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Sodium in PDB 3zx3: Crystal Structure and Domain Rotation of NTPDASE1 CD39

Enzymatic activity of Crystal Structure and Domain Rotation of NTPDASE1 CD39

All present enzymatic activity of Crystal Structure and Domain Rotation of NTPDASE1 CD39:
3.6.1.5;

Protein crystallography data

The structure of Crystal Structure and Domain Rotation of NTPDASE1 CD39, PDB code: 3zx3 was solved by M.Zebisch, P.Schaefer, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 146.62 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 163.133, 81.136, 165.465, 90.00, 117.61, 90.00
R / Rfree (%) 17.6 / 23.3

Other elements in 3zx3:

The structure of Crystal Structure and Domain Rotation of NTPDASE1 CD39 also contains other interesting chemical elements:

Chlorine (Cl) 27 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure and Domain Rotation of NTPDASE1 CD39 (pdb code 3zx3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure and Domain Rotation of NTPDASE1 CD39, PDB code: 3zx3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3zx3

Go back to Sodium Binding Sites List in 3zx3
Sodium binding site 1 out of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na521

b:51.8
occ:1.00
 OD1 B:ASN429 2.4 64.9 1.0
O B:GLN426 2.5 52.7 1.0
O B:ALA343 2.6 38.3 1.0
O B:GLY427 2.7 43.1 1.0
O B:CYS342 3.2 44.9 1.0
CG B:ASN429 3.5 59.4 1.0
C B:GLY427 3.5 41.2 1.0
C B:ALA343 3.6 37.5 1.0
C B:GLN426 3.7 47.6 1.0
CA B:ALA343 3.9 37.6 1.0
ND2 B:ASN429 3.9 58.2 1.0
CA B:GLY427 4.0 40.3 1.0
C B:CYS342 4.2 41.2 1.0
O B:HOH2152 4.2 50.1 1.0
OXT B:ACY512 4.3 57.3 1.0
N B:GLY427 4.3 41.8 1.0
ND2 B:ASN334 4.3 54.0 1.0
N B:ASN429 4.5 41.4 1.0
N B:ALA343 4.5 37.1 1.0
O B:HOH2123 4.6 59.4 1.0
N B:TYR428 4.6 38.9 1.0
CB B:ASN429 4.7 56.8 1.0
N B:PHE344 4.8 33.1 1.0
CA B:GLN426 4.9 44.5 1.0
CA B:ASN429 4.9 48.3 1.0

Sodium binding site 2 out of 5 in 3zx3

Go back to Sodium Binding Sites List in 3zx3
Sodium binding site 2 out of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na521

b:52.5
occ:1.00
 O C:PHE332 2.5 36.8 1.0
O C:LEU329 2.6 38.6 1.0
O C:HOH2136 2.7 55.1 1.0
O C:HOH2137 2.9 43.5 1.0
C C:LEU329 3.5 39.1 1.0
C C:PHE332 3.6 35.2 1.0
CA C:LYS330 4.1 41.0 1.0
N C:LYS330 4.1 36.7 1.0
OD1 C:ASN334 4.3 40.5 1.0
N C:PHE332 4.4 34.7 1.0
CB C:LEU329 4.4 35.2 1.0
CA C:PHE332 4.4 35.1 1.0
C C:LYS330 4.4 38.2 1.0
CA C:LEU329 4.4 35.0 1.0
O C:LYS330 4.5 40.1 1.0
O C:HOH2051 4.5 52.4 1.0
CB C:PHE332 4.5 33.1 1.0
N C:ASN333 4.6 35.2 1.0
N C:ASN334 4.6 37.8 1.0
CA C:ASN333 4.6 36.8 1.0
CD C:LYS330 4.7 67.1 1.0

Sodium binding site 3 out of 5 in 3zx3

Go back to Sodium Binding Sites List in 3zx3
Sodium binding site 3 out of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na522

b:29.3
occ:1.00
 O C:HOH2155 2.4 31.0 1.0
O C:ALA343 2.4 27.8 1.0
OD1 C:ASN429 2.4 26.8 1.0
O C:GLY427 2.5 29.0 1.0
O C:GLN426 2.5 27.7 1.0
O C:CYS342 2.6 26.5 1.0
C C:GLY427 3.3 27.2 1.0
CG C:ASN429 3.3 27.9 1.0
C C:ALA343 3.3 26.5 1.0
CA C:ALA343 3.5 26.0 1.0
C C:CYS342 3.6 25.9 1.0
C C:GLN426 3.6 26.6 1.0
ND2 C:ASN429 3.6 27.1 1.0
CA C:GLY427 3.6 27.2 1.0
N C:ALA343 4.0 24.6 1.0
N C:GLY427 4.0 26.7 1.0
O C:HOH2154 4.2 30.0 1.0
O C:HOH2186 4.4 29.4 1.0
N C:TYR428 4.4 23.8 1.0
O C:HOH2187 4.4 51.7 1.0
ND2 C:ASN334 4.4 33.7 1.0
N C:ASN429 4.5 23.9 1.0
N C:PHE344 4.6 28.9 1.0
CB C:ASN429 4.6 27.4 1.0
O C:HOH2142 4.7 31.3 1.0
CA C:CYS342 4.8 25.3 1.0
CA C:GLN426 4.8 29.0 1.0
OXT C:ACY512 4.9 32.7 1.0
CA C:ASN429 4.9 24.4 1.0
CA C:TYR428 4.9 25.6 1.0
C C:TYR428 4.9 26.2 1.0
CB C:ALA343 4.9 25.1 1.0
N C:CYS342 5.0 25.9 1.0

Sodium binding site 4 out of 5 in 3zx3

Go back to Sodium Binding Sites List in 3zx3
Sodium binding site 4 out of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na522

b:52.1
occ:1.00
 O D:HOH2194 2.1 43.0 1.0
O D:PHE332 2.3 40.1 1.0
O D:HOH2195 2.3 53.0 1.0
O D:LEU329 2.5 36.7 1.0
O D:HOH2193 2.7 48.5 1.0
O D:HOH2197 2.8 49.5 1.0
C D:PHE332 3.5 38.5 1.0
C D:LEU329 3.5 37.5 1.0
CA D:LYS330 3.9 40.1 1.0
C D:LYS330 4.1 38.9 1.0
N D:LYS330 4.1 38.8 1.0
N D:PHE332 4.2 35.3 1.0
O D:LYS330 4.2 39.5 1.0
CA D:PHE332 4.3 36.6 1.0
N D:ASN333 4.4 38.0 1.0
CB D:PHE332 4.4 34.1 1.0
CA D:ASN333 4.5 43.9 1.0
CA D:LEU329 4.5 36.5 1.0
OD1 D:ASN334 4.5 42.0 1.0
N D:ASN334 4.5 43.0 1.0
CB D:LEU329 4.5 38.5 1.0
N D:ILE331 4.8 36.1 1.0
O D:HOH2202 4.9 57.2 1.0
OD1 D:ASN333 4.9 76.3 1.0
C D:ASN333 5.0 41.8 1.0

Sodium binding site 5 out of 5 in 3zx3

Go back to Sodium Binding Sites List in 3zx3
Sodium binding site 5 out of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na521

b:35.4
occ:1.00
 O D:GLY427 2.4 35.6 1.0
O D:HOH2210 2.4 38.9 1.0
OD1 D:ASN429 2.4 36.8 1.0
O D:CYS342 2.5 34.7 1.0
O D:ALA343 2.6 33.6 1.0
O D:GLN426 2.6 39.1 1.0
C D:GLY427 3.2 32.7 1.0
CG D:ASN429 3.3 35.9 1.0
C D:ALA343 3.4 33.4 1.0
CA D:GLY427 3.5 32.8 1.0
C D:CYS342 3.5 34.7 1.0
C D:GLN426 3.5 38.9 1.0
ND2 D:ASN429 3.6 34.8 1.0
CA D:ALA343 3.6 31.8 1.0
N D:GLY427 4.0 35.5 1.0
N D:ALA343 4.0 33.1 1.0
O D:HOH2239 4.1 46.2 1.0
O D:HOH2209 4.2 38.5 1.0
N D:TYR428 4.3 33.4 1.0
ND2 D:ASN334 4.4 41.8 1.0
N D:ASN429 4.4 34.3 1.0
O D:HOH2203 4.6 44.1 1.0
CB D:ASN429 4.6 37.4 1.0
N D:PHE344 4.7 32.1 1.0
CA D:CYS342 4.8 36.7 1.0
CA D:GLN426 4.8 39.8 1.0
OXT D:ACY512 4.8 35.1 1.0
CA D:ASN429 4.8 36.0 1.0
CA D:TYR428 4.8 32.9 1.0
C D:TYR428 4.9 33.3 1.0
N D:CYS342 5.0 37.3 1.0
CB D:ALA343 5.0 29.4 1.0

Reference:

M.Zebisch, M.Krauss, P.Schafer, N.Strater. Crystallographic Evidence For A Domain Motion in Rat Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) 1. J.Mol.Biol. V. 415 288 2012.
ISSN: ISSN 0022-2836
PubMed: 22100451
DOI: 10.1016/J.JMB.2011.10.050
Page generated: Tue Dec 15 06:32:07 2020

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