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Chlorine in PDB 2is9: Structure of Yeast Dcn-1

Protein crystallography data

The structure of Structure of Yeast Dcn-1, PDB code: 2is9 was solved by X.Yang, J.Zhou, L.Sun, Z.Wei, J.Gao, W.Gong, R.M.Xu, Z.Rao, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.92
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 81.107, 81.107, 106.023, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24

Other elements in 2is9:

The structure of Structure of Yeast Dcn-1 also contains other interesting chemical elements:

Platinum (Pt) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Yeast Dcn-1 (pdb code 2is9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Yeast Dcn-1, PDB code: 2is9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2is9

Go back to Chlorine Binding Sites List in 2is9
Chlorine binding site 1 out of 4 in the Structure of Yeast Dcn-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Yeast Dcn-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1110

b:0.0
occ:1.00
PT A:PT1109 3.2 0.3 1.0
CL A:CL1118 4.2 0.1 1.0
SD A:MET230 4.8 37.9 1.0

Chlorine binding site 2 out of 4 in 2is9

Go back to Chlorine Binding Sites List in 2is9
Chlorine binding site 2 out of 4 in the Structure of Yeast Dcn-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Yeast Dcn-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1111

b:0.7
occ:1.00
O A:HOH1201 3.7 34.2 1.0
CB A:LEU233 3.7 22.9 1.0
O A:ARG229 4.2 23.4 1.0
CA A:LEU233 4.4 22.4 1.0
N A:LEU233 4.4 22.2 1.0
PT A:PT1109 4.5 0.3 1.0
CG A:LEU233 4.5 25.3 1.0
CD1 A:LEU233 4.5 27.9 1.0
CD2 A:LEU233 4.6 26.6 1.0

Chlorine binding site 3 out of 4 in 2is9

Go back to Chlorine Binding Sites List in 2is9
Chlorine binding site 3 out of 4 in the Structure of Yeast Dcn-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Yeast Dcn-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1112

b:1.0
occ:1.00
OD1 A:ASP226 3.2 26.5 1.0
CA A:ASP226 3.6 24.7 1.0
CG A:ASP226 4.0 26.5 1.0
CB A:ASP226 4.0 24.9 1.0
PT A:PT1109 4.2 0.3 1.0
CD A:ARG229 4.3 35.9 1.0
CB A:ARG229 4.3 25.7 1.0
O A:ASP226 4.3 24.4 1.0
N A:ASP226 4.4 25.0 1.0
CG A:MET230 4.4 28.1 1.0
O A:HOH1199 4.4 43.4 1.0
C A:ASP226 4.5 24.0 1.0
O A:LYS225 4.6 24.4 1.0
SD A:MET230 4.8 37.9 1.0
C A:LYS225 4.8 25.5 1.0
CG A:ARG229 4.8 29.6 1.0
CL A:CL1118 4.9 0.1 1.0

Chlorine binding site 4 out of 4 in 2is9

Go back to Chlorine Binding Sites List in 2is9
Chlorine binding site 4 out of 4 in the Structure of Yeast Dcn-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Yeast Dcn-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1118

b:0.1
occ:1.00
O A:HOH1199 2.7 43.4 1.0
SD A:MET230 3.5 37.9 1.0
PT A:PT1109 3.7 0.3 1.0
CL A:CL1110 4.2 0.0 1.0
CE A:MET230 4.4 39.1 1.0
O A:HOH1146 4.4 35.3 1.0
CG A:MET230 4.5 28.1 1.0
OD1 A:ASP226 4.7 26.5 1.0
CL A:CL1112 4.9 1.0 1.0

Reference:

X.Yang, J.Zhou, L.Sun, Z.Wei, J.Gao, W.Gong, R.M.Xu, Z.Rao, Y.Liu. Structural Basis For the Function of Dcn-1 in Protein Neddylation. J.Biol.Chem. V. 282 24490 2007.
ISSN: ISSN 0021-9258
PubMed: 17597076
DOI: 10.1074/JBC.C700038200
Page generated: Wed Oct 28 10:39:07 2020

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