Zinc in PDB 6boj: Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004, PDB code: 6boj was solved by D.Fox Iii, J.W.Fairman, M.E.Gurney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.50 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.780, 81.890, 116.790, 90.00, 110.41, 90.00
R / Rfree (%) 16.1 / 18.6

Other elements in 6boj:

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 (pdb code 6boj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004, PDB code: 6boj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6boj

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Zinc binding site 1 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:11.6
occ:1.00
 OD2 A:ASP367 2.1 9.4 1.0
OD1 A:ASP484 2.1 9.4 1.0
NE2 A:HIS330 2.1 11.2 1.0
NE2 A:HIS366 2.1 8.7 1.0
O A:HOH818 2.3 12.0 1.0
O A:HOH963 2.4 14.5 1.0
CG A:ASP484 3.0 12.2 1.0
CD2 A:HIS366 3.0 9.0 1.0
CD2 A:HIS330 3.1 11.6 1.0
CG A:ASP367 3.1 9.2 1.0
CE1 A:HIS330 3.1 11.3 1.0
CE1 A:HIS366 3.1 8.4 1.0
OD2 A:ASP484 3.3 12.9 1.0
OD1 A:ASP367 3.7 9.8 1.0
MG A:MG702 3.9 10.3 1.0
O A:HOH932 4.2 11.8 1.0
CD2 A:HIS326 4.2 11.2 1.0
CG A:HIS366 4.2 7.8 1.0
ND1 A:HIS366 4.2 8.7 1.0
ND1 A:HIS330 4.2 11.1 1.0
CG A:HIS330 4.2 11.0 1.0
O A:HOH1022 4.2 13.2 1.0
CB A:ASP367 4.3 9.2 1.0
CB A:ASP484 4.4 10.8 1.0
NE2 A:HIS326 4.4 11.2 1.0
CG2 A:VAL334 4.6 11.6 1.0
O A:HOH881 4.8 10.9 1.0
CA A:ASP484 4.9 10.8 1.0

Zinc binding site 2 out of 6 in 6boj

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Zinc binding site 2 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:13.8
occ:1.00
 NE2 A:HIS318 2.0 12.0 1.0
O A:HOH810 2.1 20.1 1.0
O A:HOH1047 2.1 18.3 1.0
O A:HOH1061 2.1 24.1 1.0
O C:HOH829 2.1 20.7 1.0
CE1 A:HIS318 2.9 12.6 1.0
CD2 A:HIS318 3.1 12.3 1.0
O C:HOH878 4.0 21.2 1.0
ND1 A:HIS318 4.1 12.7 1.0
OE2 A:GLU409 4.1 16.2 1.0
CG A:HIS318 4.2 12.8 1.0
OD2 C:ASP322 4.2 23.9 1.0
O C:HOH984 4.4 27.6 1.0
CD2 A:LEU406 4.7 12.5 1.0
O C:HOH818 4.9 37.1 1.0
O A:HOH834 5.0 30.0 1.0

Zinc binding site 3 out of 6 in 6boj

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Zinc binding site 3 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:13.9
occ:1.00
 NE2 B:HIS366 2.1 12.5 1.0
OD1 B:ASP484 2.1 12.0 1.0
NE2 B:HIS330 2.1 12.1 1.0
OD2 B:ASP367 2.1 12.1 1.0
O B:HOH1031 2.3 15.0 1.0
O B:HOH1131 2.6 19.5 1.0
CD2 B:HIS366 3.0 11.9 1.0
CG B:ASP484 3.0 14.1 1.0
CD2 B:HIS330 3.1 12.4 1.0
CE1 B:HIS366 3.1 11.4 1.0
CE1 B:HIS330 3.1 12.2 1.0
CG B:ASP367 3.2 11.8 1.0
OD2 B:ASP484 3.3 15.0 1.0
OD1 B:ASP367 3.7 12.8 1.0
MG B:MG702 3.9 10.1 1.0
CG B:HIS366 4.2 10.8 1.0
ND1 B:HIS366 4.2 11.7 1.0
O B:HOH1087 4.2 15.2 1.0
ND1 B:HIS330 4.2 12.1 1.0
O B:HOH1193 4.2 18.8 1.0
CD2 B:HIS326 4.2 13.1 1.0
CG B:HIS330 4.2 12.6 1.0
CB B:ASP367 4.3 11.2 1.0
CB B:ASP484 4.4 13.9 1.0
NE2 B:HIS326 4.5 14.2 1.0
CG2 B:VAL334 4.5 12.5 1.0
O B:HOH1063 4.7 14.1 1.0
CA B:ASP484 4.9 14.2 1.0

Zinc binding site 4 out of 6 in 6boj

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Zinc binding site 4 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:11.9
occ:1.00
 NE2 C:HIS330 2.1 9.6 1.0
OD2 C:ASP367 2.1 9.2 1.0
NE2 C:HIS366 2.1 10.9 1.0
OD1 C:ASP484 2.1 10.3 1.0
O C:HOH840 2.2 13.1 1.0
O C:HOH974 2.4 16.8 1.0
CD2 C:HIS366 3.0 10.6 1.0
CG C:ASP484 3.0 12.2 1.0
CD2 C:HIS330 3.1 9.6 1.0
CE1 C:HIS330 3.1 9.6 1.0
CG C:ASP367 3.1 9.5 1.0
CE1 C:HIS366 3.1 10.4 1.0
OD2 C:ASP484 3.3 13.0 1.0
OD1 C:ASP367 3.7 10.3 1.0
MG C:MG702 3.9 10.3 1.0
O C:HOH939 4.2 12.8 1.0
O C:HOH1034 4.2 15.3 1.0
ND1 C:HIS330 4.2 9.4 1.0
CG C:HIS366 4.2 10.3 1.0
CG C:HIS330 4.2 9.3 1.0
ND1 C:HIS366 4.2 10.6 1.0
CD2 C:HIS326 4.2 10.8 1.0
CB C:ASP367 4.3 9.3 1.0
CB C:ASP484 4.4 11.2 1.0
NE2 C:HIS326 4.5 11.0 1.0
CG2 C:VAL334 4.6 10.1 1.0
O C:HOH868 4.8 11.6 1.0
CA C:ASP484 4.9 10.9 1.0

Zinc binding site 5 out of 6 in 6boj

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Zinc binding site 5 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:14.2
occ:1.00
 OD2 D:ASP367 2.1 12.2 1.0
OD1 D:ASP484 2.1 11.7 1.0
NE2 D:HIS330 2.1 11.7 1.0
NE2 D:HIS366 2.1 11.6 1.0
O D:HOH829 2.3 16.3 1.0
O D:HOH937 2.4 19.7 1.0
CD2 D:HIS366 3.0 11.8 1.0
CD2 D:HIS330 3.1 12.1 1.0
CG D:ASP484 3.1 13.7 1.0
CG D:ASP367 3.1 12.1 1.0
CE1 D:HIS330 3.1 11.6 1.0
CE1 D:HIS366 3.1 11.4 1.0
OD2 D:ASP484 3.4 14.0 1.0
OD1 D:ASP367 3.6 13.0 1.0
MG D:MG702 3.9 11.6 1.0
O D:HOH902 4.2 15.7 1.0
O D:HOH967 4.2 16.5 1.0
CD2 D:HIS326 4.2 14.1 1.0
CG D:HIS366 4.2 10.5 1.0
ND1 D:HIS330 4.2 12.2 1.0
ND1 D:HIS366 4.2 12.0 1.0
CG D:HIS330 4.2 11.7 1.0
CB D:ASP367 4.3 11.3 1.0
CB D:ASP484 4.5 12.6 1.0
NE2 D:HIS326 4.5 14.5 1.0
CG2 D:VAL334 4.6 13.4 1.0
O D:HOH864 4.8 14.3 1.0
CA D:ASP484 4.9 12.6 1.0

Zinc binding site 6 out of 6 in 6boj

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Zinc binding site 6 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn704

b:16.9
occ:1.00
 O D:HOH821 1.9 21.1 1.0
NE2 D:HIS318 2.1 14.2 1.0
O D:HOH1000 2.1 25.4 1.0
O D:HOH1011 2.1 29.2 1.0
O B:HOH1008 2.2 26.1 1.0
CE1 D:HIS318 2.9 16.2 1.0
CD2 D:HIS318 3.1 14.7 1.0
O B:HOH1136 4.1 25.6 1.0
OE2 D:GLU409 4.1 18.4 1.0
ND1 D:HIS318 4.1 14.9 1.0
O D:HOH1030 4.1 30.6 1.0
OD2 B:ASP322 4.2 25.4 1.0
CG D:HIS318 4.2 13.4 1.0
O D:HOH924 4.4 31.8 1.0
O D:HOH808 4.6 33.5 1.0
CD2 D:LEU406 4.7 14.8 1.0

Reference:

C.Zhang, Y.Xu, A.Chowdhary, D.Fox 3Rd., M.E.Gurney, H.T.Zhang, B.D.Auerbach, R.J.Salvi, M.Yang, G.Li, J.M.O'donnell. Memory Enhancing Effects of BPN14770, An Allosteric Inhibitor of Phosphodiesterase-4D, in Wild-Type and Humanized Mice. Neuropsychopharmacology V. 43 2299 2018.
ISSN: ISSN 1740-634X
PubMed: 30131563
DOI: 10.1038/S41386-018-0178-6
Page generated: Wed Dec 16 11:32:52 2020

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