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Cadmium in PDB 3whj: Crystal Structure of NAS2 N-Terminal Domain

Protein crystallography data

The structure of Crystal Structure of NAS2 N-Terminal Domain, PDB code: 3whj was solved by T.Satoh, Y.Saeki, T.Hiromoto, Y.-H.Wang, Y.Uekusa, H.Yagi, H.Yoshihara, M.Yagi-Utsumi, T.Mizushima, K.Tanaka, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.65
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 64.590, 64.590, 149.760, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 19.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of NAS2 N-Terminal Domain (pdb code 3whj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of NAS2 N-Terminal Domain, PDB code: 3whj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3whj

Go back to Cadmium Binding Sites List in 3whj
Cadmium binding site 1 out of 5 in the Crystal Structure of NAS2 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of NAS2 N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:21.8
occ:1.00
O A:HOH305 2.3 24.7 1.0
OD2 A:ASP92 2.4 19.1 1.0
OD1 A:ASP92 2.5 19.7 1.0
CG A:ASP92 2.8 17.9 1.0
O A:HOH351 4.1 56.0 1.0
O A:MET88 4.3 20.2 1.0
CB A:ASP92 4.3 18.6 1.0
CG2 A:ILE23 4.6 18.3 1.0
O A:HOH306 4.6 21.3 1.0
O A:HOH339 4.8 37.0 1.0
O A:HOH384 4.8 57.0 1.0
C A:MET88 5.0 19.8 1.0
CB A:MET88 5.0 19.2 1.0

Cadmium binding site 2 out of 5 in 3whj

Go back to Cadmium Binding Sites List in 3whj
Cadmium binding site 2 out of 5 in the Crystal Structure of NAS2 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of NAS2 N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:18.4
occ:1.00
OD1 A:ASP27 2.2 22.3 1.0
NE2 A:HIS95 2.3 17.6 1.0
O1 A:SO4201 2.3 22.6 0.8
O2 A:SO4201 2.7 20.4 0.8
OD2 A:ASP27 2.7 18.4 1.0
CG A:ASP27 2.8 16.6 1.0
S A:SO4201 2.8 32.2 0.8
CD2 A:HIS95 3.2 18.0 1.0
CE1 A:HIS95 3.3 17.6 1.0
O4 A:SO4201 3.4 57.8 0.8
O3 A:SO4201 4.3 24.7 0.8
CB A:ASP27 4.3 16.9 1.0
O A:HOH320 4.3 26.4 1.0
CG A:HIS95 4.4 16.0 1.0
ND1 A:HIS95 4.4 18.5 1.0
CB A:ARG99 4.7 16.8 1.0
CD A:ARG99 4.8 16.1 1.0
CG2 A:ILE26 4.9 17.5 1.0

Cadmium binding site 3 out of 5 in 3whj

Go back to Cadmium Binding Sites List in 3whj
Cadmium binding site 3 out of 5 in the Crystal Structure of NAS2 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of NAS2 N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:24.4
occ:1.00
NZ A:LYS38 2.3 22.2 1.0
O A:HOH330 2.3 31.4 1.0
OE1 A:GLU42 2.4 25.7 1.0
O3 A:SO4202 2.4 41.8 0.6
OE2 A:GLU42 2.4 20.5 1.0
CD A:GLU42 2.7 21.3 1.0
O2 A:SO4202 2.7 51.4 0.6
S A:SO4202 3.1 42.7 0.6
CE A:LYS38 3.3 21.3 1.0
CD A:LYS38 3.7 20.2 1.0
O1 A:SO4202 3.7 42.4 0.6
CG A:LYS38 4.1 18.5 1.0
O A:HOH335 4.2 32.2 1.0
CG A:GLU42 4.2 20.7 1.0
O4 A:SO4202 4.3 35.9 0.6
O A:HOH308 4.5 28.1 1.0

Cadmium binding site 4 out of 5 in 3whj

Go back to Cadmium Binding Sites List in 3whj
Cadmium binding site 4 out of 5 in the Crystal Structure of NAS2 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of NAS2 N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:77.1
occ:0.60
OE2 A:GLU5 2.0 69.7 1.0
O A:HOH382 2.7 56.5 1.0
CD A:GLU5 2.8 63.2 1.0
OE1 A:GLU5 3.0 53.7 1.0
CG A:GLU5 4.0 52.3 1.0
N A:MET1 5.0 61.8 1.0

Cadmium binding site 5 out of 5 in 3whj

Go back to Cadmium Binding Sites List in 3whj
Cadmium binding site 5 out of 5 in the Crystal Structure of NAS2 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of NAS2 N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:30.4
occ:0.40
OD2 A:ASP109 2.1 0.1 1.0
CG A:ASP109 3.0 33.4 1.0
OD1 A:ASP109 3.1 38.0 1.0
CB A:ASP109 4.4 27.9 1.0
O A:ASN105 4.5 23.2 1.0
O A:HOH316 4.6 44.2 1.0
O A:HOH380 4.7 48.4 1.0
CB A:ASN105 4.7 27.2 1.0
C A:ASN105 4.9 20.5 1.0

Reference:

T.Satoh, Y.Saeki, T.Hiromoto, Y.H.Wang, Y.Uekusa, H.Yagi, H.Yoshihara, M.Yagi-Utsumi, T.Mizushima, K.Tanaka, K.Kato. Structural Basis For Proteasome Formation Controlled By An Assembly Chaperone NAS2 Structure 2014.
ISSN: ISSN 0969-2126
PubMed: 24685148
DOI: 10.1016/J.STR.2014.02.014
Page generated: Sun Jan 24 09:56:19 2021

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