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

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

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

Magnesium

(Mg)

8 atoms

The binding sites of Manganese 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 Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of An Rna Domain From Hepatitis C Virus., PDB code: 2nok:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn119 b:92.0 occ:1.00 O2 A:C55 2.3 54.0 1.0 C2 A:C55 3.3 51.9 1.0 N3 A:C55 3.6 48.9 1.0 N1 A:A54 4.3 58.2 1.0 O6 B:G110 4.4 55.4 1.0 N6 B:A109 4.5 57.6 1.0 N1 A:C55 4.5 51.5 1.0 N7 B:A109 4.7 56.9 1.0 C2 A:A54 4.7 58.0 1.0 C1' A:C55 4.8 54.5 1.0 C4 A:C55 5.0 50.5 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 A:Mn128 b:70.3 occ:1.00 N7 A:G52 2.3 61.6 1.0 C8 A:G52 3.0 61.9 1.0 C5 A:G52 3.5 60.8 1.0 O6 A:G52 4.0 62.2 1.0 C6 A:G52 4.2 62.0 1.0 N9 A:G52 4.3 60.6 1.0 OP2 A:G52 4.4 61.2 1.0 N7 A:A53 4.5 56.7 1.0 C4 A:G52 4.6 60.9 1.0 N7 A:G51 4.9 53.2 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 C:Mn118 b:74.8 occ:1.00 OP1 C:C55 2.0 61.7 1.0 OP1 A:C55 2.2 63.0 1.0 P C:C55 3.4 60.7 1.0 P A:C55 3.7 59.2 1.0 O5' C:C55 4.1 59.7 1.0 OP2 C:C55 4.3 60.7 1.0 C5' C:C55 4.3 59.3 1.0 O5' A:C55 4.4 60.2 1.0 C5' A:C55 4.4 61.5 1.0 O3' C:A54 4.4 59.7 1.0 O3' A:A54 4.5 60.4 1.0 OP2 A:C55 4.5 61.0 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of An Rna Domain From Hepatitis C Virus.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 C:Mn120 b:88.2 occ:1.00 O2 C:C55 2.2 57.3 1.0 C2 C:C55 2.9 56.0 1.0 N3 C:C55 3.0 55.1 1.0 N1 C:A54 3.8 60.9 1.0 C2 C:A54 4.2 60.3 1.0 N1 C:C55 4.2 54.9 1.0 C4 C:C55 4.3 54.9 1.0 O6 D:G110 4.5 54.1 1.0 N7 D:A109 4.5 55.8 1.0 N7 D:G110 4.7 53.8 1.0 C6 C:A54 4.8 60.9 1.0 N6 D:A109 4.9 55.7 1.0 C1' C:C55 4.9 55.5 1.0 N4 C:C55 4.9 55.8 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 C:Mn123 b:73.3 occ:1.00 N7 C:G52 2.3 65.2 1.0 C8 C:G52 3.3 64.8 1.0 C5 C:G52 3.3 63.9 1.0 O6 C:G52 3.4 65.1 1.0 C6 C:G52 3.7 64.7 1.0 OP2 C:G52 4.3 62.9 1.0 N9 C:G52 4.5 64.9 1.0 C4 C:G52 4.5 64.7 1.0 N7 C:A53 4.6 59.0 1.0 N7 C:G51 4.6 55.2 1.0 C5 C:G51 4.9 54.9 1.0

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