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Calcium in PDB 3g5i: Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor

Enzymatic activity of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor

All present enzymatic activity of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor:
3.2.2.8;

Protein crystallography data

The structure of Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor, PDB code: 3g5i was solved by G.Garau, L.Muzzolini, P.Tornaghi, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.50 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.350, 82.910, 93.870, 90.00, 112.15, 90.00
R / Rfree (%) 20.3 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor (pdb code 3g5i). 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 the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor, PDB code: 3g5i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3g5i

Go back to Calcium Binding Sites List in 3g5i
Calcium binding site 1 out of 4 in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor


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 the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:16.3
occ:1.00
O A:HOH312 2.4 15.8 1.0
O A:THR124 2.4 24.5 1.0
OD1 A:ASP10 2.4 30.5 1.0
OD2 A:ASP241 2.4 27.4 1.0
OD1 A:ASP15 2.5 22.9 1.0
O2' A:DNB502 2.5 28.3 1.0
OD2 A:ASP15 2.5 24.5 1.0
O3' A:DNB502 2.8 16.2 1.0
CG A:ASP15 2.9 26.7 1.0
ND2 A:ASN39 3.3 38.4 1.0
CG A:ASP241 3.4 28.2 1.0
C A:THR124 3.5 24.8 1.0
CG A:ASP10 3.5 29.2 1.0
C2' A:DNB502 3.7 29.1 1.0
C3' A:DNB502 3.7 27.0 1.0
OD1 A:ASP241 3.7 28.8 1.0
OD2 A:ASP10 3.9 28.9 1.0
N A:GLY125 4.2 23.6 1.0
CA A:GLY125 4.2 24.3 1.0
OG1 A:THR124 4.3 24.4 1.0
CB A:ASP15 4.4 26.6 1.0
CG A:ASN39 4.4 40.7 1.0
C1' A:DNB502 4.4 32.6 1.0
OD1 A:ASP14 4.4 37.1 1.0
CB A:THR124 4.4 25.4 1.0
N A:ASP10 4.5 25.0 1.0
ND2 A:ASN166 4.5 24.1 1.0
O A:ASP10 4.5 26.1 1.0
OD1 A:ASN166 4.5 22.8 1.0
CA A:THR124 4.5 24.9 1.0
N4' A:DNB502 4.6 26.1 1.0
C4' A:DNB502 4.8 28.6 1.0
CB A:ASP10 4.8 25.9 1.0
C A:ASP10 4.8 26.3 1.0
OD2 A:ASP14 4.8 39.5 1.0
CB A:ASP241 4.8 25.7 1.0
N A:ASP15 4.8 27.2 1.0
OD1 A:ASN39 4.9 41.0 1.0
CA A:ASP10 4.9 26.0 1.0
CG A:ASP14 4.9 32.9 1.0
CG A:ASN166 5.0 25.0 1.0
CA A:ASP15 5.0 27.2 1.0

Calcium binding site 2 out of 4 in 3g5i

Go back to Calcium Binding Sites List in 3g5i
Calcium binding site 2 out of 4 in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor


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 the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:19.8
occ:1.00
O2' B:DNB502 2.4 27.1 0.7
OD1 B:ASP10 2.4 30.3 1.0
OD2 B:ASP241 2.5 26.8 1.0
OD2 B:ASP15 2.5 25.4 1.0
OD1 B:ASP15 2.5 22.1 1.0
O B:THR124 2.5 24.1 1.0
O B:HOH455 2.5 24.4 1.0
O3' B:DNB502 2.6 16.9 0.7
CG B:ASP15 2.8 26.6 1.0
ND2 B:ASN39 3.2 38.8 1.0
CG B:ASP241 3.5 28.6 1.0
CG B:ASP10 3.5 28.8 1.0
C B:THR124 3.6 24.8 1.0
C2' B:DNB502 3.6 26.7 0.7
C3' B:DNB502 3.6 25.2 0.7
OD1 B:ASP241 3.8 28.2 1.0
OD2 B:ASP10 4.0 28.8 1.0
N B:GLY125 4.2 24.1 1.0
CA B:GLY125 4.2 24.0 1.0
CG B:ASN39 4.3 41.1 1.0
CB B:ASP15 4.3 26.3 1.0
O B:ASP10 4.3 26.9 1.0
OG1 B:THR124 4.4 24.5 1.0
C1' B:DNB502 4.4 30.0 0.7
OD1 B:ASP14 4.5 37.2 1.0
CB B:THR124 4.5 25.1 1.0
N B:ASP10 4.5 25.2 1.0
OD2 B:ASP14 4.6 39.6 1.0
OD1 B:ASN166 4.6 23.0 1.0
ND2 B:ASN166 4.6 22.9 1.0
CA B:THR124 4.7 24.5 1.0
C4' B:DNB502 4.7 26.6 0.7
N4' B:DNB502 4.7 27.2 0.7
C B:ASP10 4.7 26.8 1.0
OD1 B:ASN39 4.7 41.6 1.0
N B:ASP15 4.8 27.6 1.0
CB B:ASP10 4.8 26.0 1.0
CB B:ASP241 4.8 25.9 1.0
CG B:ASP14 4.8 33.2 1.0
CA B:ASP10 4.9 26.0 1.0
CA B:ASP15 4.9 27.1 1.0

Calcium binding site 3 out of 4 in 3g5i

Go back to Calcium Binding Sites List in 3g5i
Calcium binding site 3 out of 4 in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor


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 the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:19.5
occ:1.00
O C:THR124 2.4 24.6 1.0
O C:HOH573 2.4 22.5 1.0
OD2 C:ASP241 2.4 27.1 1.0
OD1 C:ASP15 2.4 22.9 1.0
OD2 C:ASP15 2.5 25.2 1.0
OD1 C:ASP10 2.5 31.1 1.0
O3' C:DNB502 2.6 25.0 0.7
O2' C:DNB502 2.6 32.1 0.7
CG C:ASP15 2.8 26.7 1.0
CG C:ASP241 3.4 28.1 1.0
ND2 C:ASN39 3.4 39.2 1.0
C C:THR124 3.5 25.2 1.0
CG C:ASP10 3.6 28.6 1.0
OD1 C:ASP241 3.7 27.7 1.0
C2' C:DNB502 3.7 34.8 0.7
C3' C:DNB502 3.7 32.6 0.7
OD2 C:ASP10 4.1 28.5 1.0
OG1 C:THR124 4.2 25.0 1.0
CB C:ASP15 4.2 26.9 1.0
N C:GLY125 4.3 24.2 1.0
CA C:GLY125 4.3 24.2 1.0
O C:ASP10 4.3 26.8 1.0
CB C:THR124 4.3 25.2 1.0
OD1 C:ASP14 4.4 37.8 1.0
C1' C:DNB502 4.5 37.7 0.7
CG C:ASN39 4.5 40.9 1.0
N C:ASP10 4.6 25.5 1.0
CA C:THR124 4.6 25.1 1.0
OD2 C:ASP14 4.6 39.7 1.0
ND2 C:ASN166 4.6 22.9 1.0
C4' C:DNB502 4.7 33.8 0.7
C C:ASP10 4.7 26.6 1.0
N4' C:DNB502 4.7 35.8 0.7
CB C:ASP241 4.7 26.0 1.0
N C:ASP15 4.7 27.2 1.0
OD1 C:ASN166 4.8 23.4 1.0
CG C:ASP14 4.8 33.5 1.0
CA C:ASP15 4.9 27.1 1.0
CB C:ASP10 4.9 25.8 1.0
OD1 C:ASN39 4.9 41.6 1.0
CA C:ASP10 4.9 25.9 1.0

Calcium binding site 4 out of 4 in 3g5i

Go back to Calcium Binding Sites List in 3g5i
Calcium binding site 4 out of 4 in the Crystal Structure of the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor


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 the E.Coli Riha Pyrimidine Nucleosidase Bound to A Iminoribitol-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:20.2
occ:1.00
O D:HOH390 2.4 17.9 1.0
OD1 D:ASP10 2.4 30.8 1.0
O D:THR124 2.5 24.9 1.0
OD2 D:ASP15 2.5 25.1 1.0
OD2 D:ASP241 2.5 27.2 1.0
OD1 D:ASP15 2.5 22.2 1.0
O2' D:DNB502 2.5 40.5 1.0
CG D:ASP15 2.8 26.5 1.0
O3' D:DNB502 2.9 30.7 1.0
ND2 D:ASN39 3.3 39.0 1.0
CG D:ASP10 3.5 28.6 1.0
CG D:ASP241 3.5 28.5 1.0
C D:THR124 3.6 24.9 1.0
C2' D:DNB502 3.7 39.0 1.0
OD1 D:ASP241 3.8 28.9 1.0
C3' D:DNB502 3.8 37.2 1.0
OD2 D:ASP10 3.9 28.8 1.0
CA D:GLY125 4.2 24.1 1.0
N D:GLY125 4.2 24.4 1.0
CG D:ASN39 4.3 40.9 1.0
CB D:ASP15 4.3 26.5 1.0
C1' D:DNB502 4.4 42.6 1.0
O D:ASP10 4.4 26.6 1.0
N D:ASP10 4.4 24.9 1.0
OG1 D:THR124 4.4 25.0 1.0
OD1 D:ASP14 4.5 37.5 1.0
CB D:THR124 4.5 25.1 1.0
N4' D:DNB502 4.6 39.2 1.0
OD1 D:ASN166 4.6 22.7 1.0
CA D:THR124 4.6 24.7 1.0
ND2 D:ASN166 4.7 23.3 1.0
C D:ASP10 4.7 26.4 1.0
OD2 D:ASP14 4.7 39.5 1.0
CB D:ASP10 4.7 25.9 1.0
C4' D:DNB502 4.8 38.2 1.0
OD1 D:ASN39 4.8 41.4 1.0
CA D:ASP10 4.8 25.8 1.0
N D:ASP15 4.8 27.3 1.0
CB D:ASP241 4.9 26.1 1.0
CG D:ASP14 4.9 33.3 1.0
CA D:ASP15 5.0 26.8 1.0

Reference:

G.Garau, L.Muzzolini, P.Tornaghi, M.Degano. Crystal Structure of the Riha Nucleoside Hydrolase Bound to A Competitive Inhibitor To Be Published.
Page generated: Tue Jul 8 12:36:31 2025

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