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Calcium in PDB 1yoe: Crystal Structure of A the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose

Enzymatic activity of Crystal Structure of A the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose

All present enzymatic activity of Crystal Structure of A the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose:
3.2.2.8;

Protein crystallography data

The structure of Crystal Structure of A the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose, PDB code: 1yoe was solved by L.Muzzolini, W.Versees, J.Steyaert, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.78
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.466, 84.062, 112.483, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose (pdb code 1yoe). 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 A the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose, PDB code: 1yoe:

Calcium binding site 1 out of 1 in 1yoe

Go back to Calcium Binding Sites List in 1yoe
Calcium binding site 1 out of 1 in the Crystal Structure of A the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose


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 A the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:11.6
occ:1.00
 O A:THR124 2.4 9.4 1.0
OD2 A:ASP241 2.4 9.2 1.0
O2' A:RIB2001 2.4 9.3 0.7
OD1 A:ASP10 2.5 10.2 1.0
OD1 A:ASP15 2.5 9.0 1.0
OD2 A:ASP15 2.5 10.1 1.0
O A:HOH2002 2.5 10.8 1.0
O3' A:RIB2001 2.6 8.8 0.7
O3' A:RIB2001 2.7 16.5 0.3
O2' A:RIB2001 2.7 17.0 0.3
CG A:ASP15 2.8 10.2 1.0
C A:THR124 3.4 9.7 1.0
CG A:ASP241 3.4 9.7 1.0
C2' A:RIB2001 3.4 11.5 0.7
C3' A:RIB2001 3.6 11.6 0.7
ND2 A:ASN39 3.6 15.2 1.0
CG A:ASP10 3.6 9.6 1.0
OD1 A:ASP241 3.7 11.5 1.0
C3' A:RIB2001 3.8 16.9 0.3
C2' A:RIB2001 3.8 17.7 0.3
OD2 A:ASP10 3.9 9.7 1.0
CA A:GLY125 4.1 9.9 1.0
C1' A:RIB2001 4.1 17.2 0.7
N A:GLY125 4.1 10.1 1.0
OD1 A:ASP14 4.3 16.2 1.0
CB A:ASP15 4.3 8.8 1.0
OG1 A:THR124 4.3 11.1 1.0
O1' A:RIB2001 4.3 17.7 0.3
CB A:THR124 4.4 9.6 1.0
ND2 A:ASN166 4.4 9.0 1.0
O A:ASP10 4.5 10.2 1.0
CA A:THR124 4.5 10.2 1.0
OD1 A:ASN166 4.5 11.9 1.0
C4' A:RIB2001 4.6 14.5 0.7
N A:ASP10 4.6 9.5 1.0
C1' A:RIB2001 4.7 18.2 0.3
CG A:ASN39 4.7 18.2 1.0
OD2 A:ASP14 4.7 14.4 1.0
CB A:ASP241 4.8 9.9 1.0
N A:ASP15 4.8 9.8 1.0
C A:ASP10 4.9 10.2 1.0
C4' A:RIB2001 4.9 17.0 0.3
CG A:ASP14 4.9 12.7 1.0
CB A:ASP10 4.9 10.1 1.0
O4' A:RIB2001 4.9 20.4 0.7
CA A:ASP15 4.9 8.8 1.0
CG A:ASN166 4.9 11.0 1.0

Reference:

L.Muzzolini, W.Versees, J.Steyaert, M.Degano. Crystal Structure of the E. Coli Pyrimidine Nucleoside Hydrolase Ybek with Bound Ribose To Be Published.
Page generated: Fri Jul 12 08:08:16 2024

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