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Cobalt in PDB 2p7d: A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution

Protein crystallography data

The structure of A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution, PDB code: 2p7d was solved by A.T.Torelli, J.Krucinska, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.10 / 2.25
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.900, 93.900, 134.400, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 23.7

Other elements in 2p7d:

The structure of A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution also contains other interesting chemical elements:

Sodium (Na) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution (pdb code 2p7d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution, PDB code: 2p7d:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 2p7d

Go back to Cobalt Binding Sites List in 2p7d
Cobalt binding site 1 out of 2 in the A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:72.2
occ:0.25
CO B:NCO102 0.0 72.2 0.2
N4 B:NCO102 1.9 69.8 0.2
N5 B:NCO102 2.0 69.6 0.2
N3 B:NCO102 2.0 69.2 0.2
N2 B:NCO102 2.0 68.8 0.2
N6 B:NCO102 2.0 70.6 0.2
N1 B:NCO102 2.0 69.3 0.2
O6 B:G12 4.1 57.4 1.0
O2 A:SO4103 4.2 81.8 0.4
O6 B:G13 4.3 56.1 1.0
N7 B:G12 4.6 56.5 1.0
O6 B:G11 4.8 63.0 1.0
O1 A:SO4103 4.9 81.8 0.4
N7 B:G11 4.9 62.5 1.0
S A:SO4103 4.9 84.7 0.4
O3 A:SO4103 4.9 81.0 0.4
N4 A:C2 4.9 54.1 1.0

Cobalt binding site 2 out of 2 in 2p7d

Go back to Cobalt Binding Sites List in 2p7d
Cobalt binding site 2 out of 2 in the A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co101

b:76.3
occ:0.85
CO D:NCO101 0.0 76.3 0.8
N5 D:NCO101 1.9 70.5 0.8
N4 D:NCO101 2.0 71.5 0.8
N3 D:NCO101 2.0 70.1 0.8
N1 D:NCO101 2.0 70.8 0.8
N2 D:NCO101 2.0 68.2 0.8
N6 D:NCO101 2.0 67.3 0.8
OP2 D:U41 3.7 67.2 1.0
OP1 D:A40 3.8 74.1 1.0
OP2 C:A20 3.9 81.0 1.0
O6 C:G21 4.2 62.1 1.0
N7 C:G21 4.4 63.2 1.0
P D:A40 4.7 74.8 1.0
OP2 D:A40 4.7 70.8 1.0

Reference:

A.T.Torelli, J.Krucinska, J.E.Wedekind. A Comparison of Vanadate to A 2'-5' Linkage at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization Rna V. 13 1052 2007.
ISSN: ISSN 1355-8382
PubMed: 17488874
DOI: 10.1261/RNA.510807
Page generated: Sun Dec 13 10:38:34 2020

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