Zinc in PDB 7opi: Structure of A Minimal SF3B Core in Complex with the Inactive Modulator Spliceostatin E (Form I)

Protein crystallography data

The structure of Structure of A Minimal SF3B Core in Complex with the Inactive Modulator Spliceostatin E (Form I), PDB code: 7opi 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) 48.43 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.535, 108.28, 253.202, 90, 90, 90
R / Rfree (%) 22.8 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Minimal SF3B Core in Complex with the Inactive Modulator Spliceostatin E (Form I) (pdb code 7opi). 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 the Inactive Modulator Spliceostatin E (Form I), PDB code: 7opi:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7opi

Go back to Zinc Binding Sites List in 7opi
Zinc binding site 1 out of 3 in the Structure of A Minimal SF3B Core in Complex with the Inactive Modulator Spliceostatin E (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 the Inactive Modulator Spliceostatin E (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:100.9
occ:1.00
SG D:CYS61 2.3 106.1 1.0
SG D:CYS23 2.3 107.5 1.0
SG D:CYS58 2.3 100.9 1.0
SG D:CYS26 2.3 108.0 1.0
CB D:CYS26 3.3 111.2 1.0
CB D:CYS58 3.4 106.6 1.0
CB D:CYS23 3.7 110.8 1.0
CB D:CYS61 3.7 114.6 1.0
N D:CYS61 3.9 108.4 1.0
N D:CYS26 4.0 103.8 1.0
N D:CYS23 4.2 94.9 1.0
CA D:CYS26 4.3 108.9 1.0
CA D:CYS61 4.3 108.5 1.0
N D:GLY62 4.4 107.2 1.0
CA D:CYS23 4.5 103.8 1.0
N D:GLY63 4.7 104.0 1.0
CB D:ILE60 4.7 99.6 1.0
CA D:CYS58 4.8 100.9 1.0
C D:CYS61 4.9 110.3 1.0
C D:ILE60 5.0 109.8 1.0
N D:ILE60 5.0 89.3 1.0
CB D:LYS25 5.0 114.5 1.0

Zinc binding site 2 out of 3 in 7opi

Go back to Zinc Binding Sites List in 7opi
Zinc binding site 2 out of 3 in the Structure of A Minimal SF3B Core in Complex with the Inactive Modulator Spliceostatin E (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 the Inactive Modulator Spliceostatin E (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn102

b:96.0
occ:1.00
SG D:CYS46 2.3 76.1 1.0
SG D:CYS11 2.3 80.9 1.0
SG D:CYS49 2.3 90.7 1.0
SG D:CYS85 2.3 90.5 1.0
CB D:CYS11 3.1 80.5 1.0
CB D:CYS49 3.1 92.4 1.0
CB D:CYS85 3.1 93.2 1.0
CB D:CYS46 3.6 95.2 1.0
N D:CYS46 4.0 94.3 1.0
N D:CYS49 4.2 103.7 1.0
CA D:CYS49 4.2 98.2 1.0
CA D:CYS46 4.4 97.7 1.0
CB D:LYS13 4.5 93.6 1.0
CA D:CYS11 4.5 81.0 1.0
CA D:CYS85 4.6 87.5 1.0
CB D:LYS87 4.6 95.4 1.0
O D:CYS46 4.8 107.8 1.0
C D:CYS46 4.9 103.0 1.0
CG D:LYS13 4.9 97.4 1.0
N D:LYS13 5.0 89.8 1.0

Zinc binding site 3 out of 3 in 7opi

Go back to Zinc Binding Sites List in 7opi
Zinc binding site 3 out of 3 in the Structure of A Minimal SF3B Core in Complex with the Inactive Modulator Spliceostatin E (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 the Inactive Modulator Spliceostatin E (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn103

b:114.0
occ:1.00
SG D:CYS33 2.3 92.6 1.0
SG D:CYS30 2.3 88.3 1.0
SG D:CYS75 2.3 88.7 1.0
SG D:CYS72 2.3 99.9 1.0
CB D:CYS30 3.4 94.0 1.0
CB D:CYS72 3.4 81.7 1.0
CB D:CYS75 3.6 79.7 1.0
CB D:CYS33 3.6 92.5 1.0
N D:CYS33 3.9 86.0 1.0
N D:CYS72 4.0 90.2 1.0
CA D:CYS72 4.2 79.6 1.0
N D:CYS75 4.2 91.5 1.0
CA D:CYS33 4.3 87.3 1.0
CA D:CYS75 4.5 82.4 1.0
CB D:ILE32 4.6 73.6 1.0
CB D:SER35 4.7 96.3 1.0
CA D:CYS30 4.8 85.6 1.0
C D:CYS72 4.8 90.4 1.0
O D:CYS72 4.9 97.8 1.0
C D:CYS33 4.9 86.8 1.0
C D:ILE32 5.0 81.7 1.0
N D:ILE32 5.0 80.1 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 09:53:08 2021

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