Zinc in PDB 7eg4: Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex

Enzymatic activity of Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex

All present enzymatic activity of Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex:
3.1.4.17;

Other elements in 7eg4:

The structure of Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex (pdb code 7eg4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex, PDB code: 7eg4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7eg4

Go back to Zinc Binding Sites List in 7eg4
Zinc binding site 1 out of 2 in the Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:86.3
occ:1.00
ND1 D:HIS275 2.1 47.4 1.0
SG D:CYS312 2.4 45.9 1.0
SG D:CYS277 2.4 63.6 1.0
SG D:CYS311 2.4 50.5 1.0
CG D:HIS275 2.9 47.4 1.0
CB D:HIS275 3.0 47.4 1.0
CB D:CYS312 3.2 45.9 1.0
CA D:HIS275 3.2 47.4 1.0
CE1 D:HIS275 3.3 47.4 1.0
CB D:CYS311 3.7 50.5 1.0
CB D:CYS277 3.8 63.6 1.0
N D:PHE276 3.9 46.8 1.0
N D:CYS312 3.9 45.9 1.0
N D:CYS277 4.0 63.6 1.0
C D:HIS275 4.0 47.4 1.0
C D:CYS311 4.0 50.5 1.0
CD2 D:HIS275 4.1 47.4 1.0
CA D:CYS312 4.2 45.9 1.0
NE2 D:HIS275 4.3 47.4 1.0
N D:HIS275 4.4 47.4 1.0
O D:CYS311 4.4 50.5 1.0
CA D:CYS311 4.5 50.5 1.0
CA D:CYS277 4.5 63.6 1.0
O D:HIS274 4.6 38.5 1.0
O D:GLU279 4.7 72.3 1.0
CE2 D:PHE310 4.7 47.2 1.0
C D:HIS274 4.9 38.5 1.0
C D:PHE276 5.0 46.8 1.0
CA D:PHE276 5.0 46.8 1.0

Zinc binding site 2 out of 2 in 7eg4

Go back to Zinc Binding Sites List in 7eg4
Zinc binding site 2 out of 2 in the Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:86.3
occ:1.00
ND1 B:HIS275 2.1 47.4 1.0
SG B:CYS312 2.4 45.9 1.0
SG B:CYS277 2.4 63.6 1.0
SG B:CYS311 2.4 50.5 1.0
CG B:HIS275 2.9 47.4 1.0
CB B:HIS275 3.0 47.4 1.0
CB B:CYS312 3.2 45.9 1.0
CA B:HIS275 3.2 47.4 1.0
CE1 B:HIS275 3.3 47.4 1.0
CB B:CYS311 3.7 50.5 1.0
CB B:CYS277 3.8 63.6 1.0
N B:PHE276 3.9 46.8 1.0
N B:CYS312 3.9 45.9 1.0
N B:CYS277 4.0 63.6 1.0
C B:HIS275 4.0 47.4 1.0
C B:CYS311 4.0 50.5 1.0
CD2 B:HIS275 4.1 47.4 1.0
CA B:CYS312 4.2 45.9 1.0
NE2 B:HIS275 4.3 47.4 1.0
N B:HIS275 4.4 47.4 1.0
O B:CYS311 4.4 50.5 1.0
CA B:CYS311 4.5 50.5 1.0
CA B:CYS277 4.5 63.6 1.0
O B:HIS274 4.6 38.5 1.0
O B:GLU279 4.7 72.3 1.0
CE2 B:PHE310 4.7 47.2 1.0
C B:HIS274 4.9 38.5 1.0
C B:PHE276 5.0 46.8 1.0
CA B:PHE276 5.0 46.8 1.0

Reference:

J.Chen, N.Liu, L.Dianrong, W.Yuanxun, S.Yuxing, W.Qingcui, H.Yinpin, H.W.Wang, H.Niu, Q.Xiangbing, X.D.Wang. Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Fri Nov 5 16:51:07 2021

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