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Calcium in PDB 2mas: Purine Nucleoside Hydrolase with A Transition State Inhibitor

Enzymatic activity of Purine Nucleoside Hydrolase with A Transition State Inhibitor

All present enzymatic activity of Purine Nucleoside Hydrolase with A Transition State Inhibitor:
3.2.2.1;

Protein crystallography data

The structure of Purine Nucleoside Hydrolase with A Transition State Inhibitor, PDB code: 2mas was solved by M.Degano, V.L.Schramm, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.630, 159.760, 206.380, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Purine Nucleoside Hydrolase with A Transition State Inhibitor (pdb code 2mas). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Purine Nucleoside Hydrolase with A Transition State Inhibitor, PDB code: 2mas:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2mas

Go back to Calcium Binding Sites List in 2mas
Calcium binding site 1 out of 4 in the Purine Nucleoside Hydrolase with A Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Purine Nucleoside Hydrolase with A Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca316

b:22.0
occ:1.00
 O A:THR126 2.3 10.7 1.0
O A:HOH436 2.4 15.8 1.0
OD1 A:ASP15 2.5 18.2 1.0
O2' A:PIR400 2.5 18.8 1.0
OD1 A:ASP10 2.5 25.4 1.0
O3' A:PIR400 2.5 16.2 1.0
OD2 A:ASP242 2.6 25.6 1.0
OD2 A:ASP15 2.6 14.4 1.0
CG A:ASP15 2.9 18.4 1.0
OD1 A:ASN39 3.3 31.8 1.0
C2' A:PIR400 3.5 20.6 1.0
C3' A:PIR400 3.6 19.7 1.0
C A:THR126 3.6 16.8 1.0
CG A:ASP242 3.6 27.2 1.0
CG A:ASP10 3.6 24.7 1.0
OD1 A:ASP242 3.8 29.9 1.0
OD2 A:ASP10 4.0 17.3 1.0
C1' A:PIR400 4.2 22.8 1.0
OG1 A:THR126 4.2 15.0 1.0
CA A:GLY127 4.3 16.0 1.0
N A:GLY127 4.3 18.8 1.0
CB A:ASP15 4.3 18.0 1.0
N4' A:PIR400 4.5 23.1 1.0
CG A:ASN39 4.5 30.3 1.0
CB A:THR126 4.5 16.5 1.0
OD1 A:ASN168 4.5 13.4 1.0
O A:ASP10 4.6 20.1 1.0
OD1 A:ASP14 4.6 27.7 1.0
C4' A:PIR400 4.6 19.3 1.0
N A:ASP10 4.6 18.4 1.0
CA A:THR126 4.6 15.1 1.0
ND2 A:ASN168 4.7 13.0 1.0
OD2 A:ASP14 4.7 24.8 1.0
CB A:ASP10 4.9 21.4 1.0
C A:ASP10 4.9 20.7 1.0
CG A:ASP14 5.0 26.9 1.0
CB A:ASP242 5.0 25.2 1.0
N A:ASP15 5.0 24.8 1.0
CA A:ASP15 5.0 21.2 1.0
ND2 A:ASN39 5.0 27.0 1.0

Calcium binding site 2 out of 4 in 2mas

Go back to Calcium Binding Sites List in 2mas
Calcium binding site 2 out of 4 in the Purine Nucleoside Hydrolase with A Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Purine Nucleoside Hydrolase with A Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca316

b:25.3
occ:1.00
 O B:THR126 2.2 13.4 1.0
O B:HOH428 2.4 21.3 1.0
O3' B:PIR400 2.5 24.0 1.0
OD2 B:ASP242 2.5 20.4 1.0
OD1 B:ASP10 2.5 30.7 1.0
OD2 B:ASP15 2.6 21.1 1.0
OD1 B:ASP15 2.6 16.0 1.0
O2' B:PIR400 2.7 21.1 1.0
CG B:ASP15 2.9 23.7 1.0
C B:THR126 3.4 15.8 1.0
CG B:ASP242 3.5 28.9 1.0
OD1 B:ASN39 3.5 34.1 1.0
C3' B:PIR400 3.6 21.9 1.0
CG B:ASP10 3.6 28.7 1.0
C2' B:PIR400 3.7 18.9 1.0
OD1 B:ASP242 3.7 33.9 1.0
OG1 B:THR126 4.0 10.3 1.0
OD2 B:ASP10 4.0 24.8 1.0
CA B:GLY127 4.1 16.0 1.0
N B:GLY127 4.2 15.0 1.0
C1' B:PIR400 4.3 24.6 1.0
CB B:THR126 4.3 16.2 1.0
CB B:ASP15 4.4 26.0 1.0
CA B:THR126 4.5 14.8 1.0
OD1 B:ASN168 4.5 10.4 1.0
ND2 B:ASN168 4.5 14.6 1.0
N4' B:PIR400 4.5 22.7 1.0
N B:ASP10 4.6 19.9 1.0
C4' B:PIR400 4.6 22.4 1.0
CG B:ASN39 4.6 32.1 1.0
O B:ASP10 4.7 24.8 1.0
OD2 B:ASP14 4.8 32.4 1.0
OD1 B:ASP14 4.8 37.3 1.0
CB B:ASP10 4.9 25.7 1.0
CB B:ASP242 4.9 26.3 1.0
C B:ASP10 5.0 24.5 1.0
CG B:ASN168 5.0 13.2 1.0

Calcium binding site 3 out of 4 in 2mas

Go back to Calcium Binding Sites List in 2mas
Calcium binding site 3 out of 4 in the Purine Nucleoside Hydrolase with A Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Purine Nucleoside Hydrolase with A Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca316

b:15.0
occ:1.00
 O C:THR126 2.2 8.9 1.0
O C:HOH451 2.4 17.1 1.0
OD1 C:ASP10 2.5 18.7 1.0
O3' C:PIR400 2.5 15.0 1.0
OD1 C:ASP15 2.6 11.1 1.0
OD2 C:ASP242 2.6 24.0 1.0
OD2 C:ASP15 2.7 15.9 1.0
O2' C:PIR400 2.7 15.6 1.0
CG C:ASP15 3.0 15.3 1.0
C C:THR126 3.4 12.2 1.0
CG C:ASP10 3.6 22.6 1.0
OD1 C:ASN39 3.6 26.1 1.0
C3' C:PIR400 3.6 14.6 1.0
CG C:ASP242 3.6 21.6 1.0
C2' C:PIR400 3.6 13.8 1.0
OD1 C:ASP242 3.9 24.1 1.0
OD2 C:ASP10 3.9 23.3 1.0
OG1 C:THR126 4.1 10.9 1.0
CA C:GLY127 4.1 10.5 1.0
N C:GLY127 4.2 9.7 1.0
C1' C:PIR400 4.3 17.4 1.0
CB C:THR126 4.4 13.8 1.0
CB C:ASP15 4.4 14.7 1.0
OD1 C:ASN168 4.5 8.8 1.0
CA C:THR126 4.5 9.3 1.0
N4' C:PIR400 4.5 13.2 1.0
ND2 C:ASN168 4.5 12.1 1.0
N C:ASP10 4.6 15.3 1.0
C4' C:PIR400 4.6 19.8 1.0
O C:ASP10 4.6 12.2 1.0
CG C:ASN39 4.6 21.5 1.0
OD1 C:ASP14 4.8 18.4 1.0
OD2 C:ASP14 4.8 19.6 1.0
CB C:ASP10 4.9 18.6 1.0
C C:ASP10 4.9 18.6 1.0
CB C:ASP242 4.9 19.5 1.0
CG C:ASN168 4.9 14.4 1.0

Calcium binding site 4 out of 4 in 2mas

Go back to Calcium Binding Sites List in 2mas
Calcium binding site 4 out of 4 in the Purine Nucleoside Hydrolase with A Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Purine Nucleoside Hydrolase with A Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca316

b:17.7
occ:1.00
 O D:THR126 2.3 10.2 1.0
O3' D:PIR400 2.5 24.9 1.0
O D:HOH441 2.5 28.8 1.0
OD1 D:ASP15 2.5 12.7 1.0
O2' D:PIR400 2.5 18.9 1.0
OD2 D:ASP242 2.5 21.1 1.0
OD1 D:ASP10 2.5 28.6 1.0
OD2 D:ASP15 2.7 15.4 1.0
CG D:ASP15 2.9 20.6 1.0
OD1 D:ASN39 3.5 35.2 1.0
C D:THR126 3.5 15.6 1.0
C3' D:PIR400 3.5 23.6 1.0
C2' D:PIR400 3.5 22.9 1.0
CG D:ASP242 3.5 22.9 1.0
CG D:ASP10 3.6 24.0 1.0
OD1 D:ASP242 3.8 20.6 1.0
OD2 D:ASP10 4.0 26.2 1.0
OG1 D:THR126 4.1 14.7 1.0
C1' D:PIR400 4.2 22.4 1.0
CA D:GLY127 4.2 17.7 1.0
N D:GLY127 4.3 14.1 1.0
CB D:ASP15 4.4 18.3 1.0
CB D:THR126 4.4 17.0 1.0
OD1 D:ASN168 4.5 14.7 1.0
N4' D:PIR400 4.5 22.8 1.0
ND2 D:ASN168 4.6 15.6 1.0
CA D:THR126 4.6 13.4 1.0
C4' D:PIR400 4.6 26.7 1.0
O D:ASP10 4.6 20.3 1.0
CG D:ASN39 4.6 28.6 1.0
N D:ASP10 4.6 18.9 1.0
OD1 D:ASP14 4.7 25.6 1.0
OD2 D:ASP14 4.8 18.6 1.0
CB D:ASP242 4.9 22.4 1.0
CB D:ASP10 4.9 23.2 1.0
C D:ASP10 5.0 23.1 1.0
CG D:ASN168 5.0 17.2 1.0
CA D:ASP15 5.0 15.5 1.0

Reference:

M.Degano, S.C.Almo, J.C.Sacchettini, V.L.Schramm. Trypanosomal Nucleoside Hydrolase. A Novel Mechanism From the Structure with A Transition-State Inhibitor. Biochemistry V. 37 6277 1998.
ISSN: ISSN 0006-2960
PubMed: 9572842
DOI: 10.1021/BI973012E
Page generated: Tue Jul 8 07:04:40 2025

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