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Sodium in PDB 3g8q: A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea

Protein crystallography data

The structure of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea, PDB code: 3g8q was solved by Y.Xiong, B.J.Stanley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.465, 77.060, 109.082, 90.00, 103.57, 90.00
R / Rfree (%) 20.2 / 26.5

Other elements in 3g8q:

The structure of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea (pdb code 3g8q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea, PDB code: 3g8q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3g8q

Go back to Sodium Binding Sites List in 3g8q
Sodium binding site 1 out of 7 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:45.0
occ:1.00
 OG1 A:THR125 2.6 36.0 1.0
O A:ARG189 3.0 38.5 1.0
O A:LEU123 3.0 28.6 1.0
N A:THR125 3.1 33.3 1.0
CG2 A:THR125 3.4 32.2 1.0
CB A:THR125 3.4 31.3 1.0
NH2 A:ARG191 3.4 63.1 1.0
NE A:ARG191 3.4 55.2 1.0
C A:ARG189 3.6 37.2 1.0
C A:LEU123 3.6 29.3 1.0
CG A:ARG189 3.8 45.2 1.0
CZ A:ARG191 3.8 57.6 1.0
C A:LEU124 3.8 33.4 1.0
CA A:THR125 3.8 36.1 1.0
CG A:LEU123 3.9 32.4 1.0
CB A:ARG189 3.9 41.2 1.0
CA A:LEU124 4.0 33.6 1.0
N A:LEU124 4.1 28.0 1.0
N A:ILE190 4.1 41.5 1.0
CD2 A:LEU123 4.2 29.8 1.0
N A:ARG191 4.2 39.5 1.0
CB A:LEU123 4.3 30.8 1.0
CA A:ILE190 4.3 42.9 1.0
CG A:ARG191 4.4 49.1 1.0
CA A:ARG189 4.4 42.5 1.0
CB A:ARG191 4.5 41.0 1.0
CD A:ARG191 4.5 50.8 1.0
CA A:LEU123 4.6 29.8 1.0
C A:ILE190 4.6 39.5 1.0
O A:LEU124 4.7 32.9 1.0
C A:THR125 4.8 35.5 1.0
O A:THR125 4.8 41.5 1.0
NH1 A:ARG191 5.0 54.2 1.0
CA A:ARG191 5.0 37.6 1.0
CD A:ARG189 5.0 53.3 1.0

Sodium binding site 2 out of 7 in 3g8q

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Sodium binding site 2 out of 7 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:55.1
occ:1.00
 O B:HOH310 2.8 0.0 1.0
OD1 B:ASP175 2.8 84.0 1.0
OD2 B:ASP173 2.8 88.1 1.0
OD1 B:ASP173 3.1 88.4 1.0
CG B:ASP175 3.3 81.2 1.0
CG B:ASP173 3.3 83.9 1.0
CB B:ASP175 3.6 74.3 1.0
OD2 B:ASP175 4.1 82.9 1.0
N B:ASP175 4.7 69.7 1.0
CA B:ASP175 4.8 70.3 1.0
CB B:ASP173 4.9 78.0 1.0

Sodium binding site 3 out of 7 in 3g8q

Go back to Sodium Binding Sites List in 3g8q
Sodium binding site 3 out of 7 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:43.9
occ:1.00
 CD C:ARG270 2.6 49.8 1.0
OG C:SER272 2.7 29.2 1.0
OD2 C:ASP265 2.8 35.9 1.0
O C:ASP265 2.8 35.9 1.0
NH1 C:ARG270 2.9 29.4 1.0
O C:ARG270 3.2 44.9 1.0
NE C:ARG270 3.5 43.0 1.0
CZ C:ARG270 3.6 38.4 1.0
C C:ASP265 3.6 34.9 1.0
CB C:SER272 3.6 34.5 1.0
N C:SER272 3.8 33.5 1.0
C C:ARG270 3.8 44.6 1.0
CG C:ARG270 3.8 45.9 1.0
CG C:ASP265 3.8 37.5 1.0
CD2 C:LEU120 4.0 36.6 1.0
C C:VAL271 4.0 37.7 1.0
CB C:ASP265 4.1 35.3 1.0
N C:LEU267 4.1 37.0 1.0
CA C:VAL271 4.1 41.0 1.0
N C:VAL266 4.1 35.5 1.0
N C:VAL271 4.2 43.7 1.0
CA C:VAL266 4.2 37.9 1.0
CB C:LEU267 4.3 36.7 1.0
CB C:ARG270 4.3 46.0 1.0
CA C:SER272 4.4 35.6 1.0
C C:VAL266 4.4 36.4 1.0
CA C:ASP265 4.5 34.5 1.0
OG C:SER196 4.7 40.4 1.0
CA C:ARG270 4.7 45.0 1.0
O C:VAL271 4.7 36.0 1.0
CB C:LEU120 4.8 40.0 1.0
CA C:LEU267 4.8 36.9 1.0
NH2 C:ARG270 4.8 36.9 1.0
OD1 C:ASP265 5.0 37.4 1.0

Sodium binding site 4 out of 7 in 3g8q

Go back to Sodium Binding Sites List in 3g8q
Sodium binding site 4 out of 7 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:55.2
occ:1.00
 OD1 C:ASP173 2.2 74.7 1.0
O C:HOH335 2.4 74.2 1.0
OD2 C:ASP175 2.7 72.9 1.0
OD2 C:ASP173 2.8 83.0 1.0
CG C:ASP173 2.8 74.6 1.0
CG C:ASP175 3.8 67.2 1.0
NH2 C:ARG192 3.9 68.7 1.0
CB C:ASP175 4.3 63.5 1.0
CB C:ASP173 4.3 69.4 1.0
N C:ASP175 4.5 59.4 1.0
CD C:PRO174 4.5 59.2 1.0
OD1 C:ASP175 4.8 59.6 1.0
N C:PRO174 4.8 58.9 1.0
CA C:ASP173 4.9 65.7 1.0

Sodium binding site 5 out of 7 in 3g8q

Go back to Sodium Binding Sites List in 3g8q
Sodium binding site 5 out of 7 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:38.8
occ:1.00
 O D:HOH342 2.5 67.0 1.0
O D:HOH341 2.5 56.3 1.0
OD1 D:ASP115 2.5 52.4 1.0
OD1 D:ASN17 2.6 74.8 1.0
O D:ASN17 2.6 71.6 1.0
CG D:ASN17 3.1 74.7 1.0
C D:ASN17 3.3 65.7 1.0
O D:GLY113 3.3 47.2 1.0
CG D:ASP115 3.6 54.7 1.0
CA D:ASN17 3.7 66.2 1.0
ND2 D:ASN17 3.7 80.5 1.0
O D:HOH346 3.8 52.2 1.0
OD2 D:ASP115 3.9 59.8 1.0
CB D:ASN17 4.0 70.8 1.0
NZ D:LYS21 4.3 58.5 1.0
N D:GLU18 4.3 62.7 1.0
C D:GLY113 4.4 51.4 1.0
CA D:GLU18 4.8 64.0 1.0
CB D:ASP115 4.8 51.4 1.0
N D:ASP115 4.9 48.5 1.0
C D:TYR114 4.9 51.0 1.0

Sodium binding site 6 out of 7 in 3g8q

Go back to Sodium Binding Sites List in 3g8q
Sodium binding site 6 out of 7 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:51.8
occ:1.00
 O D:HOH338 1.9 79.4 1.0
OE2 D:GLU179 2.8 71.5 1.0
OE1 D:GLU176 2.9 68.4 1.0
OE1 D:GLU179 3.0 75.2 1.0
CD D:GLU179 3.2 71.8 1.0
OE2 D:GLU176 3.3 75.0 1.0
CD D:GLU176 3.5 70.1 1.0
O D:HOH336 4.0 83.0 1.0
NA D:NA304 4.7 41.3 1.0
CG D:GLU179 4.7 64.2 1.0
CG D:GLU176 5.0 64.7 1.0

Sodium binding site 7 out of 7 in 3g8q

Go back to Sodium Binding Sites List in 3g8q
Sodium binding site 7 out of 7 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:41.3
occ:1.00
 OE2 D:GLU179 2.4 71.5 1.0
O D:HOH336 2.6 83.0 1.0
O D:HOH359 2.7 66.2 1.0
CD D:GLU179 3.5 71.8 1.0
O D:HOH358 3.8 78.2 1.0
CG D:GLU179 3.8 64.2 1.0
O D:HOH337 4.3 73.9 1.0
OE1 D:GLU179 4.6 75.2 1.0
NA D:NA303 4.7 51.8 1.0

Reference:

L.Randau, B.J.Stanley, A.Kohlway, S.Mechta, Y.Xiong, D.Soll. A Cytidine Deaminase Edits C to U in Transfer Rnas in Archaea Science V. 324 657 2009.
ISSN: ISSN 0036-8075
PubMed: 19407206
DOI: 10.1126/SCIENCE.1170123
Page generated: Mon Oct 7 09:56:43 2024

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