Atomistry » Zinc » PDB 7b8e-7bos » 7b92
Atomistry »
  Zinc »
    PDB 7b8e-7bos »
      7b92 »

Zinc in PDB 7b92: Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form II)

Protein crystallography data

The structure of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form II), PDB code: 7b92 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) 46.52 / 3.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.429, 107.429, 361.474, 90, 90, 120
R / Rfree (%) 22.3 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form II) (pdb code 7b92). 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 II), PDB code: 7b92:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7b92

Go back to Zinc Binding Sites List in 7b92
Zinc binding site 1 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (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 Sudemycin D6 (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:78.4
occ:1.00
SG D:CYS49 2.2 81.4 1.0
SG D:CYS11 2.3 69.4 1.0
SG D:CYS46 2.3 72.2 1.0
SG D:CYS85 2.7 83.6 1.0
CB D:CYS11 3.1 74.1 1.0
CB D:CYS85 3.3 74.9 1.0
CB D:CYS49 3.3 83.3 1.0
CB D:CYS46 3.7 79.0 1.0
CB D:LYS87 4.1 75.7 1.0
N D:CYS46 4.1 77.4 1.0
N D:CYS49 4.4 85.6 1.0
CA D:CYS46 4.4 79.0 1.0
CA D:CYS49 4.5 81.8 1.0
CA D:CYS11 4.6 83.1 1.0
CB D:LYS13 4.6 82.7 1.0
O D:CYS46 4.7 79.1 1.0
CA D:CYS85 4.8 67.3 1.0
CG D:LYS87 4.8 82.3 1.0
C D:CYS46 4.9 80.6 1.0
CD D:LYS13 4.9 75.1 1.0

Zinc binding site 2 out of 3 in 7b92

Go back to Zinc Binding Sites List in 7b92
Zinc binding site 2 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (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 Sudemycin D6 (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn102

b:69.7
occ:1.00
SG D:CYS75 2.3 74.7 1.0
SG D:CYS33 2.4 75.7 1.0
SG D:CYS72 2.4 67.4 1.0
SG D:CYS30 2.5 81.3 1.0
CB D:CYS75 3.4 70.4 1.0
CB D:CYS72 3.4 55.8 1.0
CB D:CYS33 3.4 81.4 1.0
CB D:CYS30 3.6 76.9 1.0
N D:CYS33 3.7 77.4 1.0
N D:CYS72 3.7 73.3 1.0
CA D:CYS72 4.1 65.6 1.0
CA D:CYS33 4.1 78.1 1.0
N D:CYS75 4.2 75.3 1.0
CB D:ILE32 4.3 75.0 1.0
CA D:CYS75 4.4 69.3 1.0
C D:ILE32 4.7 77.0 1.0
N D:ILE32 4.7 71.5 1.0
CA D:ILE32 4.8 74.9 1.0
C D:CYS72 4.8 70.3 1.0
C D:CYS33 4.8 81.0 1.0
CG2 D:ILE32 4.8 76.0 1.0
O D:CYS72 4.8 70.3 1.0
C D:TYR71 4.8 69.3 1.0
CA D:CYS30 5.0 71.5 1.0
CB D:SER35 5.0 80.0 1.0

Zinc binding site 3 out of 3 in 7b92

Go back to Zinc Binding Sites List in 7b92
Zinc binding site 3 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (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 Sudemycin D6 (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn103

b:97.9
occ:1.00
O D:HOH201 2.1 97.2 1.0
SG D:CYS61 2.3 101.2 1.0
SG D:CYS23 2.3 89.2 1.0
SG D:CYS58 2.7 84.5 1.0
CB D:CYS61 2.7 103.1 1.0
N D:CYS61 3.5 99.3 1.0
CA D:CYS61 3.7 106.8 1.0
CB D:CYS58 3.8 89.8 1.0
CB D:CYS23 3.8 93.9 1.0
N D:GLY62 4.3 101.2 1.0
CD D:LYS25 4.3 107.7 1.0
CB D:CYS26 4.4 94.3 1.0
C D:CYS61 4.5 107.2 1.0
CG D:LYS25 4.6 108.3 1.0
N D:CYS23 4.6 80.7 1.0
N D:CYS26 4.7 100.5 1.0
C D:ILE60 4.7 97.7 1.0
CB D:ILE60 4.7 85.2 1.0
CB D:LYS25 4.7 109.2 1.0
NZ D:LYS25 4.8 110.8 1.0
CA D:CYS23 4.8 87.1 1.0
N D:GLY63 4.8 100.5 1.0
C2 D:T2W104 5.0 101.5 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: Tue Oct 29 17:32:04 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy