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Cobalt in PDB 2p7f: The Novel Use of A 2',5'-Phosphodiester Linkage As A Reaction Intermediate at the Active Site of A Small Ribozyme

Protein crystallography data

The structure of The Novel Use of A 2',5'-Phosphodiester Linkage As A Reaction Intermediate at the Active Site of A Small Ribozyme, PDB code: 2p7f 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) 29.38 / 2.35
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.100, 94.100, 127.200, 90.00, 90.00, 120.00
R / Rfree (%) 22.7 / 25.2

Cobalt Binding Sites:

The binding sites of Cobalt atom in the The Novel Use of A 2',5'-Phosphodiester Linkage As A Reaction Intermediate at the Active Site of A Small Ribozyme (pdb code 2p7f). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the The Novel Use of A 2',5'-Phosphodiester Linkage As A Reaction Intermediate at the Active Site of A Small Ribozyme, PDB code: 2p7f:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 2p7f

Go back to Cobalt Binding Sites List in 2p7f
Cobalt binding site 1 out of 2 in the The Novel Use of A 2',5'-Phosphodiester Linkage As A Reaction Intermediate at the Active Site of A Small Ribozyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Novel Use of A 2',5'-Phosphodiester Linkage As A Reaction Intermediate at the Active Site of A Small Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:73.1
occ:0.25
CO B:NCO102 0.0 73.1 0.2
N4 B:NCO102 1.9 69.6 0.2
N5 B:NCO102 1.9 70.1 0.2
N3 B:NCO102 2.0 70.3 0.2
N2 B:NCO102 2.0 70.8 0.2
N6 B:NCO102 2.0 72.0 0.2
N1 B:NCO102 2.0 69.9 0.2
O6 B:G12 4.1 60.5 1.0
O6 B:G13 4.2 65.8 1.0
N7 B:G12 4.4 62.2 1.0
O2 A:SO4103 4.5 56.4 0.3
C6 B:G12 4.9 61.9 1.0

Cobalt binding site 2 out of 2 in 2p7f

Go back to Cobalt Binding Sites List in 2p7f
Cobalt binding site 2 out of 2 in the The Novel Use of A 2',5'-Phosphodiester Linkage As A Reaction Intermediate at the Active Site of A Small Ribozyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Novel Use of A 2',5'-Phosphodiester Linkage As A Reaction Intermediate at the Active Site of A Small Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co101

b:75.7
occ:0.75
CO D:NCO101 0.0 75.7 0.8
N4 D:NCO101 1.9 62.0 0.8
N5 D:NCO101 1.9 56.4 0.8
N3 D:NCO101 2.0 61.3 0.8
N2 D:NCO101 2.0 58.0 0.8
N6 D:NCO101 2.0 61.6 0.8
N1 D:NCO101 2.0 56.4 0.8
OP2 D:U41 3.7 76.9 1.0
OP1 D:A40 3.7 78.2 1.0
OP2 C:A20 4.1 96.5 1.0
O6 C:G21 4.3 71.7 1.0
N7 C:G21 4.4 70.9 1.0
P D:A40 4.6 82.9 1.0
OP2 D:A40 4.8 77.0 1.0
O5' D:A40 4.9 83.5 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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