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Gold in PDB 4b8b: N-Terminal Domain of the Yeast NOT1

Protein crystallography data

The structure of N-Terminal Domain of the Yeast NOT1, PDB code: 4b8b was solved by J.Basquin, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.050 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.097, 164.507, 86.141, 90.00, 100.05, 90.00
R / Rfree (%) 23.76 / 27.57

Gold Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Gold atom in the N-Terminal Domain of the Yeast NOT1 (pdb code 4b8b). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 29 binding sites of Gold where determined in the N-Terminal Domain of the Yeast NOT1, PDB code: 4b8b:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gold binding site 1 out of 29 in 4b8b

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Gold binding site 1 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1747

b:66.7
occ:0.45
O A:PRO424 3.4 54.2 1.0
OG A:SER461 3.6 62.4 1.0
CB A:ASN457 3.8 66.4 1.0
C A:ASN457 3.8 65.9 1.0
O A:ASN457 3.9 65.9 1.0
N A:PHE458 3.9 64.5 1.0
CB A:PRO424 4.0 54.3 1.0
CA A:PHE458 4.0 62.7 1.0
C A:PRO424 4.1 53.4 1.0
CB A:PHE427 4.3 52.7 1.0
CA A:PRO424 4.4 52.3 1.0
CA A:ASN457 4.5 68.0 1.0
CD2 A:HIS420 4.6 54.7 1.0
CB A:SER461 4.6 62.6 1.0
CB A:PHE458 4.7 61.6 1.0
NE2 A:HIS420 4.9 56.5 1.0
CG A:PHE427 4.9 52.7 1.0
CD2 A:PHE427 5.0 54.7 1.0

Gold binding site 2 out of 29 in 4b8b

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Gold binding site 2 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1748

b:77.9
occ:0.24
SG A:CYS549 2.3 74.3 1.0
CD A:PRO505 2.5 0.4 1.0
N A:PRO505 2.7 0.3 1.0
C A:SER504 3.2 83.7 1.0
CB A:CYS549 3.3 71.3 1.0
CA A:PRO505 3.3 0.2 1.0
CG A:PRO505 3.5 0.8 1.0
CB A:PRO505 3.5 0.9 1.0
CA A:SER504 3.6 85.2 1.0
CD A:PRO550 3.6 77.8 1.0
CG1 A:VAL508 4.0 62.9 1.0
O A:SER504 4.0 82.1 1.0
O A:VAL503 4.1 81.3 1.0
CA A:CYS549 4.1 72.0 1.0
N A:PRO550 4.2 74.7 1.0
N A:SER504 4.3 83.0 1.0
C A:VAL503 4.5 80.8 1.0
C A:CYS549 4.6 72.5 1.0
CG A:PRO550 4.7 80.9 1.0
CB A:SER504 4.8 88.9 1.0
C A:PRO505 4.8 0.6 1.0

Gold binding site 3 out of 29 in 4b8b

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Gold binding site 3 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1749

b:5.9
occ:0.08
SG A:CYS486 2.3 63.6 1.0
CD2 A:LEU531 2.8 62.1 1.0
O A:CYS486 3.2 63.3 1.0
CG1 A:ILE490 3.5 77.7 1.0
CD1 A:ILE490 3.5 77.6 1.0
CB A:CYS486 3.6 61.4 1.0
CA A:CYS486 3.7 60.4 1.0
C A:CYS486 3.8 62.0 1.0
CG A:LEU531 3.9 61.8 1.0
CB A:ALA456 3.9 74.3 1.0
CD1 A:LEU531 3.9 63.7 1.0
CB A:GLN489 4.0 71.8 1.0
CA A:ALA456 4.3 72.2 1.0
CB A:LEU531 4.4 59.9 1.0
N A:ILE490 4.6 75.2 1.0
O A:ILE455 4.7 87.3 1.0
CB A:ILE490 4.8 78.3 1.0
C A:GLN489 4.8 75.4 1.0
CA A:LEU531 5.0 57.9 1.0
CG A:GLN489 5.0 69.6 1.0

Gold binding site 4 out of 29 in 4b8b

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Gold binding site 4 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1750

b:0.6
occ:0.21
CB A:ASN238 2.2 60.3 1.0
CA A:ASN238 2.9 59.8 1.0
C A:ASN238 3.1 60.4 1.0
O A:ASN238 3.4 60.8 1.0
N A:ASN238 3.5 59.9 1.0
CG A:ASN238 3.5 59.7 1.0
N A:VAL239 3.7 60.8 1.0
NH2 A:ARG242 3.9 78.9 1.0
ND2 A:ASN238 4.1 60.1 1.0
OD1 A:ASN238 4.4 59.3 1.0
O A:ASN235 4.4 0.0 1.0
CA A:VAL239 4.8 61.2 1.0
O A:THR234 4.8 0.6 1.0
C A:GLY237 4.8 88.1 1.0
CZ A:ARG242 5.0 79.2 1.0

Gold binding site 5 out of 29 in 4b8b

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Gold binding site 5 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1751

b:1.0
occ:0.30
SG A:CYS639 2.3 44.7 1.0
O A:CYS639 3.2 39.3 1.0
CE A:MET601 3.3 56.7 1.0
CB A:CYS639 3.5 44.0 1.0
CA A:CYS639 3.6 41.7 1.0
C A:CYS639 3.7 40.2 1.0
CD2 A:HIS642 4.0 38.6 1.0
SD A:MET601 4.0 58.4 1.0
CG A:GLU598 4.1 88.7 1.0
CB A:ALA643 4.2 38.2 1.0
CG A:MET601 4.5 62.5 1.0
N A:ALA643 4.7 36.5 1.0
CA A:ALA643 4.7 36.9 1.0
N A:ILE640 4.8 40.3 1.0
CA A:GLU598 4.9 91.0 1.0
NE2 A:HIS642 4.9 39.0 1.0
CG1 A:ILE593 5.0 66.2 1.0
CG A:HIS642 5.0 37.5 1.0
N A:CYS639 5.0 41.7 1.0

Gold binding site 6 out of 29 in 4b8b

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Gold binding site 6 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1752

b:71.5
occ:0.24
NZ A:LYS439 3.4 66.7 1.0
CD2 A:LEU412 3.5 50.3 1.0
CE A:MET395 3.8 52.6 1.0
CG2 A:VAL392 4.1 44.6 1.0
CG2 A:ILE434 4.1 52.8 1.0
CG1 A:ILE434 4.2 49.4 1.0
CE A:LYS439 4.4 66.7 1.0
CB A:ILE434 4.5 51.9 1.0
CD A:LYS439 4.5 67.1 1.0
CA A:ILE434 4.6 52.9 1.0
CG1 A:VAL392 4.6 46.4 1.0
CG A:LEU412 4.7 48.9 1.0
N A:THR435 4.7 56.0 1.0
CD1 A:ILE434 4.8 48.5 1.0
CD1 A:LEU412 4.8 47.7 1.0
CB A:VAL392 4.9 44.3 1.0
SD A:MET395 4.9 50.8 1.0
N A:ASP436 4.9 73.5 1.0
CB A:ASP436 5.0 72.6 1.0

Gold binding site 7 out of 29 in 4b8b

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Gold binding site 7 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1753

b:71.3
occ:0.25
NE2 A:GLN705 2.8 34.6 1.0
CD A:GLN705 3.8 35.1 1.0
CD2 A:LEU656 3.8 35.4 1.0
CB A:LYS701 3.8 52.8 1.0
O A:LEU656 3.9 33.5 1.0
CD A:LYS701 4.0 55.8 1.0
CD2 A:LEU659 4.1 32.8 1.0
OE1 A:GLN705 4.1 36.4 1.0
CB A:ALA660 4.2 31.9 1.0
CG A:LYS701 4.4 55.8 1.0
CA A:ALA660 4.5 30.8 1.0
N A:ALA660 4.5 31.8 1.0
CG A:LEU659 4.6 32.2 1.0
CB A:LEU656 4.6 36.3 1.0
CG A:LEU656 4.7 36.9 1.0
C A:LEU656 4.8 35.1 1.0
CA A:LEU656 4.8 36.1 1.0
C A:LYS701 4.8 49.0 1.0
O A:LYS701 4.8 47.7 1.0
CG A:GLN705 4.9 34.3 1.0
CB A:LEU659 4.9 33.1 1.0
CA A:LYS701 4.9 52.3 1.0

Gold binding site 8 out of 29 in 4b8b

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Gold binding site 8 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1754

b:1.0
occ:0.31
CE A:LYS482 3.8 63.5 1.0
CB A:ALA453 3.9 0.5 1.0
O A:LYS482 4.4 58.2 1.0
CG A:LYS532 4.5 56.7 1.0
NZ A:LYS482 4.5 65.8 1.0
CG A:LYS482 4.7 60.9 1.0
CD A:LYS482 4.8 63.2 1.0
CE A:LYS532 4.9 59.6 1.0
CA A:ALA453 4.9 0.6 1.0
O A:LEU531 5.0 56.8 1.0

Gold binding site 9 out of 29 in 4b8b

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Gold binding site 9 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 9 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1755

b:0.8
occ:0.28
CZ A:PHE357 3.5 48.7 1.0
CE2 A:PHE357 3.9 46.5 1.0
CE1 A:PHE380 4.0 39.9 1.0
CE1 A:PHE377 4.1 61.6 1.0
CD1 A:PHE380 4.2 38.7 1.0
CZ A:PHE380 4.3 41.1 1.0
CE2 A:PHE376 4.5 35.5 1.0
CE1 A:PHE357 4.5 49.5 1.0
CG2 A:THR414 4.6 45.6 1.0
CG A:PHE380 4.6 38.8 1.0
CE2 A:PHE380 4.7 41.2 1.0
CD1 A:PHE377 4.8 60.1 1.0
CD1 A:ILE411 4.8 58.1 1.0
CD2 A:PHE380 4.8 40.1 1.0
CZ A:PHE377 4.9 64.2 1.0

Gold binding site 10 out of 29 in 4b8b

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Gold binding site 10 out of 29 in the N-Terminal Domain of the Yeast NOT1


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 10 of N-Terminal Domain of the Yeast NOT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1756

b:0.7
occ:0.26
O A:ALA569 3.3 41.9 1.0
NH2 A:ARG529 3.8 62.3 1.0
NH1 A:ARG529 3.9 60.9 1.0
C A:ALA569 4.1 40.7 1.0
CA A:ALA569 4.1 40.4 1.0
CZ A:ARG529 4.2 62.3 1.0
CB A:ALA569 4.3 41.1 1.0
O A:MET521 4.3 48.3 1.0
CE1 A:PHE570 5.0 44.1 1.0

Reference:

J.Basquin, V.V.Roudko, M.Rode, C.Basquin, B.Seraphin, E.Conti. Architecture of the Nuclease Module of the Yeast CCR4-Not Complex: the NOT1-CAF1-CCR4 Interaction. Mol.Cell V. 48 207 2012.
ISSN: ISSN 1097-2765
PubMed: 22959269
DOI: 10.1016/J.MOLCEL.2012.08.014
Page generated: Sat Dec 12 01:54:01 2020

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