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Calcium in PDB 3ahw: Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-Monophosphate

Enzymatic activity of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-Monophosphate

All present enzymatic activity of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-Monophosphate:
3.1.27.4;

Protein crystallography data

The structure of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-Monophosphate, PDB code: 3ahw was solved by S.Noguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.14 / 1.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.994, 35.940, 36.151, 90.00, 103.42, 90.00
R / Rfree (%) 13.7 / 14.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-Monophosphate (pdb code 3ahw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-Monophosphate, PDB code: 3ahw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3ahw

Go back to Calcium Binding Sites List in 3ahw
Calcium binding site 1 out of 4 in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-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 2'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca122

b:7.7
occ:1.00
OD1 A:ASN32 2.3 9.8 1.0
OD1 A:ASP29 2.3 8.6 1.0
O A:VAL30 2.3 8.3 1.0
OD2 A:ASP37 2.3 8.5 1.0
O A:HOH187 2.4 7.9 1.0
O A:HOH190 2.4 9.0 1.0
CG A:ASP37 3.2 7.6 1.0
CG A:ASP29 3.4 8.2 1.0
CG A:ASN32 3.5 8.7 1.0
C A:VAL30 3.5 7.7 1.0
N A:VAL30 3.8 7.7 1.0
OD1 A:ASP37 4.0 8.7 1.0
OD2 A:ASP29 4.0 10.6 1.0
OH A:TYR72 4.0 10.1 1.0
CB A:ASP37 4.0 7.3 1.0
ND2 A:ASN32 4.2 10.1 1.0
O A:HOH205 4.2 8.3 1.0
O A:HOH172 4.2 7.6 1.0
CA A:VAL30 4.3 8.8 1.0
O A:HOH227 4.3 16.5 1.0
CE1 A:TYR72 4.5 9.2 1.0
N A:ASN32 4.5 8.0 1.0
N A:ALA31 4.5 8.0 1.0
CB A:ASP29 4.5 7.4 1.0
C A:ALA31 4.5 8.0 1.0
CB A:ASN32 4.5 8.9 1.0
C A:ASP29 4.6 7.4 1.0
CA A:ASP29 4.6 7.4 1.0
CA A:ALA31 4.7 8.4 1.0
N A:ASP37 4.7 7.0 1.0
CZ A:TYR72 4.8 9.2 1.0

Calcium binding site 2 out of 4 in 3ahw

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Calcium binding site 2 out of 4 in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-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 2'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca123

b:13.2
occ:0.60
O A:HOH230 2.4 18.2 0.6
OD1 A:ASP45 2.4 15.1 1.0
O A:HOH149 2.5 9.6 1.0
O A:ILE51 2.5 10.6 1.0
O A:HOH179 2.6 24.9 1.0
CG A:ASP45 3.4 14.9 1.0
C A:ILE51 3.6 7.8 1.0
OD2 A:ASP45 3.7 20.1 1.0
O A:HOH226 3.7 14.3 1.0
N A:ILE51 3.8 7.7 1.0
CA A:ILE51 4.3 7.2 1.0
N A:THR52 4.6 7.9 1.0
O A:GLU46 4.7 10.3 1.0
C A:ASP50 4.7 8.6 1.0
CB A:ASP45 4.7 13.0 1.0
CB A:ILE51 4.8 7.5 1.0
CA A:ASP50 4.9 9.4 1.0
O A:HOH153 4.9 9.7 1.0
CA A:THR52 4.9 9.5 1.0

Calcium binding site 3 out of 4 in 3ahw

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Calcium binding site 3 out of 4 in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-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 2'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca124

b:18.4
occ:0.70
O A:HOH283 2.1 15.5 0.3
O A:HOH220 2.3 22.8 1.0
O A:HOH262 2.4 19.4 1.0
O A:HOH283 2.4 14.7 0.3
OD1 A:ASN16 2.4 10.5 1.0
CG A:ASN16 3.4 7.8 1.0
ND2 A:ASN16 3.7 11.3 1.0
O A:HOH249 3.8 27.9 1.0
OD2 A:ASP17 4.3 14.8 1.0
NE2 A:GLN5 4.4 17.2 1.0
CB A:SER15 4.5 8.4 1.0
O A:GLN5 4.6 8.3 1.0
CB A:ASN16 4.7 7.3 1.0
N A:ASN16 4.8 6.7 1.0

Calcium binding site 4 out of 4 in 3ahw

Go back to Calcium Binding Sites List in 3ahw
Calcium binding site 4 out of 4 in the Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Ustilago Sphaerogena Ribonuclease U2 Complexed with Adenosine 2'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca125

b:13.2
occ:0.50
O A:HOH279 2.1 12.4 0.5
O A:HOH234 2.4 29.8 1.0
OE2 A:GLU94 2.5 11.2 1.0
O A:HOH271 2.6 15.4 1.0
CD A:GLU94 3.4 9.5 1.0
OE1 A:GLU94 3.6 13.5 1.0
N A:CYS1 4.3 8.6 1.0
O A:CYS54 4.5 9.3 1.0
CA A:CYS1 4.6 7.8 1.0
CG A:GLU94 4.7 8.3 1.0
O A:HOH191 4.8 28.6 1.0

Reference:

S.Noguchi, S.Noguchi. N/A N/A.
ISSN: ISSN 0929-8665
PubMed: 20858208
DOI: 10.2174/0929866511009011559
Page generated: Sat Dec 12 04:04:04 2020

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