Manganese in PDB 1vby: Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound

The structure of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound, PDB code: 1vby was solved by A.Ke, K.Zhou, F.Ding, J.H.D.Cate, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.16 / 2.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	108.589, 108.589, 190.519, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 28.4

The structure of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound (pdb code 1vby). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound, PDB code: 1vby:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound


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 the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:81.5 occ:1.00 O4 B:U163 2.5 77.1 1.0 O2 B:U120 3.2 69.8 1.0 OP1 B:U123 3.3 94.1 1.0 OP2 B:G101 3.4 0.3 1.0 C4 B:U163 3.6 77.5 1.0 OP2 B:C122 4.4 73.3 1.0 C2 B:U120 4.4 69.7 1.0 N3 B:U163 4.5 78.4 1.0 P B:G101 4.5 0.6 1.0 O5' B:G101 4.5 0.9 1.0 C5 B:U163 4.6 76.9 1.0 P B:U123 4.7 96.3 1.0 C5' B:C122 4.8 78.6 1.0 O3' B:U100 4.9 0.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound


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 the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:0.8 occ:1.00 OP2 B:A166 1.9 90.1 1.0 P B:A166 3.2 90.3 1.0 O5' B:A165 3.6 84.2 1.0 OP1 B:A166 3.8 90.6 1.0 C3' B:A165 4.1 83.9 1.0 C5' B:A165 4.1 84.0 1.0 O3' B:A165 4.2 86.7 1.0 O5' B:A166 4.2 90.5 1.0 OP1 B:A165 4.4 83.0 1.0 OP1 B:C132 4.4 0.0 1.0 N7 B:A166 4.5 82.9 1.0 P B:A165 4.5 83.7 1.0 C4' B:A165 4.7 83.5 1.0 C8 B:A166 4.7 83.7 1.0

A.Ke, K.Zhou, F.Ding, J.H.D.Cate, J.A.Doudna. A Conformational Switch Controls Hepatitis Delta Virus Ribozyme Catalysis Nature V. 429 201 2004.
ISSN: ISSN 0028-0836
PubMed: 15141216
DOI: 10.1038/NATURE02522