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Cobalt in PDB 2p7e: Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization

Protein crystallography data

The structure of Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization, PDB code: 2p7e 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) 29.93 / 2.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.100, 94.100, 132.400, 90.00, 90.00, 120.00
R / Rfree (%) 25.8 / 27.1

Other elements in 2p7e:

The structure of Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization also contains other interesting chemical elements:

Vanadium (V) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization (pdb code 2p7e). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization, PDB code: 2p7e:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 2p7e

Go back to Cobalt Binding Sites List in 2p7e
Cobalt binding site 1 out of 2 in the Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:75.9
occ:0.35
CO B:NCO102 0.0 75.9 0.3
N4 B:NCO102 2.0 71.6 0.3
N5 B:NCO102 2.0 71.4 0.3
N3 B:NCO102 2.0 71.5 0.3
N2 B:NCO102 2.0 72.5 0.3
N6 B:NCO102 2.0 72.5 0.3
N1 B:NCO102 2.0 71.9 0.3
O6 B:G12 3.8 43.0 1.0
N7 B:G12 4.2 43.5 1.0
O2 A:SO4103 4.3 75.0 0.5
O6 B:G13 4.4 43.3 1.0
O6 B:G11 4.5 52.5 1.0
N7 B:G11 4.5 51.4 1.0
C6 B:G12 4.6 39.7 1.0
C6 B:G11 4.8 51.5 1.0
C5 B:G12 4.8 38.4 1.0
C5 B:G11 4.8 50.1 1.0
N4 A:C2 5.0 40.8 1.0
O3 A:SO4103 5.0 78.8 0.5

Cobalt binding site 2 out of 2 in 2p7e

Go back to Cobalt Binding Sites List in 2p7e
Cobalt binding site 2 out of 2 in the Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co101

b:53.4
occ:0.75
CO C:NCO101 0.0 53.4 0.8
N5 C:NCO101 1.9 46.6 0.8
N4 C:NCO101 1.9 44.5 0.8
N3 C:NCO101 2.0 46.3 0.8
N2 C:NCO101 2.0 46.9 0.8
N6 C:NCO101 2.0 43.7 0.8
N1 C:NCO101 2.0 45.9 0.8
OP1 D:A40 3.8 62.0 1.0
OP2 D:U41 3.8 49.6 1.0
O6 C:G21 3.9 52.8 1.0
OP2 C:A20 4.0 63.7 1.0
N7 C:G21 4.3 49.9 1.0
OP2 D:A40 4.6 59.2 1.0
P D:A40 4.6 60.5 1.0
C6 C:G21 4.8 46.8 1.0
C5 C:G21 5.0 47.1 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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