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Strontium in PDB 4prf: A Second Look at the Hdv Ribozyme Structure and Dynamics.

Protein crystallography data

The structure of A Second Look at the Hdv Ribozyme Structure and Dynamics., PDB code: 4prf was solved by G.J.Kapral, S.Jain, J.Noeske, J.A.Doudna, D.C.Richardson, J.S.Richardson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.53 / 2.40
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 (%) 19.8 / 25.2

Strontium Binding Sites:

The binding sites of Strontium atom in the A Second Look at the Hdv Ribozyme Structure and Dynamics. (pdb code 4prf). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 2 binding sites of Strontium where determined in the A Second Look at the Hdv Ribozyme Structure and Dynamics., PDB code: 4prf:
Jump to Strontium binding site number: 1; 2;

Strontium binding site 1 out of 2 in 4prf

Go back to Strontium Binding Sites List in 4prf
Strontium binding site 1 out of 2 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr201

b:0.8
occ:1.00
O4 B:U163 2.4 0.4 1.0
O2 B:U120 3.1 0.2 1.0
H22 B:G128 3.5 0.9 1.0
C4 B:U163 3.6 0.6 1.0
OP1 B:U123 3.6 0.4 1.0
H3 B:U163 3.9 0.2 1.0
O6 B:G125 4.1 0.1 1.0
N2 B:G128 4.2 100.0 1.0
N3 B:U163 4.2 0.8 1.0
OP2 B:G101 4.2 0.6 1.0
C2 B:U120 4.3 99.3 1.0
H21 B:G128 4.6 0.9 1.0
H1' B:U120 4.6 0.9 1.0
H3 B:U120 4.6 0.9 1.0
C5 B:U163 4.7 0.5 1.0
H5 B:U163 4.8 0.1 1.0
P B:U123 4.8 0.8 1.0
N3 B:G128 4.8 0.9 1.0
C2 B:G128 4.9 0.4 1.0
N3 B:U120 4.9 99.9 1.0
OP2 B:C122 5.0 83.8 1.0

Strontium binding site 2 out of 2 in 4prf

Go back to Strontium Binding Sites List in 4prf
Strontium binding site 2 out of 2 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr202

b:0.6
occ:1.00
O2' B:C141 2.5 0.3 1.0
H2' B:C141 3.3 0.6 1.0
C2' B:C141 3.4 0.5 1.0
H3' B:C141 4.1 0.1 1.0
C3' B:C141 4.2 0.2 1.0
O6 B:G159 4.3 61.3 1.0
N7 B:G159 4.6 70.7 1.0
O3' B:C141 4.7 0.8 1.0
O4 B:U160 4.7 56.7 1.0
C1' B:C141 4.7 0.9 1.0
H61 B:A145 4.9 78.2 1.0
H62 B:A145 4.9 78.2 1.0

Reference:

G.J.Kapral, S.Jain, J.Noeske, J.A.Doudna, D.C.Richardson, J.S.Richardson. New Tools Provide A Second Look at Hdv Ribozyme Structure, Dynamics and Cleavage. Nucleic Acids Res. 2014.
ISSN: ESSN 1362-4962
PubMed: 25326328
DOI: 10.1093/NAR/GKU992
Page generated: Wed Dec 16 02:24:05 2020

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