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Chlorine in PDB 5cyk: Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E

Protein crystallography data

The structure of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E, PDB code: 5cyk was solved by M.Wegrecki, J.Bravo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.38 / 3.00
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 170.750, 170.750, 155.660, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 26.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E (pdb code 5cyk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E, PDB code: 5cyk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5cyk

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Chlorine binding site 1 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:83.9
occ:1.00
NH2 A:ARG454 2.9 67.7 1.0
NH2 A:ARG414 3.3 61.5 1.0
NH1 A:ARG414 3.7 66.4 1.0
CZ A:ARG414 3.9 65.3 1.0
CZ A:ARG454 4.1 73.2 1.0
NH1 A:ARG454 4.4 76.4 1.0
O A:GLY386 4.8 73.2 1.0

Chlorine binding site 2 out of 5 in 5cyk

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Chlorine binding site 2 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:82.2
occ:1.00
NH2 A:ARG287 2.6 91.8 1.0
CZ A:ARG287 3.6 95.0 1.0
NH1 A:ARG287 3.9 0.5 1.0
CB A:ALA285 4.2 66.7 1.0
NZ A:LYS256 4.5 0.8 1.0
CA A:ALA285 4.7 74.8 1.0
CE A:LYS256 4.8 0.5 1.0
NE A:ARG287 4.8 75.5 1.0

Chlorine binding site 3 out of 5 in 5cyk

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Chlorine binding site 3 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl901

b:93.6
occ:1.00
NH1 B:ARG575 3.3 0.7 1.0
CD B:ARG575 3.7 0.8 1.0
NH2 B:ARG584 4.2 0.6 1.0
CG B:ARG575 4.2 0.9 1.0
CZ B:ARG575 4.3 0.7 1.0
NE B:ARG575 4.4 0.5 1.0
O B:LEU493 4.7 0.6 1.0
CA B:GLY573 5.0 0.8 1.0

Chlorine binding site 4 out of 5 in 5cyk

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Chlorine binding site 4 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl902

b:75.8
occ:1.00
NH2 B:ARG450 3.0 0.4 1.0
NH1 B:ARG450 3.4 0.9 1.0
NH2 B:ARG798 3.6 83.1 1.0
CZ B:ARG450 3.7 92.4 1.0
CG B:LYS769 4.6 0.1 1.0
CZ B:ARG798 4.6 82.4 1.0
NH1 B:ARG798 4.8 91.7 1.0
NZ B:LYS769 4.9 0.2 1.0
NE B:ARG450 5.0 62.6 1.0

Chlorine binding site 5 out of 5 in 5cyk

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Chlorine binding site 5 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl903

b:87.8
occ:1.00
NE2 B:GLN487 3.5 68.5 1.0
N B:SER490 4.1 77.4 1.0
CB B:SER490 4.2 82.4 1.0
CA B:TRP489 4.3 78.1 1.0
C B:TRP489 4.3 75.0 1.0
O B:GLN487 4.5 63.5 1.0
N B:TRP489 4.5 74.1 1.0
O B:VAL488 4.5 80.3 1.0
CD B:GLN487 4.6 75.8 1.0
C B:VAL488 4.6 75.2 1.0
CG B:GLN487 4.7 66.8 1.0
CA B:SER490 4.8 73.5 1.0

Reference:

M.Wegrecki, O.Rodriguez-Galan, J.De La Cruz, J.Bravo. The Structure of ERB1-YTM1 Complex Reveals the Functional Importance of A High-Affinity Binding Between Two Beta-Propellers During the Assembly of Large Ribosomal Subunits in Eukaryotes. Nucleic Acids Res. V. 43 11017 2015.
ISSN: ESSN 1362-4962
PubMed: 26476442
DOI: 10.1093/NAR/GKV1043
Page generated: Fri Jul 26 06:21:11 2024

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