Atomistry » Chlorine » PDB 5afy-5anv » 5amh
Atomistry »
  Chlorine »
    PDB 5afy-5anv »
      5amh »

Chlorine in PDB 5amh: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form

Protein crystallography data

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form, PDB code: 5amh was solved by M.D.Hartmann, A.N.Lupas, B.Hernandez Alvarez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.77 / 1.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.720, 51.720, 84.710, 90.00, 90.00, 120.00
R / Rfree (%) 12.565 / 15.737

Other elements in 5amh:

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Zinc (Zn) 1 atom
Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form (pdb code 5amh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form, PDB code: 5amh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5amh

Go back to Chlorine Binding Sites List in 5amh
Chlorine binding site 1 out of 7 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1127

b:19.8
occ:1.00
 O A:HOH2089 3.0 45.1 1.0
O A:HOH2086 3.1 38.1 1.0
O A:HOH2088 3.2 33.1 1.0
N A:ARG57 3.2 15.0 1.0
N A:ASP116 3.3 16.2 1.0
CB A:ASP116 3.6 23.6 1.0
CG2 A:ILE114 3.7 16.4 1.0
O A:ARG57 3.8 17.0 1.0
CA A:PHE56 3.9 16.1 1.0
N A:LYS115 4.0 14.7 1.0
CB A:LYS115 4.0 17.2 1.0
C A:PHE56 4.1 15.3 1.0
CA A:ASP116 4.1 17.9 1.0
CA A:ARG57 4.1 14.7 1.0
CB A:ARG57 4.1 17.4 1.0
O A:HOH2146 4.2 73.9 1.0
C A:LYS115 4.3 16.4 1.0
CA A:LYS115 4.3 16.0 1.0
CB A:PHE56 4.4 16.2 1.0
C A:ARG57 4.5 14.4 1.0
CD1 A:PHE56 4.6 19.9 1.0
CD A:ARG57 4.7 29.5 1.0
O A:ILE55 4.7 20.5 1.0
C A:ILE114 4.7 13.4 1.0
CG A:ASP116 4.9 33.0 1.0
CG A:LYS115 4.9 20.6 1.0

Chlorine binding site 2 out of 7 in 5amh

Go back to Chlorine Binding Sites List in 5amh
Chlorine binding site 2 out of 7 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1128

b:24.4
occ:1.00
 NE1 A:TRP99 3.1 15.9 1.0
C4 A:EF2151 3.5 18.9 1.0
CE1 A:HIS96 3.6 14.0 1.0
O16 A:EF2151 3.8 23.2 1.0
N09 A:EF2151 3.8 18.9 1.0
CE2 A:TRP99 3.8 15.7 1.0
CZ2 A:TRP99 3.9 16.9 1.0
CG1 A:ILE87 4.0 16.8 1.0
C13 A:EF2151 4.0 23.9 1.0
CD1 A:ILE87 4.0 18.6 1.0
C07 A:EF2151 4.1 16.3 1.0
CD1 A:TRP99 4.3 15.0 1.0
C08 A:EF2151 4.3 16.9 1.0
NE2 A:HIS96 4.3 13.9 1.0
C14 A:EF2151 4.4 22.9 1.0
O A:HOH2079 4.4 25.9 1.0
C3 A:EF2151 4.4 22.4 1.0
C12 A:EF2151 4.6 25.0 1.0
ND1 A:HIS96 4.6 13.9 1.0
CZ3 A:TRP85 4.7 19.9 1.0
CH2 A:TRP85 5.0 22.2 1.0

Chlorine binding site 3 out of 7 in 5amh

Go back to Chlorine Binding Sites List in 5amh
Chlorine binding site 3 out of 7 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1129

b:16.6
occ:1.00
 N A:VAL47 3.2 15.1 1.0
O A:HOH2067 3.2 16.1 1.0
O A:HOH2066 3.3 21.1 1.0
O A:HOH2075 3.4 29.2 1.0
CA A:HIS46 3.5 15.2 1.0
O A:HOH2073 3.6 43.5 1.0
CB A:HIS46 3.8 14.8 1.0
O A:VAL47 3.8 17.4 1.0
C A:HIS46 3.8 15.9 1.0
CG A:HIS46 4.0 16.0 1.0
OD2 A:ASP43 4.0 20.1 1.0
ND1 A:HIS46 4.1 18.6 1.0
CA A:VAL47 4.2 14.8 1.0
CB A:VAL47 4.3 17.3 1.0
C A:VAL47 4.4 15.8 1.0
O A:GLU45 4.6 17.7 1.0
O A:HOH2074 4.7 32.6 1.0
CG2 A:VAL47 4.7 21.6 1.0
N A:HIS46 4.8 15.3 1.0
CE1 A:HIS46 4.9 18.7 1.0
CD2 A:HIS46 4.9 17.0 1.0
CA A:CA1126 4.9 15.5 1.0

Chlorine binding site 4 out of 7 in 5amh

Go back to Chlorine Binding Sites List in 5amh
Chlorine binding site 4 out of 7 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1130

b:28.8
occ:1.00
 O A:HOH2001 3.1 36.2 1.0
N A:ASP35 3.2 20.8 1.0
N A:SER20 3.3 30.4 1.0
O A:HOH2043 3.4 59.2 1.0
N A:ARG34 3.6 20.3 1.0
CB A:ASP35 3.6 28.1 1.0
O A:SER20 3.7 27.0 1.0
CA A:ALA19 3.7 46.8 1.0
CB A:ARG33 3.7 24.9 1.0
CB A:ARG34 4.0 24.6 1.0
CB A:ALA19 4.0 53.0 1.0
CA A:ASP35 4.0 22.9 1.0
C A:ALA19 4.0 44.9 1.0
CA A:ARG34 4.0 21.5 1.0
C A:ARG34 4.1 20.6 1.0
CD A:ARG33 4.1 34.0 1.0
CG A:ARG33 4.1 24.4 1.0
CA A:SER20 4.2 27.3 1.0
C A:SER20 4.3 23.4 1.0
C A:ARG33 4.3 18.7 1.0
CB A:SER20 4.5 35.3 1.0
CA A:ARG33 4.6 21.4 1.0
O A:HOH2007 4.6 47.3 1.0
O A:GLY18 4.8 73.9 1.0
CG A:ASP35 5.0 58.9 1.0
N A:ALA19 5.0 54.7 1.0

Chlorine binding site 5 out of 7 in 5amh

Go back to Chlorine Binding Sites List in 5amh
Chlorine binding site 5 out of 7 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1131

b:20.0
occ:0.50
 O A:HOH2021 2.7 40.0 1.0
OG A:SER95 3.2 15.8 1.0
N A:HIS96 3.2 12.2 1.0
CA A:SER95 3.7 12.8 1.0
CB A:SER95 3.9 14.4 1.0
C A:SER95 3.9 12.4 1.0
CA A:HIS96 4.2 12.2 1.0
CB A:HIS96 4.3 12.7 1.0
CD A:ARG117 4.4 23.6 1.0
NH1 A:ARG117 4.4 20.4 1.0
O A:HIS96 4.5 14.2 1.0
NE A:ARG117 4.6 25.5 1.0
CZ A:ARG117 4.7 21.7 1.0
C A:HIS96 4.7 12.0 1.0
N A:SER95 4.9 12.8 1.0

Chlorine binding site 6 out of 7 in 5amh

Go back to Chlorine Binding Sites List in 5amh
Chlorine binding site 6 out of 7 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1132

b:28.8
occ:1.00
 O A:HOH2039 2.8 43.5 1.0
O A:HOH2076 2.9 41.7 1.0
N A:PHE49 3.2 15.7 1.0
CA A:VAL48 3.7 15.9 1.0
CD1 A:TRP79 3.8 17.4 1.0
CD1 A:PHE49 3.9 24.4 1.0
C A:VAL48 4.0 14.7 1.0
NE1 A:TRP79 4.0 16.6 1.0
CB A:VAL48 4.1 15.8 1.0
O A:PHE49 4.1 16.8 1.0
CB A:PHE49 4.1 18.5 1.0
CA A:PHE49 4.2 16.4 1.0
O A:VAL47 4.5 17.4 1.0
O A:HOH2075 4.5 29.2 1.0
CG A:PHE49 4.5 22.3 1.0
CG1 A:VAL48 4.6 18.8 1.0
O A:HOH2121 4.6 52.5 1.0
C A:PHE49 4.7 16.2 1.0
O A:HOH2122 4.8 41.3 1.0
N A:VAL48 4.8 15.1 1.0
CG A:TRP79 4.9 17.4 1.0
CE1 A:PHE49 5.0 33.1 1.0

Chlorine binding site 7 out of 7 in 5amh

Go back to Chlorine Binding Sites List in 5amh
Chlorine binding site 7 out of 7 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1133

b:28.2
occ:1.00
 O A:HOH2123 3.0 38.0 1.0
O A:HOH2124 3.3 40.8 1.0
CE1 A:HIS46 3.6 18.7 1.0
CD1 A:PHE80 3.8 21.6 1.0
CA A:GLY41 3.8 19.5 1.0
CG A:MET40 3.8 22.8 0.5
N A:GLY41 3.8 18.6 1.0
C A:MET40 4.0 18.4 1.0
O A:MET40 4.1 18.6 1.0
SD A:MET40 4.1 27.5 0.5
CE1 A:PHE80 4.4 22.4 1.0
CB A:MET40 4.4 20.9 0.5
NE2 A:HIS46 4.5 17.4 1.0
O A:HOH2063 4.5 34.2 1.0
ND1 A:HIS46 4.5 18.6 1.0
O A:HOH2125 4.6 49.6 1.0
CG A:PHE80 4.8 18.4 1.0
CB A:MET40 4.8 19.7 0.5
CA A:PHE80 4.9 20.9 1.0
CA A:MET40 4.9 19.0 0.5
CB A:PHE80 4.9 19.1 1.0
CA A:MET40 5.0 18.2 0.5

Reference:

M.D.Hartmann, I.Boichenko, M.Coles, A.N.Lupas, B.Hernandez Alvarez. Structural Dynamics of the Cereblon Ligand Binding Domain. Plos One V. 10 28342 2015.
ISSN: ISSN 1932-6203
PubMed: 26024445
DOI: 10.1371/JOURNAL.PONE.0128342
Page generated: Fri Jul 26 05:20:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy