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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: Tue Dec 15 05:46:22 2020

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