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Zinc in PDB 6r1k: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C

Protein crystallography data

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C, PDB code: 6r1k 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) 47.46 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.230, 60.080, 88.520, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.2

Other elements in 6r1k:

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C (pdb code 6r1k). 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 7C, PDB code: 6r1k:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6r1k

Go back to Zinc Binding Sites List in 6r1k
Zinc binding site 1 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


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 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:30.2
occ:1.00
SG A:CYS93 2.3 30.5 1.0
SG A:CYS24 2.3 30.6 1.0
SG A:CYS27 2.3 29.0 1.0
SG A:CYS90 2.3 29.0 1.0
CB A:CYS90 3.2 27.4 1.0
CB A:CYS24 3.2 29.3 1.0
CB A:CYS93 3.3 30.6 1.0
CB A:CYS27 3.5 31.4 1.0
N A:CYS93 3.8 29.6 1.0
N A:CYS27 3.8 32.0 1.0
CA A:CYS93 4.0 31.7 1.0
CA A:CYS27 4.2 33.1 1.0
CB A:GLN26 4.4 41.3 1.0
CB A:GLN29 4.5 31.0 1.0
CB A:SER95 4.6 31.3 0.5
CA A:CYS24 4.6 28.8 1.0
CA A:CYS90 4.6 27.1 1.0
C A:GLN26 4.6 38.5 1.0
CB A:GLN92 4.7 30.2 1.0
OG A:SER95 4.7 33.4 0.5
CB A:SER95 4.7 32.7 0.5
C A:CYS93 4.7 31.6 1.0
CA A:GLN26 4.8 38.8 1.0
N A:GLY94 4.9 31.7 1.0
C A:GLN92 4.9 31.0 1.0
C A:CYS27 4.9 33.0 1.0
N A:GLN26 4.9 35.7 1.0
N A:GLN29 4.9 29.5 1.0
N A:GLY28 4.9 32.7 1.0
N A:SER95 5.0 32.6 1.0

Zinc binding site 2 out of 3 in 6r1k

Go back to Zinc Binding Sites List in 6r1k
Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


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 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:37.1
occ:1.00
SG B:CYS93 2.3 39.0 1.0
SG B:CYS90 2.3 35.9 1.0
SG B:CYS27 2.3 37.9 1.0
SG B:CYS24 2.3 36.8 1.0
CB B:CYS90 3.2 33.5 1.0
CB B:CYS24 3.2 35.2 1.0
CB B:CYS93 3.2 40.4 1.0
CB B:CYS27 3.4 41.5 1.0
N B:CYS93 3.7 37.5 1.0
N B:CYS27 3.8 41.6 1.0
CA B:CYS93 4.0 40.0 1.0
CA B:CYS27 4.1 40.7 1.0
CB B:GLN92 4.5 36.2 1.0
CB B:GLN26 4.6 45.9 1.0
CA B:CYS90 4.6 31.6 1.0
CA B:CYS24 4.6 32.4 1.0
C B:GLN26 4.7 44.7 1.0
C B:GLN92 4.8 38.4 1.0
C B:CYS93 4.8 38.1 1.0
CB B:SER95 4.8 36.6 1.0
C B:CYS27 4.8 38.9 1.0
CB B:GLN29 4.8 37.0 1.0
N B:GLY28 4.9 36.0 1.0
N B:GLY94 4.9 38.1 1.0
CA B:GLN26 5.0 43.6 1.0

Zinc binding site 3 out of 3 in 6r1k

Go back to Zinc Binding Sites List in 6r1k
Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


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 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:36.9
occ:1.00
SG C:CYS27 2.3 35.3 1.0
SG C:CYS93 2.3 40.0 1.0
SG C:CYS24 2.3 38.1 1.0
SG C:CYS90 2.3 36.8 1.0
CB C:CYS90 3.1 39.1 1.0
CB C:CYS24 3.2 34.9 1.0
CB C:CYS93 3.3 40.6 1.0
CB C:CYS27 3.4 41.2 1.0
N C:CYS93 3.7 37.5 1.0
N C:CYS27 3.8 45.0 1.0
CA C:CYS93 4.1 39.8 1.0
CA C:CYS27 4.2 42.4 1.0
CB C:GLN29 4.4 36.5 1.0
CB C:GLN26 4.5 48.8 1.0
CB C:SER95 4.6 45.4 1.0
CB C:GLN92 4.6 33.4 1.0
CA C:CYS90 4.6 37.1 1.0
CA C:CYS24 4.6 35.6 1.0
C C:GLN26 4.7 47.6 1.0
C C:CYS93 4.7 40.8 1.0
C C:GLN92 4.8 36.6 1.0
C C:CYS27 4.8 41.7 1.0
N C:GLY94 4.8 39.5 1.0
N C:GLN29 4.9 34.6 1.0
N C:GLY28 4.9 36.6 1.0
N C:SER95 4.9 43.4 1.0
CA C:GLN26 4.9 49.0 1.0
N C:GLN26 5.0 47.7 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 12:35:34 2020

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