Atomistry » Sodium » PDB 3fvs-3gdg » 3g8q
Atomistry »
  Sodium »
    PDB 3fvs-3gdg »
      3g8q »

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

Go back to Sodium Binding Sites List in 3g8q
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: Tue Dec 15 06:12:17 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy