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Gold in PDB 5cvl: WDR48 (Uaf-1), Residues 2-580

Protein crystallography data

The structure of WDR48 (Uaf-1), Residues 2-580, PDB code: 5cvl was solved by S.F.Harris, J.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.33 / 3.00
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 139.520, 139.520, 235.109, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.3

Gold Binding Sites:

The binding sites of Gold atom in the WDR48 (Uaf-1), Residues 2-580 (pdb code 5cvl). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 7 binding sites of Gold where determined in the WDR48 (Uaf-1), Residues 2-580, PDB code: 5cvl:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7;

Gold binding site 1 out of 7 in 5cvl

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Gold binding site 1 out of 7 in the WDR48 (Uaf-1), Residues 2-580


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of WDR48 (Uaf-1), Residues 2-580 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au603

b:0.7
occ:0.81
SG A:CYS278 2.3 69.4 1.0
AU A:AU609 3.3 0.4 0.5
CB A:CYS278 3.4 65.0 1.0
OH A:TYR268 3.5 78.5 1.0
CG2 A:ILE329 3.9 0.7 1.0
CG A:HIS266 3.9 75.0 1.0
CB A:HIS266 4.0 70.3 1.0
CZ A:TYR268 4.0 70.6 1.0
CE2 A:TYR268 4.2 59.3 1.0
CD2 A:HIS266 4.2 77.4 1.0
CD1 A:ILE329 4.3 0.8 1.0
ND1 A:HIS266 4.4 77.0 1.0
CA A:CYS278 4.8 63.6 1.0
NE2 A:HIS266 4.8 77.1 1.0
CB A:ILE329 4.8 0.7 1.0
CE1 A:HIS266 4.9 76.7 1.0
CE1 A:TYR268 4.9 59.3 1.0

Gold binding site 2 out of 7 in 5cvl

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Gold binding site 2 out of 7 in the WDR48 (Uaf-1), Residues 2-580


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of WDR48 (Uaf-1), Residues 2-580 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au604

b:0.7
occ:0.82
SG A:CYS85 2.4 86.6 1.0
CB A:CYS85 3.4 82.0 1.0
ND2 A:ASN147 3.5 0.8 1.0
CG A:GLU130 3.6 77.2 1.0
CG A:ASN147 4.0 0.6 1.0
OD1 A:ASN147 4.0 0.4 1.0
CA A:CYS85 4.2 80.7 1.0
CD A:GLU130 4.2 91.2 1.0
CG1 A:VAL146 4.2 78.5 1.0
CB A:VAL146 4.5 78.8 1.0
CB A:GLU130 4.5 70.8 1.0
OE1 A:GLU130 4.5 74.9 1.0
N A:ASN147 4.6 77.7 1.0
N A:CYS85 4.6 79.8 1.0
OE2 A:GLU130 4.8 83.7 1.0
CA A:ASN147 4.9 77.6 1.0
C A:VAL146 4.9 79.7 1.0

Gold binding site 3 out of 7 in 5cvl

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Gold binding site 3 out of 7 in the WDR48 (Uaf-1), Residues 2-580


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of WDR48 (Uaf-1), Residues 2-580 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au605

b:88.5
occ:0.36
SG A:CYS366 2.4 50.9 1.0
CB A:CYS366 2.8 45.7 1.0
AU A:AU608 3.4 0.9 0.3
CG A:LEU424 3.6 40.5 1.0
CD1 A:LEU424 3.6 39.6 1.0
CA A:CYS366 3.8 44.1 1.0
CD2 A:LEU424 3.9 43.7 1.0
N A:CYS366 4.0 43.6 1.0
CG1 A:VAL422 4.0 51.3 1.0
O A:CYS366 4.1 48.1 1.0
C A:CYS366 4.2 47.8 1.0
CB A:VAL422 4.5 51.7 1.0
C A:GLN365 4.9 46.7 1.0
CB A:LEU424 4.9 36.7 1.0

Gold binding site 4 out of 7 in 5cvl

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Gold binding site 4 out of 7 in the WDR48 (Uaf-1), Residues 2-580


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of WDR48 (Uaf-1), Residues 2-580 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au606

b:0.8
occ:0.38
SG A:CYS109 2.5 67.1 1.0
OG1 A:THR112 2.9 81.8 1.0
C A:SER111 3.6 69.2 1.0
CB A:CYS109 3.8 63.1 1.0
O A:SER111 3.8 68.4 1.0
N A:THR112 3.9 64.2 1.0
CB A:THR112 4.0 75.5 1.0
N A:SER111 4.0 67.7 1.0
CA A:SER111 4.0 66.8 1.0
ND1 A:HIS73 4.0 77.5 1.0
C A:MET110 4.1 71.2 1.0
O A:MET110 4.2 71.9 1.0
CE1 A:HIS73 4.2 77.8 1.0
NZ A:LYS100 4.4 60.3 1.0
N A:MET110 4.4 64.6 1.0
CA A:THR112 4.4 63.6 1.0
C A:CYS109 4.5 68.2 1.0
CA A:CYS109 4.7 62.6 1.0
O A:HOH829 4.8 61.2 1.0
CA A:MET110 4.8 64.5 1.0
O A:CYS109 4.9 69.3 1.0
CD A:LYS100 4.9 45.2 1.0

Gold binding site 5 out of 7 in 5cvl

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Gold binding site 5 out of 7 in the WDR48 (Uaf-1), Residues 2-580


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of WDR48 (Uaf-1), Residues 2-580 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au607

b:0.4
occ:0.37
SG A:CYS244 2.6 82.6 1.0
OG1 A:THR247 2.7 61.0 1.0
NH1 A:ARG235 3.1 0.9 1.0
O A:HOH792 3.2 59.1 1.0
NE A:ARG235 3.4 97.2 1.0
CZ A:ARG235 3.6 0.0 1.0
CB A:CYS244 3.8 78.7 1.0
CB A:THR247 3.8 58.1 1.0
NH1 A:ARG243 3.8 0.6 1.0
O A:CYS244 4.4 78.7 1.0
O A:HOH722 4.5 53.1 1.0
CD A:ARG235 4.5 85.7 1.0
CG2 A:THR247 4.6 51.7 1.0
CZ A:ARG243 4.6 0.3 1.0
NH2 A:ARG235 4.7 98.5 1.0
CG A:ARG235 4.7 73.9 1.0
O A:ALA246 4.8 63.5 1.0
C A:ALA246 4.9 63.9 1.0
N A:THR247 4.9 57.2 1.0
CA A:THR247 4.9 55.9 1.0
NH2 A:ARG243 4.9 0.1 1.0
C A:CYS244 5.0 78.4 1.0
CA A:CYS244 5.0 78.4 1.0

Gold binding site 6 out of 7 in 5cvl

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Gold binding site 6 out of 7 in the WDR48 (Uaf-1), Residues 2-580


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of WDR48 (Uaf-1), Residues 2-580 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au608

b:0.9
occ:0.29
O A:HOH796 3.0 54.6 1.0
SG A:CYS366 3.0 50.9 1.0
AU A:AU605 3.4 88.5 0.4
O A:CYS366 3.7 48.1 1.0
O A:HOH814 3.7 52.1 1.0
CG1 A:ILE368 3.8 38.0 1.0
CD1 A:ILE368 3.8 39.1 1.0
C A:CYS366 4.1 47.8 1.0
N A:ILE368 4.2 38.5 1.0
N A:HIS367 4.5 43.9 1.0
CB A:CYS366 4.5 45.7 1.0
CA A:HIS367 4.5 43.5 1.0
CB A:VAL422 4.5 51.7 1.0
CB A:ILE368 4.7 38.4 1.0
C A:HIS367 4.7 44.9 1.0
CG2 A:VAL422 4.8 51.4 1.0
CA A:CYS366 4.9 44.1 1.0
CG1 A:VAL422 5.0 51.3 1.0

Gold binding site 7 out of 7 in 5cvl

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Gold binding site 7 out of 7 in the WDR48 (Uaf-1), Residues 2-580


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of WDR48 (Uaf-1), Residues 2-580 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au609

b:0.4
occ:0.48
SG A:CYS278 2.6 69.4 1.0
AU A:AU603 3.3 0.7 0.8
O A:CYS278 3.6 70.4 1.0
CD2 A:HIS266 3.6 77.4 1.0
CB A:CYS278 3.7 65.0 1.0
C A:CYS278 3.8 70.3 1.0
CG2 A:ILE286 3.9 82.7 1.0
CD A:ARG333 3.9 0.4 1.0
N A:ASP280 4.0 68.2 1.0
N A:THR279 4.1 68.1 1.0
NE2 A:HIS266 4.2 77.1 1.0
C A:THR279 4.3 72.7 1.0
CG2 A:VAL288 4.3 77.7 1.0
NH1 A:ARG333 4.3 0.8 1.0
CG A:HIS266 4.4 75.0 1.0
CA A:THR279 4.4 68.2 1.0
CA A:CYS278 4.4 63.6 1.0
O A:ILE286 4.5 80.8 1.0
NE A:ARG333 4.5 0.7 1.0
CB A:ASP280 4.6 68.9 1.0
CA A:ASP280 4.6 67.5 1.0
CZ A:ARG333 4.7 0.6 1.0
CB A:VAL288 4.8 77.8 1.0
CG2 A:ILE329 4.8 0.7 1.0
N A:VAL288 4.8 74.9 1.0
CB A:HIS266 4.9 70.3 1.0
C A:ILE286 4.9 80.7 1.0
O A:THR279 4.9 72.6 1.0

Reference:

J.Yin, A.J.Schoeffler, K.Wickliffe, K.Newton, M.A.Starovasnik, E.C.Dueber, S.F.Harris. Structural Insights Into Wd-Repeat 48 Activation of Ubiquitin-Specific Protease 46. Structure V. 23 2043 2015.
ISSN: ISSN 0969-2126
PubMed: 26388029
DOI: 10.1016/J.STR.2015.08.010
Page generated: Sat Dec 12 01:54:13 2020

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