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Sodium in PDB 3cqx: Chaperone Complex

Protein crystallography data

The structure of Chaperone Complex, PDB code: 3cqx was solved by Z.Xu, J.C.Nix, S.Misra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.13 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.846, 105.808, 210.683, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Chaperone Complex (pdb code 3cqx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Chaperone Complex, PDB code: 3cqx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3cqx

Go back to Sodium Binding Sites List in 3cqx
Sodium binding site 1 out of 4 in the Chaperone Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Chaperone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:59.2
occ:1.00
N A:GLY75 2.8 39.3 1.0
OE2 A:GLU117 2.9 44.8 1.0
CA A:GLY75 3.6 40.3 1.0
NH2 A:ARG100 3.8 59.4 1.0
C A:ILE74 3.8 38.2 1.0
CG A:PRO116 3.8 39.9 1.0
CA A:ILE74 3.9 36.3 1.0
CB A:PRO116 3.9 40.1 1.0
CD A:PRO116 3.9 39.8 1.0
CD A:GLU117 4.0 45.7 1.0
O A:LEU73 4.2 35.3 1.0
CB A:ALA157 4.3 24.0 1.0
N A:ARG76 4.4 40.9 1.0
C A:GLY75 4.4 40.3 1.0
CG1 A:ILE74 4.5 36.0 1.0
N A:GLU117 4.6 38.6 1.0
OE1 A:GLU117 4.6 48.3 1.0
O A:ARG76 4.7 43.3 1.0
N A:PRO116 4.7 40.3 1.0
N A:ILE74 4.7 35.2 1.0
C A:LEU73 4.8 33.6 1.0
CB A:ILE74 4.8 36.0 1.0
CA A:PRO116 4.8 39.3 1.0
CZ A:ARG100 4.8 59.9 1.0
NE A:ARG100 5.0 58.5 1.0
O A:ILE74 5.0 39.2 1.0

Sodium binding site 2 out of 4 in 3cqx

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Sodium binding site 2 out of 4 in the Chaperone Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Chaperone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:49.5
occ:1.00
O A:ILE74 2.8 39.2 1.0
OE1 A:GLN154 2.9 32.8 1.0
O A:LYS71 3.0 29.4 1.0
NE A:ARG76 3.2 38.8 1.0
O A:ARG72 3.6 30.1 1.0
CG2 A:ILE74 3.7 33.2 1.0
C A:ARG72 3.7 29.3 1.0
C A:ILE74 3.8 38.2 1.0
N A:ILE74 3.8 35.2 1.0
CD A:ARG76 3.8 38.1 1.0
CD A:GLN154 3.8 31.2 1.0
CG A:ARG76 3.8 41.0 1.0
CZ A:PHE150 3.9 25.5 1.0
CZ A:ARG76 3.9 37.8 1.0
C A:LEU73 4.0 33.6 1.0
CE2 A:PHE150 4.0 26.8 1.0
CG A:GLN154 4.0 28.4 1.0
C A:LYS71 4.1 29.6 1.0
NH2 A:ARG76 4.1 39.2 1.0
N A:LEU73 4.1 31.5 1.0
CA A:ILE74 4.2 36.3 1.0
CA A:ARG72 4.2 29.7 1.0
O A:LEU73 4.3 35.3 1.0
CA A:LEU73 4.4 32.9 1.0
CB A:ILE74 4.6 36.0 1.0
N A:ARG72 4.6 28.7 1.0
CE1 A:PHE150 4.7 25.6 1.0
CB A:GLN154 4.7 28.7 1.0
N A:GLY75 4.9 39.3 1.0
CD2 A:PHE150 4.9 26.1 1.0
NH1 A:ARG76 4.9 40.5 1.0
CB A:ARG76 5.0 39.8 1.0

Sodium binding site 3 out of 4 in 3cqx

Go back to Sodium Binding Sites List in 3cqx
Sodium binding site 3 out of 4 in the Chaperone Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Chaperone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:66.4
occ:1.00
O A:ILE130 2.9 41.3 1.0
O A:ALA30 2.9 38.8 1.0
CG2 A:ILE130 3.6 40.7 1.0
CB A:ALA133 3.6 44.2 1.0
C A:ILE130 3.8 41.6 1.0
CA A:ILE130 3.9 41.6 1.0
C A:ALA30 4.1 39.3 1.0
CG2 A:ILE29 4.1 35.7 1.0
CA A:ASN31 4.1 44.1 1.0
N A:TYR134 4.1 45.8 1.0
C A:ASN31 4.3 46.0 1.0
CB A:ILE130 4.3 42.1 1.0
CB A:TYR134 4.4 46.9 1.0
C A:ALA133 4.4 46.7 1.0
CA A:ALA133 4.5 46.3 1.0
N A:ASN31 4.6 40.9 1.0
O A:ASN31 4.7 46.6 1.0
CA A:TYR134 4.7 46.5 1.0
N A:ASP32 4.7 49.0 1.0
O A:HOH526 4.8 41.9 1.0
N A:ALA133 5.0 45.9 1.0
CG1 A:ILE130 5.0 42.4 1.0
N A:ALA131 5.0 41.6 1.0

Sodium binding site 4 out of 4 in 3cqx

Go back to Sodium Binding Sites List in 3cqx
Sodium binding site 4 out of 4 in the Chaperone Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Chaperone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na504

b:57.8
occ:1.00
OD2 A:ASP285 2.8 42.2 1.0
O D:HOH507 3.0 32.5 1.0
O D:GLN167 3.1 42.9 1.0
O D:CYS142 3.3 36.4 1.0
CB D:CYS142 3.5 36.4 1.0
C D:GLN167 3.6 43.3 1.0
CB D:LYS171 3.7 44.4 1.0
CG A:ASP285 3.7 41.5 1.0
CB D:GLN167 3.8 38.1 1.0
CB A:ASP285 3.8 39.9 1.0
CA D:CYS142 3.9 36.0 1.0
CD D:LYS171 4.0 46.7 1.0
C D:CYS142 4.0 35.5 1.0
CA D:GLN167 4.1 43.2 1.0
SG D:CYS142 4.3 40.3 1.0
O D:HOH505 4.3 40.8 1.0
CG1 D:VAL159 4.4 40.3 1.0
CG D:LYS171 4.4 45.6 1.0
NH2 A:ARG262 4.4 29.7 1.0
N D:LYS168 4.4 42.6 1.0
OE1 D:GLN167 4.5 31.4 1.0
CG D:GLN167 4.8 34.7 1.0
CA D:LYS168 4.8 43.9 1.0
CA D:LYS171 4.8 44.8 1.0
N D:LYS171 4.9 43.5 1.0
OD1 A:ASP285 4.9 40.9 1.0

Reference:

Z.Xu, R.C.Page, M.M.Gomes, E.Kohli, J.C.Nix, A.B.Herr, C.Patterson, S.Misra. Structural Basis of Nucleotide Exchange and Client Binding By the HSP70 Cochaperone BAG2 Nat.Struct.Mol.Biol. V. 15 1309 2008.
ISSN: ISSN 1545-9993
PubMed: 19029896
DOI: 10.1038/NSMB.1518
Page generated: Tue Dec 15 06:08:00 2020

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