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Barium in PDB 1vbz: Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in BA2+ Solution

Protein crystallography data

The structure of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in BA2+ Solution, PDB code: 1vbz 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) 33.43 / 2.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 108.630, 108.630, 190.072, 90.00, 90.00, 120.00
R / Rfree (%) 25.3 / 26.8

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in BA2+ Solution (pdb code 1vbz). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 2 binding sites of Barium where determined in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in BA2+ Solution, PDB code: 1vbz:
Jump to Barium binding site number: 1; 2;

Barium binding site 1 out of 2 in 1vbz

Go back to Barium Binding Sites List in 1vbz
Barium binding site 1 out of 2 in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in BA2+ Solution


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in BA2+ Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba201

b:84.7
occ:1.00
O4 B:U163 2.8 72.7 1.0
O2 B:U120 3.0 62.1 1.0
OP2 B:G101 3.5 99.8 1.0
OP1 B:U123 3.8 87.7 1.0
C4 B:U163 3.9 72.2 1.0
C2 B:U120 4.2 63.8 1.0
N3 B:U163 4.4 71.9 1.0
N2 B:G128 4.6 92.4 1.0
N3 B:U120 4.8 63.1 1.0
P B:G101 4.8 98.8 1.0
P B:U123 5.0 89.0 1.0

Barium binding site 2 out of 2 in 1vbz

Go back to Barium Binding Sites List in 1vbz
Barium binding site 2 out of 2 in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in BA2+ Solution


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, in BA2+ Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba202

b:96.9
occ:0.60
O2' B:C141 2.9 76.3 1.0
C2' B:C141 3.7 74.6 1.0
O6 B:G159 4.5 51.6 1.0
C3' B:C141 4.6 75.9 1.0
O A:HOH105 4.8 40.1 1.0
N7 B:G159 4.9 52.9 1.0
O4 B:U160 5.0 56.8 1.0
C1' B:C141 5.0 72.5 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: Sat Dec 12 01:55:04 2020

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