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Cadmium in PDB 4v0k: Crystal Structure of the CRARL6DN in the Gdp Bound Form

Protein crystallography data

The structure of Crystal Structure of the CRARL6DN in the Gdp Bound Form, PDB code: 4v0k was solved by A.Mourao, E.Lorentzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.504 / 1.44
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.725, 65.725, 185.377, 90.00, 90.00, 120.00
R / Rfree (%) 15.47 / 18.39

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the CRARL6DN in the Gdp Bound Form (pdb code 4v0k). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Crystal Structure of the CRARL6DN in the Gdp Bound Form, PDB code: 4v0k:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 4v0k

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Cadmium binding site 1 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


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A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1181

b:20.6
occ:0.80
 NE2 A:HIS111 2.4 24.3 1.0
OD2 A:ASP107 2.4 22.2 1.0
OD1 A:ASP107 2.5 23.5 1.0
CG A:ASP107 2.8 21.9 1.0
CD2 A:HIS111 3.2 23.6 1.0
CE1 A:HIS111 3.4 25.6 1.0
NH2 A:ARG77 4.0 25.6 1.0
O A:HOH2085 4.2 26.4 1.0
CB A:ASP107 4.3 20.6 1.0
CG A:HIS111 4.4 22.8 1.0
CZ A:ARG77 4.4 26.0 1.0
ND1 A:HIS111 4.5 24.5 1.0
NH1 A:ARG77 4.6 27.1 1.0
O A:HOH2135 4.7 41.9 1.0
O A:HOH2136 4.8 32.7 1.0
O A:ASP107 4.9 20.4 1.0

Cadmium binding site 2 out of 10 in 4v0k

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Cadmium binding site 2 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1182

b:46.5
occ:0.77
 OG1 A:THR31 2.3 39.0 1.0
O3B A:GDP700 2.4 34.9 1.0
O A:HOH2059 2.4 38.0 1.0
CD A:CD1183 2.5 40.7 0.1
O A:HOH2023 2.6 37.6 1.0
CB A:THR31 3.3 35.9 1.0
PB A:GDP700 3.4 34.8 1.0
O1B A:GDP700 3.4 37.0 1.0
OD1 A:ASP69 4.0 33.2 1.0
O A:HOH2022 4.0 38.0 1.0
O A:HOH2024 4.1 46.6 1.0
N A:THR31 4.2 32.2 1.0
O A:HOH2061 4.2 48.8 1.0
O A:HOH2040 4.2 49.9 1.0
O1A A:GDP700 4.2 40.0 1.0
CG2 A:THR31 4.3 35.9 1.0
OD2 A:ASP69 4.3 34.5 1.0
CA A:THR31 4.3 34.0 1.0
O A:HOH2056 4.3 39.2 1.0
O2B A:GDP700 4.3 33.1 1.0
O A:HOH2016 4.4 50.5 1.0
CG A:LYS30 4.4 29.0 1.0
O3A A:GDP700 4.5 37.2 1.0
CG A:ASP69 4.6 32.3 1.0
PA A:GDP700 4.7 37.2 1.0
O2A A:GDP700 4.8 37.6 1.0
O A:HOH2014 5.0 42.3 1.0

Cadmium binding site 3 out of 10 in 4v0k

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Cadmium binding site 3 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1183

b:40.7
occ:0.15
 CD A:CD1182 2.5 46.5 0.8
OD1 A:ASP69 2.6 33.2 1.0
O A:HOH2056 2.7 39.2 1.0
CG A:ASP69 3.4 32.3 1.0
OG1 A:THR31 3.5 39.0 1.0
CD A:LYS30 3.5 26.8 1.0
CG A:LYS30 3.5 29.0 1.0
O A:HOH2059 3.5 38.0 1.0
OD2 A:ASP69 3.6 34.5 1.0
O A:HOH2061 3.7 48.8 1.0
O3B A:GDP700 3.8 34.9 1.0
O A:HOH2022 3.9 38.0 1.0
CG1 A:VAL67 4.1 30.2 1.0
N A:ASP69 4.1 29.9 1.0
C A:PHE68 4.1 28.9 1.0
NZ A:LYS30 4.1 27.5 1.0
CA A:PHE68 4.3 27.3 1.0
CE A:LYS30 4.4 27.0 1.0
N A:PHE68 4.5 27.9 1.0
O A:HOH2036 4.5 35.6 1.0
O A:PHE68 4.6 28.2 1.0
PB A:GDP700 4.6 34.8 1.0
CB A:ASP69 4.6 29.4 1.0
O1B A:GDP700 4.7 37.0 1.0
CA A:ASP69 4.7 29.4 1.0
O2B A:GDP700 4.7 33.1 1.0
C A:VAL67 4.7 28.9 1.0
CB A:THR31 4.8 35.9 1.0
O A:VAL67 4.8 32.3 1.0
N A:THR31 4.8 32.2 1.0

Cadmium binding site 4 out of 10 in 4v0k

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Cadmium binding site 4 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1184

b:41.7
occ:0.17
 OD2 A:ASP88 2.5 28.6 1.0
O A:HOH2008 2.6 37.5 1.0
OD1 A:ASP88 2.6 27.4 1.0
O A:HOH2115 2.6 45.9 1.0
O A:HOH2117 2.8 43.0 1.0
CG A:ASP88 2.9 26.3 1.0
CD A:CD1186 3.2 22.0 0.1
O A:LYS17 3.5 39.2 1.0
O A:HOH2012 4.0 50.4 1.0
CB A:ASP88 4.4 23.2 1.0
O A:GLU86 4.5 25.2 1.0
C A:LYS17 4.7 34.9 1.0
NH2 A:ARG119 4.7 29.8 1.0
CA A:VAL18 4.7 25.9 1.0
O A:HOH2116 4.8 33.2 1.0
O A:HOH2216 4.9 53.4 1.0
N A:ASN19 4.9 23.8 1.0

Cadmium binding site 5 out of 10 in 4v0k

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Cadmium binding site 5 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1185

b:26.8
occ:0.15
 OE1 A:GLU108 2.8 25.3 1.0
O A:HOH2092 2.8 25.3 1.0
O A:GLU108 2.8 20.4 1.0
NE1 A:TRP80 3.1 24.3 1.0
CZ2 A:TRP80 3.6 25.5 1.0
C A:GLU108 3.6 19.4 1.0
CB A:GLU108 3.6 21.5 1.0
CA A:GLU108 3.6 20.7 1.0
CB A:HIS111 3.6 22.4 1.0
OH A:TYR84 3.6 24.4 1.0
CE2 A:TRP80 3.7 25.0 1.0
CD A:GLU108 3.8 23.5 1.0
CE A:MET70 4.0 25.7 1.0
CG A:ARG77 4.0 26.0 1.0
CD A:ARG77 4.2 25.4 1.0
NE A:ARG77 4.2 26.2 1.0
N A:MET112 4.2 21.5 1.0
CG A:GLU108 4.3 21.1 1.0
SD A:MET70 4.3 25.9 1.0
CD1 A:TRP80 4.4 25.8 1.0
CG A:HIS111 4.5 22.8 1.0
CG A:MET70 4.6 24.8 1.0
CA A:HIS111 4.7 22.4 1.0
C A:HIS111 4.7 22.7 1.0
CB A:MET112 4.7 21.0 1.0
N A:MET109 4.8 18.8 1.0
CA A:MET112 4.8 21.9 1.0
CH2 A:TRP80 4.9 27.1 1.0
OE2 A:GLU81 4.9 29.0 1.0
OE2 A:GLU108 4.9 26.0 1.0
CD2 A:HIS111 4.9 23.6 1.0
CZ A:TYR84 5.0 23.3 1.0
N A:GLU108 5.0 20.1 1.0

Cadmium binding site 6 out of 10 in 4v0k

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Cadmium binding site 6 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1186

b:22.0
occ:0.09
 O A:HOH2117 2.6 43.0 1.0
O A:HOH2217 2.6 53.3 1.0
CD A:CD1184 3.2 41.7 0.2
O A:HOH2222 3.3 54.5 1.0
O A:HOH2005 4.1 42.1 1.0
O A:HOH2115 4.3 45.9 1.0
O A:LYS17 4.4 39.2 1.0
O A:SER180 4.4 44.3 1.0
O A:HOH2216 4.9 53.4 1.0

Cadmium binding site 7 out of 10 in 4v0k

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Cadmium binding site 7 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1181

b:16.9
occ:0.75
 OD1 B:ASP169 2.4 22.8 1.0
OD2 B:ASP173 2.4 20.9 1.0
OD1 B:ASP173 2.5 20.8 1.0
OD2 B:ASP169 2.8 22.7 1.0
CG B:ASP173 2.8 21.9 1.0
CG B:ASP169 2.9 22.2 1.0
O B:HOH2231 3.7 56.8 1.0
CB B:ASP173 4.3 21.7 1.0
O B:ASP169 4.3 20.4 1.0
CB B:ASP169 4.4 19.8 1.0
O B:HOH2233 4.5 34.4 1.0
O B:HOH2230 4.5 32.9 1.0
O B:HOH2237 4.5 29.1 1.0
C B:ASP169 4.8 20.3 1.0
CA B:ASP169 4.9 20.2 1.0

Cadmium binding site 8 out of 10 in 4v0k

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Cadmium binding site 8 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1182

b:17.4
occ:0.41
 O3B B:GDP700 2.2 20.1 1.0
OG1 B:THR31 2.2 20.9 1.0
O B:HOH2080 2.3 21.7 1.0
O B:HOH2028 2.3 24.2 1.0
O B:HOH2026 2.3 22.8 1.0
O B:HOH2027 2.3 24.1 1.0
CB B:THR31 3.2 19.9 1.0
PB B:GDP700 3.3 19.4 1.0
O1B B:GDP700 3.5 20.0 1.0
O B:HOH2029 4.0 24.4 1.0
OD1 B:ASP69 4.0 22.3 1.0
O B:HOH2082 4.1 35.3 1.0
O1A B:GDP700 4.1 22.6 1.0
N B:THR31 4.1 18.1 1.0
CG2 B:THR31 4.2 21.5 1.0
CA B:THR31 4.2 19.3 1.0
O B:HOH2019 4.2 44.8 1.0
OD2 B:ASP69 4.3 22.6 1.0
O B:HOH2077 4.3 23.5 1.0
O2B B:GDP700 4.3 19.4 1.0
O3A B:GDP700 4.4 19.0 1.0
CG B:LYS30 4.5 18.5 1.0
PA B:GDP700 4.6 19.7 1.0
CG B:ASP69 4.6 21.0 1.0
O2A B:GDP700 4.8 21.0 1.0
O B:HOH2018 4.9 46.6 1.0
O B:HOH2009 4.9 31.3 1.0

Cadmium binding site 9 out of 10 in 4v0k

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Cadmium binding site 9 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1183

b:25.6
occ:0.17
 O A:HOH2189 2.5 51.1 1.0
NZ B:LYS130 3.1 26.1 1.0
ND2 B:ASN161 3.3 21.5 1.0
O A:HOH2188 3.4 34.1 1.0
CB B:ASP131 3.5 23.3 1.0
O B:HOH2250 3.6 41.1 1.0
O B:HOH2225 3.7 34.5 1.0
CA B:ASP131 3.7 21.7 1.0
OE1 A:GLN156 3.8 31.2 1.0
CG B:LYS130 3.8 20.4 1.0
CE B:LYS130 3.8 24.1 1.0
N B:ASP131 3.9 21.0 1.0
CB B:ASN161 4.0 19.5 1.0
O A:HOH2111 4.0 50.9 1.0
CG B:ASN161 4.1 21.5 1.0
OE1 B:GLU166 4.1 28.9 1.0
C B:LYS130 4.4 20.7 1.0
CD B:LYS130 4.4 21.7 1.0
CD A:GLN156 4.4 27.5 1.0
O B:LYS130 4.6 22.7 1.0
O A:HOH2120 4.6 53.8 1.0
NE2 A:GLN156 4.7 28.9 1.0
CG B:ASP131 4.7 24.6 1.0
O A:HOH2187 5.0 41.6 1.0
CB B:LYS130 5.0 20.5 1.0
OD1 B:ASP131 5.0 23.1 1.0

Cadmium binding site 10 out of 10 in 4v0k

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Cadmium binding site 10 out of 10 in the Crystal Structure of the CRARL6DN in the Gdp Bound Form


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of the CRARL6DN in the Gdp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1184

b:49.3
occ:0.16
 OD2 B:ASP88 2.6 27.8 1.0
O B:HOH2140 2.7 48.0 1.0
O B:HOH2003 2.8 42.8 1.0
OD1 B:ASP88 2.8 28.4 1.0
CG B:ASP88 3.0 27.6 1.0
O B:LYS17 3.4 41.8 1.0
O B:HOH2251 3.6 55.2 1.0
CB B:ASP88 4.5 24.7 1.0
C B:LYS17 4.5 40.6 1.0
O B:GLU86 4.6 28.3 1.0
CA B:VAL18 4.7 29.5 1.0
N B:ASN19 4.9 26.1 1.0
ND2 B:ASN19 4.9 34.5 1.0

Reference:

A.Mourao, A.R.Nager, M.V.Nachury, E.Lorentzen. Structural Basis For Membrane Targeting of the Bbsome By ARL6 Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
DOI: 10.1038/NSMB.2920
Page generated: Fri Jul 19 17:59:28 2024

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