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Sodium in PDB 3gox: Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta

Protein crystallography data

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta, PDB code: 3gox was solved by M.Sokolowska, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.60 / 1.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 90.682, 90.682, 334.933, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 18.6

Other elements in 3gox:

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta (pdb code 3gox). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta, PDB code: 3gox:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3gox

Go back to Sodium Binding Sites List in 3gox
Sodium binding site 1 out of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:18.6
occ:1.00
OP1 D:DA3 2.2 23.5 0.5
OP1 C:DT3 2.3 28.1 0.5
OD1 A:ASP148 2.3 15.2 1.0
OD1 A:ASN165 2.3 15.7 1.0
O A:HOH271 2.3 17.6 1.0
O C:HOH201 2.5 21.5 1.0
O3' D:DG2 2.8 16.7 0.5
O3' C:DG2 2.9 18.4 0.5
P D:DA3 3.1 22.5 0.5
P C:DT3 3.1 24.6 0.5
CG A:ASN165 3.3 14.9 1.0
CG A:ASP148 3.4 15.6 1.0
C3' D:DG2 3.6 14.3 0.5
C3' C:DG2 3.6 15.4 0.5
ND2 A:ASN165 3.7 15.6 1.0
O5' C:DT3 3.7 25.3 0.5
O5' D:DA3 3.9 22.6 0.5
C4' D:DG2 3.9 12.5 0.5
C4' C:DG2 3.9 13.5 0.5
NH2 A:ARG157 4.0 18.2 1.0
CB A:ASP148 4.1 17.2 1.0
CA A:ASP148 4.1 16.7 1.0
O A:HIS149 4.1 18.0 1.0
N A:HIS149 4.2 16.1 1.0
OP2 D:DA3 4.3 23.4 0.5
OD2 A:ASP173 4.4 22.7 1.0
OD2 A:ASP148 4.4 17.5 1.0
OP2 C:DT3 4.4 25.9 0.5
O A:HOH230 4.5 31.1 1.0
O A:ASN165 4.6 14.4 1.0
CB A:ASN165 4.6 13.2 1.0
C A:ASP148 4.7 16.7 1.0
C5' C:DG2 4.8 13.7 0.5
C5' D:DG2 4.8 12.8 0.5
CD1 A:LEU168 4.8 20.5 1.0
OD1 A:ASP173 4.9 23.6 1.0
CA A:ASN165 5.0 14.0 1.0
O4' D:DG2 5.0 12.0 0.5
O4' C:DG2 5.0 12.9 0.5
C2' D:DG2 5.0 12.5 0.5

Sodium binding site 2 out of 3 in 3gox

Go back to Sodium Binding Sites List in 3gox
Sodium binding site 2 out of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:18.7
occ:1.00
OP1 C:DT3 2.2 26.9 0.5
OP1 D:DA3 2.2 23.1 0.5
OD1 B:ASP148 2.3 14.9 1.0
OD1 B:ASN165 2.3 15.0 1.0
O B:HOH239 2.3 18.3 1.0
O C:HOH328 2.5 20.5 1.0
O3' D:DG2 2.8 16.5 0.5
O3' C:DG2 2.9 17.8 0.5
P D:DA3 3.1 23.9 0.5
P C:DT3 3.1 25.7 0.5
CG B:ASN165 3.3 14.9 1.0
CG B:ASP148 3.4 16.9 1.0
C3' D:DG2 3.6 14.7 0.5
C3' C:DG2 3.6 15.5 0.5
O5' C:DT3 3.7 25.9 0.5
ND2 B:ASN165 3.7 15.3 1.0
O5' D:DA3 3.9 23.3 0.5
C4' C:DG2 3.9 13.6 0.5
C4' D:DG2 3.9 13.0 0.5
NH2 B:ARG157 4.0 17.1 1.0
CB B:ASP148 4.1 16.8 1.0
CA B:ASP148 4.1 17.1 1.0
N B:HIS149 4.2 16.5 1.0
O B:HIS149 4.2 16.4 1.0
OD2 B:ASP148 4.3 16.4 1.0
OP2 D:DA3 4.3 23.6 0.5
O B:HOH247 4.4 30.7 1.0
OP2 C:DT3 4.4 25.0 0.5
OD2 B:ASP173 4.4 23.9 1.0
O B:ASN165 4.6 14.1 1.0
CB B:ASN165 4.6 14.0 1.0
C B:ASP148 4.7 16.6 1.0
C5' C:DG2 4.8 13.0 0.5
CD1 B:LEU168 4.8 20.5 1.0
C5' D:DG2 4.8 12.4 0.5
OD1 B:ASP173 4.8 22.7 1.0
CA B:ASN165 4.9 13.9 1.0

Sodium binding site 3 out of 3 in 3gox

Go back to Sodium Binding Sites List in 3gox
Sodium binding site 3 out of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na307

b:23.5
occ:1.00
O B:TYR57 2.3 16.3 1.0
O B:HOH455 2.4 36.6 1.0
O B:HOH361 2.5 27.9 1.0
O B:HOH213 2.5 21.1 1.0
OH B:TYR63 2.5 12.2 1.0
C B:TYR57 3.5 14.4 1.0
CZ B:TYR63 3.5 10.6 1.0
CE2 B:TYR63 3.7 10.7 1.0
CB B:TYR57 4.2 14.8 1.0
CA B:TYR57 4.3 14.7 1.0
N B:ARG58 4.4 12.9 1.0
CA B:ARG58 4.6 12.4 1.0
CE1 B:TYR63 4.7 8.8 1.0
CG B:ARG58 4.9 12.8 1.0
O B:HOH360 4.9 19.3 1.0
CD2 B:TYR63 5.0 10.4 1.0

Reference:

M.Sokolowska, H.Czapinska, M.Bochtler. Crystal Structure of the Beta Beta Alpha-Me Type II Restriction Endonuclease HPY99I with Target Dna. Nucleic Acids Res. V. 37 3799 2009.
ISSN: ISSN 0305-1048
PubMed: 19380375
DOI: 10.1093/NAR/GKP228
Page generated: Tue Dec 15 06:12:39 2020

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