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Calcium in PDB 3ago: Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate

Enzymatic activity of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate

All present enzymatic activity of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate:
3.1.27.4;

Protein crystallography data

The structure of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate, PDB code: 3ago was solved by S.Noguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.71 / 0.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.586, 39.425, 31.646, 90.00, 108.98, 90.00
R / Rfree (%) 15 / 16.2

Other elements in 3ago:

The structure of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate (pdb code 3ago). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate, PDB code: 3ago:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3ago

Go back to Calcium Binding Sites List in 3ago
Calcium binding site 1 out of 3 in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate


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 Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca116

b:10.2
occ:0.50
 CA A:CA116 0.0 10.2 0.5
CA A:CA116 1.5 12.0 0.5
O A:ALA31 2.3 9.2 1.0
OD1 A:ASP29 2.6 17.2 1.0
O A:TYR39 2.9 10.8 1.0
O A:HOH198 3.2 14.3 1.0
C A:ALA31 3.5 8.0 1.0
CB A:ASN38 3.5 12.8 1.0
CG A:ASP29 3.7 13.6 1.0
OD1 A:ASN32 3.9 16.3 1.0
C A:TYR39 3.9 8.5 1.0
OD2 A:ASP29 4.1 18.2 1.0
O A:HOH182 4.2 26.6 1.0
CB A:ALA31 4.3 8.4 1.0
CA A:ALA31 4.3 6.8 1.0
CG A:ASN38 4.3 13.9 1.0
OD1 A:ASN38 4.4 18.2 1.0
CD A:PRO40 4.4 8.4 1.0
C A:ASN38 4.5 10.3 1.0
N A:ALA31 4.5 6.8 1.0
N A:ASN32 4.5 9.2 1.0
N A:PRO40 4.6 7.5 1.0
O A:ASN38 4.6 11.4 1.0
N A:TYR39 4.7 8.2 1.0
CA A:ASN38 4.7 11.5 1.0
CA A:ASN32 4.7 10.9 1.0
CG A:ASN32 4.7 13.4 1.0
CB A:ASP29 4.9 10.8 1.0
CA A:TYR39 5.0 8.2 1.0

Calcium binding site 2 out of 3 in 3ago

Go back to Calcium Binding Sites List in 3ago
Calcium binding site 2 out of 3 in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca116

b:12.0
occ:0.50
 CA A:CA116 0.0 12.0 0.5
CA A:CA116 1.5 10.2 0.5
OD1 A:ASP29 2.5 17.2 1.0
O A:ALA31 2.5 9.2 1.0
OD1 A:ASN32 2.7 16.3 1.0
CG A:ASP29 3.2 13.6 1.0
OD2 A:ASP29 3.2 18.2 1.0
C A:ALA31 3.6 8.0 1.0
CG A:ASN32 3.7 13.4 1.0
O A:HOH198 4.0 14.3 1.0
CA A:ASN32 4.1 10.9 1.0
O A:TYR39 4.3 10.8 1.0
N A:ASN32 4.3 9.2 1.0
CB A:ASN38 4.3 12.8 1.0
OD1 A:ASN38 4.4 18.2 1.0
CB A:ASN32 4.4 12.2 1.0
O A:HOH160 4.5 17.6 1.0
O A:ASP29 4.6 9.1 1.0
ND2 A:ASN32 4.6 14.7 1.0
CB A:ASP29 4.6 10.8 1.0
O A:HOH182 4.7 26.6 1.0
CG A:ASN38 4.7 13.9 1.0
CA A:ALA31 4.7 6.8 1.0
N A:ALA31 4.8 6.8 1.0
C A:ASP29 5.0 7.6 1.0

Calcium binding site 3 out of 3 in 3ago

Go back to Calcium Binding Sites List in 3ago
Calcium binding site 3 out of 3 in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 3'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca117

b:10.4
occ:0.80
 O A:ILE51 2.3 8.9 1.0
OD1 A:ASP45 2.4 7.3 1.0
O A:HOH215 2.4 9.1 0.8
O A:HOH141 2.5 10.8 1.0
O A:HOH220 2.6 8.4 1.0
O A:HOH216 2.7 13.9 0.8
CG A:ASP45 3.4 6.7 1.0
C A:ILE51 3.4 7.8 1.0
O A:HOH190 3.5 10.7 1.0
OD2 A:ASP45 3.7 7.5 1.0
N A:ILE51 4.0 7.1 1.0
CA A:ILE51 4.2 7.0 1.0
N A:THR52 4.4 9.3 1.0
O A:HOH192 4.5 17.9 1.0
O A:HOH219 4.7 5.7 1.0
CA A:THR52 4.7 11.3 1.0
CB A:ILE51 4.7 7.0 1.0
CB A:ASP45 4.7 5.8 1.0
CA A:ALA47 4.8 6.6 1.0
C A:ASP50 5.0 7.4 1.0

Reference:

S.Noguchi, S.Noguchi. N/A N/A.
ISSN: ISSN 0907-4449
PubMed: 20606265
DOI: 10.1107/S0907444910019621
Page generated: Sat Jul 13 07:45:45 2024

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