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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

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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

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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

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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

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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

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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

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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

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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: Sat Jul 12 00:16:35 2025

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