Atomistry » Sodium » PDB 7s32-7si5 » 7s3a
Atomistry »
  Sodium »
    PDB 7s32-7si5 »
      7s3a »

Sodium in PDB 7s3a: Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide

Protein crystallography data

The structure of Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide, PDB code: 7s3a was solved by J.L.Jenkins, S.Henderson, C.L.Kielkopf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.76 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.245, 63.022, 77.491, 90, 90, 90
R / Rfree (%) 13.1 / 15.7

Other elements in 7s3a:

The structure of Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide also contains other interesting chemical elements:

Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide (pdb code 7s3a). 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 Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide, PDB code: 7s3a:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7s3a

Go back to Sodium Binding Sites List in 7s3a
Sodium binding site 1 out of 3 in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide


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 Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:41.2
occ:1.00
O A:HOH537 2.2 42.8 1.0
O B:HOH231 2.2 37.4 1.0
O A:SER294 2.3 26.0 1.0
O2 B:U6 2.4 21.5 1.0
HB3 A:ASN196 2.8 33.5 1.0
O A:LYS195 2.9 30.9 1.0
O A:HOH608 3.0 50.1 1.0
HB2 A:ASN196 3.3 33.5 1.0
C A:SER294 3.4 23.0 1.0
HA A:LYS195 3.4 32.6 1.0
CB A:ASN196 3.5 27.9 1.0
HB3 A:SER294 3.5 27.4 0.6
C A:LYS195 3.5 27.4 1.0
HB2 A:SER294 3.5 31.0 0.4
C2 B:U6 3.5 19.5 1.0
H3 B:U6 3.7 24.7 1.0
HA A:SER294 3.8 26.5 0.6
HA A:SER294 3.8 27.8 0.4
O B:HOH206 4.0 24.1 1.0
CA A:LYS195 4.0 27.1 1.0
HA A:ALA295 4.0 26.6 1.0
CA A:SER294 4.0 22.1 0.6
CA A:SER294 4.0 23.2 0.4
N3 B:U6 4.1 20.6 1.0
CB A:SER294 4.2 22.8 0.6
H1' B:U6 4.2 19.7 1.0
CB A:SER294 4.3 25.8 0.4
N A:ASN196 4.3 25.3 1.0
CG A:ASN196 4.4 31.9 1.0
O A:ASP194 4.4 34.2 1.0
N A:ALA295 4.4 21.7 1.0
OD1 A:ASN196 4.5 34.1 1.0
CA A:ASN196 4.5 24.6 1.0
HG A:SER294 4.5 27.6 0.6
CA A:ALA295 4.6 22.2 1.0
N1 B:U6 4.7 17.5 1.0
OG A:SER294 4.9 23.0 0.6
HB3 A:SER294 4.9 31.0 0.4
CB A:LYS195 4.9 26.9 1.0
HB2 A:SER294 4.9 27.4 0.6
C1' B:U6 5.0 16.4 1.0

Sodium binding site 2 out of 3 in 7s3a

Go back to Sodium Binding Sites List in 7s3a
Sodium binding site 2 out of 3 in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide


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 Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:31.9
occ:1.00
OD1 A:ASN155 2.8 15.3 1.0
OD1 A:ASN196 2.8 34.1 1.0
HA A:ASN155 3.0 16.1 1.0
O A:HOH617 3.0 39.8 1.0
O4 B:U6 3.0 22.0 1.0
HE22 A:GLN222 3.1 37.3 1.0
HA2 A:GLY297 3.3 27.8 1.0
HD21 A:ASN196 3.4 37.4 1.0
HG3 A:LYS292 3.5 31.1 1.0
H3 B:U6 3.5 24.7 1.0
O A:HOH608 3.5 50.1 1.0
CG A:ASN196 3.7 31.9 1.0
HZ2 A:LYS292 3.7 32.9 1.0
HZ3 A:LYS292 3.8 32.9 1.0
NE2 A:GLN222 3.9 31.1 1.0
CG A:ASN155 3.9 13.3 1.0
ND2 A:ASN196 3.9 31.2 1.0
CA A:ASN155 3.9 13.4 1.0
HA3 A:GLY297 3.9 27.8 1.0
O A:HOH510 3.9 36.0 1.0
C4 B:U6 3.9 20.2 1.0
CA A:GLY297 4.0 23.2 1.0
N3 B:U6 4.1 20.6 1.0
NZ A:LYS292 4.2 27.4 1.0
HE21 A:GLN222 4.2 37.3 1.0
HB2 A:LYS292 4.2 22.7 1.0
HB3 A:LYS292 4.3 22.7 1.0
CG A:LYS292 4.3 25.9 1.0
CB A:ASN155 4.3 13.6 1.0
C A:ASN155 4.3 13.0 1.0
HD2 A:LYS292 4.4 33.4 1.0
O A:GLY297 4.4 26.6 1.0
HB2 A:ASN155 4.5 16.3 1.0
CB A:LYS292 4.5 18.9 1.0
O A:ILE156 4.6 17.4 1.0
HD22 A:ASN196 4.6 37.4 1.0
C A:GLY297 4.7 23.2 1.0
O B:HOH213 4.7 19.7 1.0
O A:ASN155 4.7 14.1 1.0
H A:ASN155 4.7 15.4 1.0
CD A:GLN222 4.8 28.6 1.0
CD A:LYS292 4.8 27.9 1.0
O A:HOH503 4.8 40.1 1.0
O A:HOH689 4.8 47.9 1.0
OE1 A:GLN222 4.8 33.8 1.0
HZ1 A:LYS292 4.9 32.9 1.0
N A:ASN155 4.9 12.8 1.0
N A:ILE156 4.9 14.3 1.0
H A:ILE156 4.9 17.1 1.0
CB A:ASN196 5.0 27.9 1.0

Sodium binding site 3 out of 3 in 7s3a

Go back to Sodium Binding Sites List in 7s3a
Sodium binding site 3 out of 3 in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide


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 Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:25.9
occ:1.00
BR B:BRU7 2.1 24.4 1.0
C5 B:BRU7 3.0 17.3 1.0
O B:HOH209 3.1 23.1 1.0
H5'' B:U6 3.1 19.1 1.0
H3' B:U6 3.2 19.8 1.0
H6 B:BRU7 3.3 20.3 1.0
NE2 A:HIS230 3.4 18.9 1.0
C6 B:BRU7 3.5 16.9 1.0
HE1 A:HIS230 3.5 21.2 1.0
O5' B:U6 3.5 15.4 1.0
C5' B:U6 3.8 15.9 1.0
OP1 B:U6 3.8 16.8 1.0
CE1 A:HIS230 3.8 17.7 1.0
OP2 B:BRU7 3.9 20.2 1.0
P B:U6 4.0 16.0 1.0
C4 B:BRU7 4.0 15.7 1.0
C3' B:U6 4.1 16.5 1.0
O B:HOH222 4.2 20.7 1.0
OP2 B:U6 4.2 16.6 1.0
O4 B:BRU7 4.3 15.8 1.0
H2' B:BRU7 4.4 20.1 1.0
C4' B:U6 4.5 16.8 1.0
H5' B:U6 4.5 19.1 1.0
O5' B:BRU7 4.6 17.9 1.0
N1 B:BRU7 4.6 15.5 1.0
CD2 A:HIS230 4.7 18.1 1.0
H2' B:U6 4.8 20.1 1.0
P B:BRU7 4.8 18.4 1.0
O B:HOH224 4.8 22.0 1.0
H4' B:U6 4.9 20.2 1.0

Reference:

E.Glasser, D.Maji, G.Biancon, A.M.K.Puthenpeedikakkal, C.E.Cavender, T.Tebaldi, J.L.Jenkins, D.H.Mathews, S.Halene, C.L.Kielkopf. Pre-Mrna Splicing Factor U2AF2 Recognizes Distinct Conformations of Nucleotide Variants at the Center of the Pre-Mrna Splice Site Signal. Nucleic Acids Res. V. 50 5299 2022.
ISSN: ESSN 1362-4962
PubMed: 35524551
DOI: 10.1093/NAR/GKAC287
Page generated: Wed Oct 9 08:53:03 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy