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Calcium 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:

Vanadium (V) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding, PDB code: 3rnt:

Calcium binding site 1 out of 1 in 3rnt

Go back to Calcium Binding Sites List in 3rnt
Calcium 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 Calcium with other atoms in the Ca 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:Ca105

b:14.7
occ:1.00
OD2 A:ASP15 2.3 13.3 1.0
O A:HOH120 2.4 13.0 1.0
O A:HOH121 2.4 19.4 1.0
O A:HOH112 2.4 11.8 1.0
O A:HOH119 2.5 20.1 1.0
O A:HOH118 2.5 16.2 1.0
OD1 A:ASP15 2.5 12.1 1.0
O A:HOH161 2.6 25.7 1.0
CG A:ASP15 2.8 13.4 1.0
CB A:ASP15 4.3 9.0 1.0
O A:HOH148 4.4 26.1 1.0
OG A:SER12 4.5 11.8 1.0
O A:CYS10 4.6 13.1 1.0
O A:HOH117 4.7 14.9 1.0
O A:HOH143 4.7 37.3 1.0
O A:HOH209 4.7 41.1 1.0
O A:HOH144 4.7 35.5 1.0
CA A:GLY65 4.8 14.3 1.0
N A:SER12 4.9 9.3 1.0
O A:HOH168 4.9 30.7 1.0
O A:HOH142 5.0 25.1 1.0
O A:HOH251 5.0 37.7 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: Sat Dec 12 04:28:33 2020

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