng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.098, 65.351, 92.400, 90.00, 90.00, 90.00
R / Rfree (%) 25.7 / 30.2

Other elements in 2nok:

The structure of Crystal Structure of An Rna Domain From Hepatitis C Virus. also contains other interesting chemical elements:

Manganese (Mn) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Rna Domain From Hepatitis C Virus. (pdb code 2nok). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of An Rna Domain From Hepatitis C Virus., PDB code: 2nok:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2nok

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Magnesium binding site 1 out of 8 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of An Rna Domain From Hepatitis C Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg127

b:73.5
occ:1.00
 O6 A:G49 4.8 65.4 1.0
O6 A:G48 5.0 74.3 1.0

Magnesium binding site 2 out of 8 in 2nok

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Magnesium binding site 2 out of 8 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of An Rna Domain From Hepatitis C Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg122

b:70.4
occ:1.00
 N7 B:G107 2.5 69.8 1.0
C8 B:G107 3.4 70.4 1.0
O6 B:G105 3.5 0.0 1.0
C5 B:G107 3.6 69.7 1.0
O6 B:G107 3.8 70.5 1.0
C6 B:G107 4.1 70.1 1.0
N4 B:C108 4.2 60.5 1.0
C6 B:G105 4.2 0.0 1.0
N9 B:G107 4.7 70.1 1.0
OP2 B:G107 4.7 96.5 1.0
C4 B:G107 4.8 69.4 1.0
C5 B:G105 4.8 0.0 1.0
N7 B:G105 4.9 0.0 1.0

Magnesium binding site 3 out of 8 in 2nok

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Magnesium binding site 3 out of 8 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


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 An Rna Domain From Hepatitis C Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg124

b:60.4
occ:1.00
 O4' B:C111 3.7 58.5 1.0
C1' B:C111 3.8 58.3 1.0
N1 C:A57 4.0 65.3 1.0
N2 D:G110 4.1 53.9 1.0
C2 A:A53 4.4 57.0 1.0
C2 D:G110 4.4 54.1 1.0
N1 B:C111 4.6 55.1 1.0
O2 C:C58 4.7 66.4 1.0
C2 C:A57 4.7 65.3 1.0
N1 D:G110 4.8 53.3 1.0
O2' B:C111 4.9 58.7 1.0
C4' B:C111 4.9 58.1 1.0
O2 B:C111 5.0 58.0 1.0
N6 C:A57 5.0 66.0 1.0

Magnesium binding site 4 out of 8 in 2nok

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Magnesium binding site 4 out of 8 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


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 An Rna Domain From Hepatitis C Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg129

b:63.0
occ:1.00
 N7 B:G98 2.2 99.9 1.0
O6 B:G98 2.7 0.0 1.0
C5 B:G98 2.9 99.8 1.0
C6 B:G98 3.1 0.0 1.0
C8 B:G98 3.3 0.0 1.0
C4 B:G98 4.2 100.0 1.0
N9 B:G98 4.4 100.0 1.0
N1 B:G98 4.5 99.8 1.0

Magnesium binding site 5 out of 8 in 2nok

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Magnesium binding site 5 out of 8 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


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 An Rna Domain From Hepatitis C Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg130

b:58.7
occ:1.00
 O6 B:G117 2.9 78.7 1.0
N7 B:G117 3.7 78.0 1.0
C6 B:G117 3.8 78.3 1.0
C5 B:G117 4.1 77.6 1.0
O6 B:G116 4.7 61.1 1.0
C8 B:G117 4.9 78.6 1.0

Magnesium binding site 6 out of 8 in 2nok

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Magnesium binding site 6 out of 8 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


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 An Rna Domain From Hepatitis C Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg126

b:84.3
occ:1.00
 N7 C:G49 3.8 63.4 1.0
N7 C:G48 3.8 73.4 1.0
O6 C:G49 4.1 63.2 1.0
O6 C:G48 4.4 74.1 1.0
C5 C:G48 4.5 73.5 1.0
C8 C:G48 4.7 73.7 1.0
C5 C:G49 4.7 63.4 1.0
C6 C:G48 4.7 73.5 1.0
C6 C:G49 4.8 63.5 1.0
C8 C:G49 4.8 63.6 1.0

Magnesium binding site 7 out of 8 in 2nok

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Magnesium binding site 7 out of 8 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


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 An Rna Domain From Hepatitis C Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg121

b:53.1
occ:1.00
 N7 D:G107 2.4 68.5 1.0
C8 D:G107 3.1 69.3 1.0
C5 D:G107 3.7 68.8 1.0
O6 D:G105 4.1 0.0 1.0
O6 D:G107 4.2 69.5 1.0
C6 D:G107 4.3 69.6 1.0
OP2 D:G107 4.4 95.8 1.0
N9 D:G107 4.5 69.6 1.0
N4 D:C108 4.6 61.1 1.0
C4 D:G107 4.7 68.9 1.0
C6 D:G105 4.7 0.0 1.0

Magnesium binding site 8 out of 8 in 2nok

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Magnesium binding site 8 out of 8 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


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 An Rna Domain From Hepatitis C Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg125

b:61.1
occ:1.00
 N1 A:A57 3.7 66.6 1.0
C2 C:A53 3.8 59.3 1.0
C1' D:C111 4.0 58.7 1.0
O4' D:C111 4.0 58.6 1.0
C2 A:A57 4.3 67.4 1.0
N3 C:A53 4.4 60.7 1.0
N1 C:A53 4.6 58.2 1.0
O2' D:C111 4.7 58.4 1.0
C6 A:A57 4.7 67.0 1.0
N6 A:A57 4.7 67.8 1.0
N1 D:C111 4.7 58.0 1.0
O2 A:C58 4.7 68.9 1.0
N2 B:G110 4.8 54.5 1.0
C4' D:C111 4.8 58.7 1.0
C2' D:C111 5.0 58.6 1.0
C1' C:A54 5.0 60.9 1.0

Reference:

S.M.Dibrov, H.Johnston-Cox, Y.H.Weng, T.Hermann. Functional Architecture of Hcv Ires Domain II Stabilized By Divalent Metal Ions in the Crystal and in Solution. Angew.Chem.Int.Ed.Engl. V. 46 226 2007.
ISSN: ESSN 0570-0833
PubMed: 17131443
DOI: 10.1002/ANIE.200603807
Page generated: Wed Aug 14 00:53:34 2024

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