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Arsenic in PDB 2cjw: Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp

Protein crystallography data

The structure of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp, PDB code: 2cjw was solved by A.Splingard, J.Menetrey, M.Perderiset, J.Cicolari, F.Hamoudi, L.Cabanie, A.El Marjou, A.Wells, A.Houdusse, J.De Gunzburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 2.10
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 116.617, 116.617, 81.409, 90.00, 90.00, 120.00
R / Rfree (%) 20.9 / 24.1

Other elements in 2cjw:

The structure of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp (pdb code 2cjw). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 7 binding sites of Arsenic where determined in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp, PDB code: 2cjw:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7;

Arsenic binding site 1 out of 7 in 2cjw

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Arsenic binding site 1 out of 7 in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As106

b:55.9
occ:0.25
AS A:CAS106 0.0 55.9 0.2
SG A:CAS106 2.2 56.3 1.0
OE2 A:GLU115 2.9 41.8 1.0
CB A:CAS106 3.1 56.0 1.0
CA A:CAS106 3.7 55.9 1.0
N A:CAS106 3.9 56.0 1.0
CD A:GLU115 3.9 38.7 1.0
OE1 A:GLU115 4.2 41.0 1.0
CD1 A:ILE128 4.9 28.5 1.0

Arsenic binding site 2 out of 7 in 2cjw

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Arsenic binding site 2 out of 7 in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As198

b:40.4
occ:0.75
AS A:CAS198 0.0 40.4 0.8
CE2 A:CAS198 2.0 37.1 0.8
CE1 A:CAS198 2.0 39.4 0.8
SG A:CAS198 2.2 32.8 1.0
CB A:CAS198 3.0 26.2 1.0
N A:CAS198 3.9 24.9 1.0
CA A:CAS198 4.1 25.5 1.0
CB A:LEU195 4.3 21.6 1.0
CD2 A:LEU195 4.5 20.7 1.0
C A:ARG197 4.7 25.3 1.0
O A:LEU195 4.8 22.6 1.0
CA A:LEU195 4.8 21.3 1.0
CB A:ARG197 4.8 25.5 1.0
CG A:LEU195 4.8 22.2 1.0
C A:LEU195 4.9 22.4 1.0

Arsenic binding site 3 out of 7 in 2cjw

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Arsenic binding site 3 out of 7 in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As209

b:22.2
occ:0.90
AS A:CAS209 0.0 22.2 0.9
CE2 A:CAS209 2.0 23.0 0.9
CE1 A:CAS209 2.0 23.1 0.9
SG A:CAS209 2.2 22.1 1.0
CB A:CAS209 3.2 20.1 1.0
CE2 A:PHE165 3.6 18.9 1.0
CD2 A:LEU188 3.8 20.3 1.0
CZ A:PHE165 3.9 17.4 1.0
CD1 A:LEU188 4.1 21.5 1.0
CD2 A:PHE165 4.2 17.9 1.0
O A:PHE165 4.4 17.1 1.0
O A:HOH2046 4.5 25.8 1.0
CA A:CAS209 4.6 20.2 1.0
CG A:LEU188 4.6 20.0 1.0
CE1 A:PHE165 4.7 18.4 1.0
CB A:ALA168 4.8 21.4 1.0
CG A:PHE165 4.9 17.8 1.0
N A:SER169 4.9 22.8 1.0

Arsenic binding site 4 out of 7 in 2cjw

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Arsenic binding site 4 out of 7 in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As215

b:37.2
occ:0.75
AS A:CAS215 0.0 37.2 0.8
SG A:CAS215 2.2 29.5 1.0
CB A:CAS215 3.0 28.4 1.0
O A:PHE213 3.5 26.9 1.0
N A:CAS215 3.7 28.1 1.0
C A:PHE213 3.9 26.2 1.0
CA A:CAS215 3.9 27.5 1.0
CB A:PHE213 4.0 25.0 1.0
C A:ASP214 4.1 28.5 1.0
CD A:ARG172 4.3 29.4 1.0
O A:ASP214 4.4 28.3 1.0
NH2 A:ARG176 4.4 44.7 1.0
CA A:ALA210 4.4 22.0 1.0
N A:ASP214 4.4 27.1 1.0
CA A:PHE213 4.5 25.3 1.0
O A:CAS209 4.5 19.8 1.0
O A:ALA210 4.5 23.8 1.0
NH1 A:ARG176 4.7 43.1 1.0
C A:CAS215 4.7 26.7 1.0
CG2 A:ILE186 4.8 28.9 1.0
CA A:ASP214 4.9 28.7 1.0
CZ A:ARG176 4.9 44.1 1.0
CG A:ARG172 4.9 27.8 1.0
C A:ALA210 5.0 22.4 1.0

Arsenic binding site 5 out of 7 in 2cjw

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Arsenic binding site 5 out of 7 in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As146

b:52.7
occ:0.70
AS B:CAS146 0.0 52.7 0.7
CE2 B:CAS146 2.0 51.4 0.7
CE1 B:CAS146 2.0 51.0 0.7
SG B:CAS146 2.2 50.0 1.0
CB B:CAS146 3.0 46.5 1.0
CA B:CAS146 3.6 46.1 1.0
CG B:MET132 3.8 42.8 1.0
N B:CAS146 4.3 46.6 1.0
SD B:MET132 4.5 47.9 1.0
CE B:MET132 4.6 47.1 1.0
O B:MET132 4.7 41.6 1.0
CG2 B:VAL149 4.7 36.6 1.0
C B:CAS146 4.8 44.8 1.0
CB B:MET132 4.9 40.7 1.0
C B:MET132 5.0 41.4 1.0
O B:CAS146 5.0 44.0 1.0

Arsenic binding site 6 out of 7 in 2cjw

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Arsenic binding site 6 out of 7 in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As198

b:57.3
occ:0.25
AS B:CAS198 0.0 57.3 0.2
SG B:CAS198 2.2 56.2 1.0
CB B:CAS198 3.1 53.9 1.0
CA B:CAS198 3.5 53.5 1.0
O B:ARG197 4.3 53.7 1.0
N B:CAS198 4.4 53.4 1.0
O B:CAS198 4.5 52.8 1.0
C B:CAS198 4.5 52.9 1.0
C B:ARG197 4.7 53.5 1.0

Arsenic binding site 7 out of 7 in 2cjw

Go back to Arsenic Binding Sites List in 2cjw
Arsenic binding site 7 out of 7 in the Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Crystal Structure of the Small Gtpase Gem (Gemdndcam) in Complex to Mg.Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As209

b:43.8
occ:0.50
AS B:CAS209 0.0 43.8 0.5
SG B:CAS209 2.2 41.7 1.0
CB B:CAS209 3.1 36.6 1.0
CZ B:PHE213 3.5 40.7 1.0
CA B:CAS209 4.0 36.2 1.0
CE1 B:PHE213 4.1 40.3 1.0
CE2 B:PHE213 4.2 40.8 1.0
CE1 B:PHE165 4.6 42.5 1.0
OG B:SER169 4.7 38.8 1.0
CZ B:PHE165 4.7 42.4 1.0
N B:CAS209 4.9 36.0 1.0
C B:CAS209 5.0 35.0 1.0

Reference:

A.Splingard, J.Menetrey, M.Perderiset, J.Cicolari, K.Regazzoni, F.Hamoudi, L.Cabanie, A.El Marjou, A.Wells, A.Houdusse, J.De Gunzburg. Biochemical and Structural Characterization of the Gem Gtpase. J.Biol.Chem. V. 282 1905 2007.
ISSN: ISSN 0021-9258
PubMed: 17107948
DOI: 10.1074/JBC.M604363200
Page generated: Tue Oct 27 16:48:44 2020

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