Atomistry » Sodium » PDB 2bii-2c8x » 2bz8
Atomistry »
  Sodium »
    PDB 2bii-2c8x »
      2bz8 »

Sodium in PDB 2bz8: N-Terminal SH3 Domain of CIN85 Bound to Cbl-B Peptide

Protein crystallography data

The structure of N-Terminal SH3 Domain of CIN85 Bound to Cbl-B Peptide, PDB code: 2bz8 was solved by N.Cardenes, G.Moncalian, J.Bravo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 51.158, 51.158, 97.472, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 27.1

Sodium Binding Sites:

The binding sites of Sodium atom in the N-Terminal SH3 Domain of CIN85 Bound to Cbl-B Peptide (pdb code 2bz8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the N-Terminal SH3 Domain of CIN85 Bound to Cbl-B Peptide, PDB code: 2bz8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2bz8

Go back to Sodium Binding Sites List in 2bz8
Sodium binding site 1 out of 2 in the N-Terminal SH3 Domain of CIN85 Bound to Cbl-B Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of N-Terminal SH3 Domain of CIN85 Bound to Cbl-B Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1058

b:33.8
occ:1.00
O A:ASP50 2.6 26.3 1.0
O A:VAL53 2.7 29.2 1.0
O A:HOH2004 2.9 24.8 1.0
O A:HOH2038 3.0 38.6 1.0
O A:HOH2033 3.0 31.7 1.0
C A:ASP50 3.5 25.9 1.0
C A:VAL53 3.9 27.8 1.0
CA A:ASN51 4.0 24.8 1.0
OD1 A:ASP50 4.1 26.4 1.0
N A:ASN51 4.1 26.7 1.0
CH2 A:TRP37 4.2 26.9 1.0
CZ3 A:TRP37 4.4 27.5 1.0
CB A:ASP50 4.6 24.8 1.0
CA A:ASP50 4.6 25.4 1.0
C A:ASN51 4.6 25.9 1.0
O A:HOH2007 4.6 24.0 1.0
CA A:ARG54 4.6 29.5 1.0
N A:VAL53 4.7 26.6 1.0
CG2 A:VAL53 4.7 25.1 1.0
N A:ARG54 4.7 29.1 1.0
CG A:ASP50 4.8 22.3 1.0
N A:GLU55 4.9 31.1 1.0
CA A:VAL53 4.9 27.1 1.0

Sodium binding site 2 out of 2 in 2bz8

Go back to Sodium Binding Sites List in 2bz8
Sodium binding site 2 out of 2 in the N-Terminal SH3 Domain of CIN85 Bound to Cbl-B Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of N-Terminal SH3 Domain of CIN85 Bound to Cbl-B Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1059

b:46.8
occ:1.00
O B:ASP50 2.6 24.9 1.0
O B:VAL53 2.7 28.1 1.0
O B:HOH2015 3.0 38.0 1.0
O B:HOH2030 3.0 21.3 1.0
O B:HOH2027 3.2 47.6 1.0
C B:ASP50 3.5 25.2 1.0
CA B:ASN51 3.8 26.9 1.0
C B:VAL53 3.9 29.0 1.0
N B:ASN51 4.0 27.4 1.0
O B:HOH2029 4.2 29.7 1.0
C B:ASN51 4.3 24.9 1.0
OD2 B:ASP50 4.6 30.9 1.0
N B:VAL53 4.6 27.1 1.0
CA B:ASP50 4.6 25.2 1.0
CB B:ASP50 4.6 27.4 1.0
CG B:ASP50 4.6 30.8 1.0
O B:ASN51 4.7 26.4 1.0
CA B:ARG54 4.7 31.6 1.0
N B:ARG54 4.8 29.4 1.0
CG2 B:VAL53 4.8 28.4 1.0
CD B:ARG54 4.8 32.1 1.0
CA B:VAL53 4.9 28.2 1.0
N B:PHE52 4.9 23.8 1.0

Reference:

D.Jozic, N.Cardenes, Y.Lissanu-Deribe, G.Moncalian, D.Hoeller, Y.Groemping, I.Dikic, K.Rittinger, J.Bravo. Cbl Promotes Clustering of Endocytic Adaptor Proteins Nat.Struct.Mol.Biol. V. 12 972 2005.
ISSN: ISSN 1545-9993
PubMed: 16228008
DOI: 10.1038/NSMB1000
Page generated: Mon Oct 7 02:02:32 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