Zinc in PDB 7lrd: Cryo-Em of the SLFN12-PDE3A Complex: Consensus Subset Model

Enzymatic activity of Cryo-Em of the SLFN12-PDE3A Complex: Consensus Subset Model

All present enzymatic activity of Cryo-Em of the SLFN12-PDE3A Complex: Consensus Subset Model:
3.1.4.17;

Other elements in 7lrd:

The structure of Cryo-Em of the SLFN12-PDE3A Complex: Consensus Subset Model also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em of the SLFN12-PDE3A Complex: Consensus Subset Model (pdb code 7lrd). 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 of the SLFN12-PDE3A Complex: Consensus Subset Model, PDB code: 7lrd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7lrd

Go back to Zinc Binding Sites List in 7lrd
Zinc binding site 1 out of 2 in the Cryo-Em of the SLFN12-PDE3A Complex: Consensus Subset Model


Mono view


Stereo pair view

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

b:57.1
occ:1.00
ND1 A:HIS275 2.1 40.5 1.0
SG A:CYS277 2.3 52.3 1.0
SG A:CYS311 2.3 41.1 1.0
SG A:CYS312 2.3 39.9 1.0
CE1 A:HIS275 2.9 40.5 1.0
CG A:HIS275 3.2 40.5 1.0
CB A:CYS312 3.3 39.9 1.0
CB A:CYS311 3.5 41.1 1.0
CB A:CYS277 3.7 52.3 1.0
CB A:HIS275 3.7 40.5 1.0
N A:CYS312 3.9 39.9 1.0
CA A:HIS275 4.0 40.5 1.0
C A:CYS311 4.1 41.1 1.0
NE2 A:HIS275 4.1 40.5 1.0
N A:CYS277 4.1 52.3 1.0
CD2 A:HIS275 4.2 40.5 1.0
CA A:CYS312 4.2 39.9 1.0
N A:PHE276 4.3 42.6 1.0
CA A:CYS311 4.4 41.1 1.0
O A:GLU279 4.4 58.0 1.0
CA A:CYS277 4.5 52.3 1.0
O A:CYS311 4.5 41.1 1.0
C A:HIS275 4.6 40.5 1.0
CE2 A:PHE310 4.7 37.1 1.0

Zinc binding site 2 out of 2 in 7lrd

Go back to Zinc Binding Sites List in 7lrd
Zinc binding site 2 out of 2 in the Cryo-Em of the SLFN12-PDE3A Complex: Consensus Subset Model


Mono view


Stereo pair view

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

b:57.2
occ:1.00
ND1 C:HIS275 2.1 41.2 1.0
SG C:CYS277 2.3 53.5 1.0
SG C:CYS311 2.3 41.6 1.0
SG C:CYS312 2.3 40.3 1.0
CE1 C:HIS275 2.9 41.2 1.0
CG C:HIS275 3.2 41.2 1.0
CB C:CYS312 3.3 40.3 1.0
CB C:CYS311 3.5 41.6 1.0
CB C:CYS277 3.7 53.5 1.0
CB C:HIS275 3.7 41.2 1.0
N C:CYS312 3.9 40.3 1.0
CA C:HIS275 4.0 41.2 1.0
C C:CYS311 4.1 41.6 1.0
NE2 C:HIS275 4.1 41.2 1.0
N C:CYS277 4.1 53.5 1.0
CD2 C:HIS275 4.2 41.2 1.0
CA C:CYS312 4.2 40.3 1.0
N C:PHE276 4.3 43.1 1.0
CA C:CYS311 4.4 41.6 1.0
O C:GLU279 4.4 59.4 1.0
CA C:CYS277 4.5 53.5 1.0
O C:CYS311 4.5 41.6 1.0
C C:HIS275 4.6 41.2 1.0
CE2 C:PHE310 4.7 37.5 1.0

Reference:

C.W.Garvie, J.R.Fuller, C.W.Garvie, C.T.Lemke. N/A N/A.
Page generated: Mon Jul 12 17:23:23 2021

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