Zinc in PDB 7omf: Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I)

Protein crystallography data

The structure of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I), PDB code: 7omf was solved by C.Cretu, V.Pena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.03 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.355, 109.846, 253.3, 90, 90, 90
R / Rfree (%) 23.2 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I) (pdb code 7omf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I), PDB code: 7omf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7omf

Go back to Zinc Binding Sites List in 7omf
Zinc binding site 1 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:105.4
occ:1.00
SG D:CYS23 2.3 100.4 1.0
SG D:CYS58 2.3 99.8 1.0
SG D:CYS61 2.3 126.7 1.0
S D:SCN105 2.4 119.9 1.0
CB D:CYS58 3.3 101.8 1.0
CB D:CYS61 3.5 105.2 1.0
CB D:CYS23 3.8 110.2 1.0
N D:CYS61 3.9 105.2 1.0
C D:SCN105 4.1 115.6 1.0
CA D:CYS61 4.3 111.0 1.0
CB D:ILE60 4.4 112.4 1.0
N D:CYS23 4.6 93.5 1.0
C D:ILE60 4.7 109.8 1.0
SG D:CYS26 4.7 107.5 1.0
CA D:CYS58 4.8 99.6 1.0
CA D:CYS23 4.8 101.7 1.0
N D:ILE60 4.8 100.3 1.0
CB D:CYS26 4.8 100.9 1.0
CA D:ILE60 4.8 111.5 1.0
CG1 D:ILE60 5.0 107.3 1.0

Zinc binding site 2 out of 3 in 7omf

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Zinc binding site 2 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn102

b:99.6
occ:1.00
SG D:CYS46 2.3 86.3 1.0
SG D:CYS11 2.3 85.2 1.0
SG D:CYS49 2.3 91.4 1.0
SG D:CYS85 2.4 96.3 1.0
CB D:CYS11 3.0 84.8 1.0
CB D:CYS85 3.3 88.2 1.0
CB D:CYS49 3.5 93.2 1.0
CB D:CYS46 3.6 93.1 1.0
N D:CYS46 4.0 90.7 1.0
CA D:CYS46 4.4 94.4 1.0
CB D:LYS87 4.4 97.9 1.0
CA D:CYS11 4.5 85.1 1.0
N D:CYS49 4.5 104.2 1.0
CA D:CYS49 4.6 92.8 1.0
CB D:LYS13 4.7 92.3 1.0
CA D:CYS85 4.7 79.5 1.0
C D:CYS11 5.0 88.6 1.0
C D:CYS46 5.0 95.6 1.0

Zinc binding site 3 out of 3 in 7omf

Go back to Zinc Binding Sites List in 7omf
Zinc binding site 3 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn103

b:80.9
occ:1.00
SG D:CYS33 2.3 88.6 1.0
SG D:CYS75 2.3 83.2 1.0
SG D:CYS72 2.3 90.2 1.0
SG D:CYS30 2.3 84.8 1.0
CB D:CYS33 3.3 90.1 1.0
CB D:CYS75 3.3 74.7 1.0
CB D:CYS72 3.4 74.5 1.0
CB D:CYS30 3.5 91.0 1.0
N D:CYS33 3.7 90.3 1.0
N D:CYS72 3.8 80.2 1.0
CA D:CYS33 4.1 85.1 1.0
N D:CYS75 4.1 87.3 1.0
CA D:CYS72 4.2 80.8 1.0
CA D:CYS75 4.3 81.1 1.0
CB D:ILE32 4.5 77.1 1.0
C D:ILE32 4.7 87.1 1.0
C D:CYS33 4.8 86.9 1.0
N D:ILE32 4.9 87.2 1.0
CA D:CYS30 4.9 91.0 1.0
C D:CYS72 4.9 82.2 1.0
CA D:ILE32 4.9 88.1 1.0

Reference:

C.Cretu, P.Gee, X.Liu, A.Agrawal, T.V.Nguyen, A.K.Ghosh, A.Cook, M.Jurica, N.A.Larsen, V.Pena. Structural Basis of Intron Selection By U2 Snrnp in the Presence of Covalent Inhibitors. Nat Commun V. 12 4491 2021.
ISSN: ESSN 2041-1723
PubMed: 34301950
DOI: 10.1038/S41467-021-24741-1
Page generated: Sun Aug 22 09:53:11 2021

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