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Erbium in PDB 3cm6: Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er

Protein crystallography data

The structure of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er, PDB code: 3cm6 was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 130.279, 157.795, 65.244, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 26.5

Other elements in 3cm6:

The structure of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Erbium Binding Sites:

The binding sites of Erbium atom in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er (pdb code 3cm6). This binding sites where shown within 5.0 Angstroms radius around Erbium atom.
In total 2 binding sites of Erbium where determined in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er, PDB code: 3cm6:
Jump to Erbium binding site number: 1; 2;

Erbium binding site 1 out of 2 in 3cm6

Go back to Erbium Binding Sites List in 3cm6
Erbium binding site 1 out of 2 in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 1 of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Er300

b:87.0
occ:1.00
OD1 A:ASP15 2.6 46.5 1.0
OD1 A:ASP184 2.6 45.4 1.0
OD2 A:ASP15 2.7 46.1 1.0
OE2 A:GLU17 2.8 45.2 1.0
CG A:ASP15 3.0 43.2 1.0
O A:HOH341 3.3 48.3 1.0
O A:HOH346 3.3 43.3 1.0
O A:PHE16 3.5 36.9 1.0
CD A:GLU17 3.6 41.7 1.0
CG A:ASP184 3.6 46.4 1.0
OE1 A:GLU17 3.9 43.5 1.0
CB A:ASP184 4.1 46.4 1.0
CB A:ASP15 4.4 39.9 1.0
C A:PHE16 4.6 36.3 1.0
OD2 A:ASP184 4.7 47.0 1.0
OD1 A:ASP115 4.7 41.0 1.0
CG A:GLU17 4.8 38.0 1.0
CA A:HIS179 4.9 54.7 1.0
ND1 A:HIS179 4.9 54.3 1.0
N A:PHE16 4.9 37.2 1.0

Erbium binding site 2 out of 2 in 3cm6

Go back to Erbium Binding Sites List in 3cm6
Erbium binding site 2 out of 2 in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 2 of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Er within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Er300

b:88.5
occ:1.00
OD2 B:ASP184 2.6 43.3 1.0
OE2 B:GLU17 2.8 42.8 1.0
OD1 B:ASP15 2.8 37.5 1.0
OD2 B:ASP15 3.0 36.6 1.0
O B:HOH329 3.2 33.1 1.0
CG B:ASP15 3.3 33.6 1.0
CG B:ASP184 3.7 40.7 1.0
CD B:GLU17 3.7 39.1 1.0
OE1 B:GLU17 3.8 40.5 1.0
O B:PHE16 4.0 30.5 1.0
CB B:ASP184 4.2 39.1 1.0
CA B:HIS179 4.6 52.9 1.0
OD1 B:ASP184 4.7 42.5 1.0
CB B:ASP15 4.7 31.9 1.0
ND1 B:HIS179 4.8 55.7 1.0
O B:HOH365 5.0 30.5 1.0

Reference:

Y.-Y.Hsiao, A.Nakagawa, Z.Shi, S.Mitani, D.Xue, H.S.Yuan. Crystal Structure of Crn-4: Implications For Domain Function in Apoptotic Dna Degradation Mol.Cell.Biol. V. 29 448 2009.
ISSN: ISSN 0270-7306
PubMed: 18981218
DOI: 10.1128/MCB.01006-08
Page generated: Sun Dec 13 11:27:38 2020

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