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Cadmium in PDB 2ymy: Structure of the Murine NORE1-Sarah Domain

Protein crystallography data

The structure of Structure of the Murine NORE1-Sarah Domain, PDB code: 2ymy was solved by C.Makbul, D.Schwarz, D.C.Aruxandei, E.Wolf, E.Hofmann, C.Herrmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.205 / 1.69
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 70.820, 84.410, 39.240, 90.00, 90.00, 90.00
R / Rfree (%) 19.43 / 23.53

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of the Murine NORE1-Sarah Domain (pdb code 2ymy). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure of the Murine NORE1-Sarah Domain, PDB code: 2ymy:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 2ymy

Go back to Cadmium Binding Sites List in 2ymy
Cadmium binding site 1 out of 3 in the Structure of the Murine NORE1-Sarah Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of the Murine NORE1-Sarah Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1409

b:12.9
occ:0.50
OE1 A:GLU407 2.1 19.6 1.0
OE2 A:GLU407 2.1 19.0 1.0
CD A:GLU407 2.3 17.7 1.0
CG A:GLU407 3.8 18.8 1.0
HG2 A:GLU407 4.1 22.6 1.0
HG3 A:GLU407 4.3 22.6 1.0
HA A:ALA404 4.3 18.1 1.0
HB3 A:GLU407 4.5 22.8 1.0
HB2 A:GLU407 4.6 22.8 1.0
CB A:GLU407 4.6 19.0 1.0
HB2 A:ALA404 4.8 22.9 1.0

Cadmium binding site 2 out of 3 in 2ymy

Go back to Cadmium Binding Sites List in 2ymy
Cadmium binding site 2 out of 3 in the Structure of the Murine NORE1-Sarah Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of the Murine NORE1-Sarah Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1409

b:33.6
occ:0.50
HE2 B:HIS388 2.0 56.8 1.0
O B:HOH2024 2.3 38.3 1.0
O B:HOH2044 2.5 35.2 1.0
NE2 B:HIS388 2.6 47.3 1.0
HD2 B:HIS388 3.2 44.0 1.0
CD2 B:HIS388 3.2 36.6 1.0
CE1 B:HIS388 3.7 49.3 1.0
O B:HOH2023 3.8 30.9 0.5
HE1 B:HIS388 4.0 59.2 1.0
O B:HOH2031 4.3 56.5 1.0
OE1 B:GLN391 4.3 17.7 1.0
CG B:HIS388 4.4 31.6 1.0
ND1 B:HIS388 4.6 43.7 1.0
OE1 B:GLN384 4.8 39.3 1.0

Cadmium binding site 3 out of 3 in 2ymy

Go back to Cadmium Binding Sites List in 2ymy
Cadmium binding site 3 out of 3 in the Structure of the Murine NORE1-Sarah Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of the Murine NORE1-Sarah Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1410

b:17.1
occ:0.50
OE2 B:GLU407 2.1 29.7 1.0
OE2 B:GLU403 2.3 17.3 1.0
O B:HOH2042 2.3 33.7 1.0
OE1 B:GLU407 2.6 26.3 1.0
CD B:GLU407 2.6 33.3 1.0
CD B:GLU403 3.3 21.5 1.0
HG3 B:GLU403 3.4 25.6 1.0
CG B:GLU403 3.7 21.3 1.0
HG2 B:GLU403 3.8 25.6 1.0
CG B:GLU407 4.1 24.2 1.0
OE1 B:GLU403 4.4 17.7 1.0
HG2 B:GLU407 4.4 29.1 1.0
HG3 B:GLU407 4.5 29.1 1.0
HH12 B:ARG406 5.0 61.0 0.4

Reference:

C.Makbul, D.Constantinescu Aruxandei, E.Hofmann, D.Schwarz, E.Wolf, C.Herrmann. Structural and Thermodynamic Characterization of NORE1- Sarah: A Small, Helical Module Important in Signal Transduction Networks. Biochemistry V. 52 1045 2013.
ISSN: ISSN 0006-2960
PubMed: 23331050
DOI: 10.1021/BI3014642
Page generated: Sat Dec 12 08:18:45 2020

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