Zinc in PDB 6r0s: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product

Protein crystallography data

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product, PDB code: 6r0s was solved by C.Heim, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.12 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.455, 58.824, 88.234, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.3

Other elements in 6r0s:

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product (pdb code 6r0s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product, PDB code: 6r0s:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6r0s

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Zinc binding site 1 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:17.3
occ:1.00
SG A:CYS24 2.3 16.9 1.0
SG A:CYS27 2.3 17.5 1.0
SG A:CYS93 2.3 17.6 1.0
SG A:CYS90 2.4 16.5 1.0
CB A:CYS24 3.1 16.4 1.0
CB A:CYS90 3.2 16.6 1.0
CB A:CYS93 3.3 17.9 1.0
CB A:CYS27 3.4 18.3 1.0
N A:CYS93 3.8 18.5 1.0
N A:CYS27 3.9 18.5 1.0
CA A:CYS93 4.1 18.3 1.0
CA A:CYS27 4.2 18.8 1.0
CB A:SER95 4.5 18.6 1.0
CB A:GLN26 4.5 22.2 1.0
CA A:CYS24 4.5 16.1 1.0
CB A:GLN29 4.6 19.2 1.0
CA A:CYS90 4.6 16.7 1.0
C A:GLN26 4.7 20.0 1.0
CB A:GLN92 4.7 18.6 1.0
C A:CYS93 4.8 18.1 1.0
C A:CYS27 4.8 19.2 1.0
N A:GLY94 4.9 18.3 1.0
N A:GLY28 4.9 18.5 1.0
C A:GLN92 4.9 18.8 1.0
N A:GLN26 4.9 18.9 1.0
CA A:GLN26 4.9 20.2 1.0
N A:SER95 4.9 17.8 1.0
N A:GLN29 4.9 18.0 1.0
C A:CYS24 5.0 16.9 1.0

Zinc binding site 2 out of 3 in 6r0s

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Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:22.5
occ:1.00
SG B:CYS27 2.3 23.0 1.0
SG B:CYS93 2.3 23.8 1.0
SG B:CYS90 2.3 21.9 1.0
SG B:CYS24 2.4 21.3 1.0
CB B:CYS24 3.2 21.0 1.0
CB B:CYS90 3.2 21.6 1.0
CB B:CYS93 3.3 24.8 1.0
CB B:CYS27 3.4 24.4 1.0
N B:CYS93 3.7 23.1 1.0
N B:CYS27 3.8 25.1 1.0
CA B:CYS93 4.1 24.1 1.0
CA B:CYS27 4.1 24.9 1.0
CB B:GLN92 4.5 22.1 1.0
CA B:CYS90 4.6 20.6 1.0
CA B:CYS24 4.6 19.6 1.0
CB B:GLN26 4.7 29.8 1.0
CB B:SER95 4.7 23.5 1.0
C B:GLN92 4.7 22.7 1.0
C B:GLN26 4.7 27.7 1.0
CB B:GLN29 4.7 26.4 1.0
C B:CYS27 4.7 25.0 1.0
C B:CYS93 4.8 24.5 1.0
N B:GLY28 4.8 23.2 1.0
N B:GLY94 4.9 23.6 1.0
N B:GLN29 4.9 23.6 1.0

Zinc binding site 3 out of 3 in 6r0s

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Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:23.1
occ:1.00
SG C:CYS93 2.3 23.7 1.0
SG C:CYS27 2.3 23.3 1.0
SG C:CYS24 2.3 24.6 1.0
SG C:CYS90 2.3 21.9 1.0
CB C:CYS24 3.2 24.3 1.0
CB C:CYS90 3.2 22.1 1.0
CB C:CYS93 3.3 23.4 1.0
CB C:CYS27 3.4 25.5 1.0
N C:CYS93 3.7 22.5 1.0
N C:CYS27 3.8 28.6 1.0
CA C:CYS93 4.1 23.3 1.0
CA C:CYS27 4.2 27.9 1.0
CB C:SER95 4.4 27.7 1.0
CB C:GLN29 4.5 22.9 1.0
CB C:GLN26 4.5 34.9 1.0
CA C:CYS24 4.6 25.8 1.0
CA C:CYS90 4.6 21.8 1.0
CB C:GLN92 4.6 21.2 1.0
C C:GLN26 4.7 32.6 1.0
C C:CYS93 4.7 23.9 1.0
C C:GLN92 4.8 22.3 1.0
N C:GLY94 4.8 24.4 1.0
C C:CYS27 4.8 27.4 1.0
N C:SER95 4.8 25.9 1.0
N C:GLY28 4.8 27.0 1.0
N C:GLN29 4.9 24.3 1.0
N C:GLN26 4.9 32.1 1.0
CA C:GLN26 5.0 33.2 1.0

Reference:

C.Heim, D.Pliatsika, F.Mousavizadeh, K.Bar, B.Hernandez Alvarez, A.Giannis, M.D.Hartmann. De-Novo Design of Cereblon (Crbn) Effectors Guided By Natural Hydrolysis Products of Thalidomide Derivatives. J.Med.Chem. V. 62 6615 2019.
ISSN: ISSN 0022-2623
PubMed: 31251063
DOI: 10.1021/ACS.JMEDCHEM.9B00454
Page generated: Wed Dec 16 12:35:13 2020

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