Atomistry » Zinc » PDB 7ax5-7b9h » 7b9c
Atomistry »
  Zinc »
    PDB 7ax5-7b9h »
      7b9c »

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: Thu Aug 21 22:45:43 2025

Last articles

Zn in 7LVS
Zn in 7LW3
Zn in 7LPS
Zn in 7LTL
Zn in 7LUU
Zn in 7LUP
Zn in 7LT9
Zn in 7LTG
Zn in 7LTK
Zn in 7LRE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy