Zinc in PDB 7b9c: Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form I)

Protein crystallography data

The structure of Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form I), PDB code: 7b9c 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) 49.75 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 108.573, 111.066, 248.757, 90, 90, 90
R / Rfree (%) 21.6 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Minimal SF3B Core in Complex with Spliceostatin A (Form I) (pdb code 7b9c). 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 I), PDB code: 7b9c:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7b9c

Go back to Zinc Binding Sites List in 7b9c
Zinc binding site 1 out of 3 in the Structure of A Minimal SF3B Core in Complex with Spliceostatin A (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 Spliceostatin A (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:61.3
occ:1.00
SG D:CYS46 2.1 64.1 1.0
SG D:CYS49 2.3 63.0 1.0
SG D:CYS85 2.4 59.6 1.0
SG D:CYS11 2.4 55.9 1.0
CB D:CYS46 3.0 55.7 1.0
CB D:CYS85 3.2 55.0 1.0
CB D:CYS11 3.3 56.6 1.0
CB D:CYS49 3.4 64.2 1.0
N D:CYS46 3.8 48.9 1.0
CA D:CYS46 4.0 58.9 1.0
N D:CYS49 4.4 72.8 1.0
CB D:LYS87 4.4 56.9 1.0
CB D:LYS13 4.4 64.3 1.0
CA D:CYS49 4.5 71.3 1.0
CD D:LYS13 4.5 71.3 1.0
C D:CYS46 4.7 57.0 1.0
CA D:CYS85 4.7 59.6 1.0
CA D:CYS11 4.7 54.4 1.0
O D:CYS46 4.8 54.7 1.0
CG D:LYS13 4.9 58.1 1.0
O D:CYS85 4.9 60.0 1.0
N D:LYS13 4.9 56.1 1.0

Zinc binding site 2 out of 3 in 7b9c

Go back to Zinc Binding Sites List in 7b9c
Zinc binding site 2 out of 3 in the Structure of A Minimal SF3B Core in Complex with Spliceostatin A (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 Spliceostatin A (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn102

b:53.6
occ:1.00
SG D:CYS33 2.2 51.9 1.0
SG D:CYS72 2.2 55.8 1.0
SG D:CYS75 2.4 54.2 1.0
SG D:CYS30 2.4 55.1 1.0
CB D:CYS72 3.2 41.4 1.0
CB D:CYS33 3.2 43.9 1.0
CB D:CYS75 3.4 52.5 1.0
CB D:CYS30 3.5 53.0 1.0
N D:CYS72 3.7 52.1 1.0
N D:CYS33 3.7 57.4 1.0
CA D:CYS72 4.0 49.3 1.0
CA D:CYS33 4.0 55.7 1.0
N D:CYS75 4.2 46.2 1.0
CA D:CYS75 4.4 48.4 1.0
CB D:ILE32 4.5 51.3 1.0
C D:CYS72 4.6 53.6 1.0
C D:CYS33 4.7 53.5 1.0
C D:ILE32 4.7 59.0 1.0
O D:CYS72 4.8 53.2 1.0
CA D:CYS30 4.9 53.4 1.0
C D:TYR71 4.9 50.8 1.0
CB D:SER35 4.9 55.4 1.0
O C:HOH1412 5.0 62.7 1.0
CA D:ILE32 5.0 51.9 1.0

Zinc binding site 3 out of 3 in 7b9c

Go back to Zinc Binding Sites List in 7b9c
Zinc binding site 3 out of 3 in the Structure of A Minimal SF3B Core in Complex with Spliceostatin A (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 Spliceostatin A (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn103

b:57.9
occ:1.00
SG D:CYS23 2.3 54.9 1.0
SG D:CYS61 2.3 65.5 1.0
SG D:CYS58 2.4 57.7 1.0
CB D:CYS61 3.3 54.8 1.0
CB D:CYS58 3.3 59.0 1.0
CB D:CYS23 3.4 56.6 1.0
S D:SCN104 3.5 73.4 1.0
N D:CYS61 3.7 62.7 1.0
CA D:CYS61 4.1 62.9 1.0
N D:CYS23 4.2 48.4 1.0
SG D:CYS26 4.2 58.5 1.0
CB D:ILE60 4.3 66.3 1.0
CA D:CYS23 4.4 63.0 1.0
C D:ILE60 4.6 62.9 1.0
CA D:CYS58 4.8 57.7 1.0
CA D:ILE60 4.8 60.6 1.0
N D:ILE60 4.9 56.3 1.0
C D:CYS61 4.9 68.3 1.0
CG1 D:ILE60 5.0 60.4 1.0
NZ D:LYS25 5.0 92.0 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 18:00:11 2021

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