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Strontium in PDB 1vc0: Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in Imidazole and SR2+ Solution

Protein crystallography data

The structure of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in Imidazole and SR2+ Solution, PDB code: 1vc0 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) 35.53 / 2.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 108.944, 108.944, 191.754, 90.00, 90.00, 120.00
R / Rfree (%) 24.6 / 27.3

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in Imidazole and SR2+ Solution (pdb code 1vc0). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 2 binding sites of Strontium where determined in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in Imidazole and SR2+ Solution, PDB code: 1vc0:
Jump to Strontium binding site number: 1; 2;

Strontium binding site 1 out of 2 in 1vc0

Go back to Strontium Binding Sites List in 1vc0
Strontium binding site 1 out of 2 in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in Imidazole and SR2+ Solution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in Imidazole and SR2+ Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr201

b:90.6
occ:0.80
O4 B:U163 2.5 82.3 1.0
O2 B:U120 2.7 71.4 1.0
C4 B:U163 3.7 82.3 1.0
C2 B:U120 3.9 73.0 1.0
OP1 B:U123 4.2 93.7 1.0
N2 B:G128 4.3 0.3 1.0
N3 B:U120 4.5 72.2 1.0
N3 B:U163 4.5 82.6 1.0
OP2 B:G101 4.6 0.7 1.0
C5 B:U163 4.8 82.4 1.0
N3 B:G128 4.8 1.0 1.0
C2 B:G128 4.9 0.3 1.0
OP2 B:C122 4.9 78.5 1.0
O3' B:U100 4.9 0.2 1.0
O5' B:G101 5.0 1.0 1.0

Strontium binding site 2 out of 2 in 1vc0

Go back to Strontium Binding Sites List in 1vc0
Strontium binding site 2 out of 2 in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in Imidazole and SR2+ Solution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in Imidazole and SR2+ Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr202

b:0.1
occ:0.60
O2' B:C141 3.1 86.0 1.0
C2' B:C141 3.4 85.2 1.0
C3' B:C141 4.3 86.0 1.0
N7 B:G159 4.6 59.8 1.0
O6 B:G159 4.7 55.4 1.0
O4 B:U160 4.7 58.8 1.0
C1' B:C141 4.7 82.8 1.0
OP2 B:A142 4.8 88.6 1.0
N1 B:C141 5.0 78.4 1.0
O3' B:C141 5.0 86.5 1.0

Reference:

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
Page generated: Wed Dec 16 02:10:39 2020

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