Zinc in PDB 7b0i: Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form II)

Protein crystallography data

The structure of Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form II), PDB code: 7b0i 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) 45.01 / 3.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.503, 108.503, 358.938, 90, 90, 120
R / Rfree (%) 21.5 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form II) (pdb code 7b0i). 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 Spliceostatin A (Form II), PDB code: 7b0i:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7b0i

Go back to Zinc Binding Sites List in 7b0i
Zinc binding site 1 out of 3 in the Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form II)


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 Spliceostatin A (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1402

b:90.1
occ:1.00
SG D:CYS75 2.3 82.6 1.0
SG D:CYS33 2.3 87.1 1.0
SG D:CYS72 2.3 87.1 1.0
SG D:CYS30 2.3 96.8 1.0
CB D:CYS30 3.3 89.8 1.0
CB D:CYS72 3.4 71.1 1.0
CB D:CYS75 3.4 90.3 1.0
CB D:CYS33 3.6 93.6 1.0
N D:CYS72 3.9 92.0 1.0
N D:CYS33 4.0 95.2 1.0
N D:CYS75 4.1 92.5 1.0
CA D:CYS72 4.2 84.0 1.0
CA D:CYS75 4.3 84.7 1.0
CA D:CYS33 4.4 97.4 1.0
CB D:SER35 4.6 95.4 1.0
CB D:ILE32 4.6 87.2 1.0
C D:CYS72 4.7 93.4 1.0
CA D:CYS30 4.8 89.8 1.0
O D:CYS72 4.8 95.3 1.0
C D:ILE32 5.0 91.6 1.0

Zinc binding site 2 out of 3 in 7b0i

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Zinc binding site 2 out of 3 in the Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form II)


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 Spliceostatin A (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1403

b:93.4
occ:1.00
SG D:CYS46 2.3 80.2 1.0
SG D:CYS49 2.3 89.6 1.0
SG D:CYS11 2.3 82.4 1.0
SG D:CYS85 2.3 94.7 1.0
CB D:CYS85 3.1 90.7 1.0
CB D:CYS11 3.2 90.3 1.0
CB D:CYS49 3.6 96.1 1.0
CB D:CYS46 3.7 98.5 1.0
N D:CYS46 4.1 90.4 1.0
CB D:LYS87 4.2 102.1 1.0
N D:CYS49 4.4 101.9 1.0
CA D:CYS46 4.4 97.6 1.0
CB D:LYS13 4.5 94.9 1.0
CA D:CYS85 4.6 91.1 1.0
CA D:CYS11 4.6 96.6 1.0
CA D:CYS49 4.6 100.5 1.0
CD D:LYS13 4.8 116.2 1.0
O D:CYS46 4.8 96.9 1.0
C D:CYS46 4.9 97.5 1.0
CG D:LYS13 4.9 105.5 1.0
CG D:LYS87 5.0 99.2 1.0

Zinc binding site 3 out of 3 in 7b0i

Go back to Zinc Binding Sites List in 7b0i
Zinc binding site 3 out of 3 in the Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form II)


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 Spliceostatin A (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1404

b:98.8
occ:1.00
O D:HOH1501 2.1 85.2 1.0
SG D:CYS61 2.3 112.5 1.0
SG D:CYS58 2.3 100.3 1.0
SG D:CYS23 2.3 87.3 1.0
CB D:CYS61 3.3 111.1 1.0
CB D:CYS58 3.4 99.2 1.0
CB D:CYS23 3.6 95.0 1.0
N D:CYS61 3.6 101.9 1.0
CA D:CYS61 4.0 107.5 1.0
SG D:CYS26 4.1 97.2 1.0
N D:CYS23 4.2 89.7 1.0
CB D:ILE60 4.4 96.0 1.0
CA D:CYS23 4.5 95.2 1.0
N D:GLY62 4.5 100.7 1.0
C D:ILE60 4.7 98.9 1.0
C D:CYS61 4.8 104.1 1.0
CA D:CYS58 4.8 90.8 1.0
N D:GLY63 4.9 91.8 1.0
N D:ILE60 4.9 103.8 1.0
CB D:CYS26 4.9 95.2 1.0
CA D:ILE60 4.9 98.8 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: Sat Aug 21 17:59:23 2021

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