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Vanadium in PDB 3rnt: Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding

Enzymatic activity of Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding

All present enzymatic activity of Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding:
3.1.27.3;

Protein crystallography data

The structure of Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding, PDB code: 3rnt was solved by D.Kostrewa, H.-W.Choe, U.Heinemann, W.Saenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.820, 46.530, 41.200, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3rnt:

The structure of Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding (pdb code 3rnt). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total only one binding site of Vanadium was determined in the Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding, PDB code: 3rnt:

Vanadium binding site 1 out of 1 in 3rnt

Go back to Vanadium Binding Sites List in 3rnt
Vanadium binding site 1 out of 1 in the Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V106

b:39.2
occ:1.00
 V A:VO4106 0.0 39.2 1.0
O3 A:VO4106 1.7 45.6 1.0
O2 A:VO4106 1.7 44.4 1.0
O1 A:VO4106 1.7 44.0 1.0
O4 A:VO4106 1.7 48.6 1.0
OE2 A:GLU58 3.4 22.5 1.0
NE2 A:HIS92 3.5 17.5 1.0
OH A:TYR38 3.6 13.9 1.0
O A:HOH183 3.8 42.6 1.0
NE A:ARG77 3.8 11.5 1.0
OE1 A:GLU58 3.9 25.5 1.0
NH2 A:ARG77 3.9 9.2 1.0
CD A:GLU58 4.0 27.1 1.0
O A:HOH176 4.0 48.7 1.0
CE1 A:TYR38 4.2 11.4 1.0
CE1 A:HIS40 4.3 19.2 1.0
NE2 A:HIS40 4.3 20.9 1.0
CZ A:TYR38 4.4 11.4 1.0
CZ A:ARG77 4.4 13.9 1.0
CE1 A:HIS92 4.4 16.9 1.0
CZ A:PHE100 4.4 22.5 1.0
OD1 A:ASN98 4.5 39.4 0.5
CD2 A:HIS92 4.5 16.3 1.0
O A:HOH175 4.5 47.7 1.0
CD A:ARG77 4.8 12.1 1.0
O A:HOH266 4.9 57.7 1.0
CE1 A:PHE100 5.0 16.6 1.0

Reference:

D.Kostrewa, H.W.Choe, U.Heinemann, W.Saenger. Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate (V), Suggests Conformational Change Upon Substrate Binding. Biochemistry V. 28 7592 1989.
ISSN: ISSN 0006-2960
PubMed: 2514790
DOI: 10.1021/BI00445A014
Page generated: Wed Dec 16 02:30:58 2020

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