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: Sat Aug 21 18:00:02 2021

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