Atomistry » Zinc » PDB 3kee-3kr4 » 3kkt
Atomistry »
  Zinc »
    PDB 3kee-3kr4 »
      3kkt »

Zinc in PDB 3kkt: Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509.

Enzymatic activity of Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509.

All present enzymatic activity of Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509.:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509., PDB code: 3kkt was solved by R.K.Y.Cheng, L.Crawley, J.Barker, M.Whittaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.59 / 2.48
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.740, 89.740, 337.443, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 29.5

Other elements in 3kkt:

The structure of Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509. (pdb code 3kkt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509., PDB code: 3kkt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3kkt

Go back to Zinc Binding Sites List in 3kkt
Zinc binding site 1 out of 2 in the Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509.


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 Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:31.2
occ:1.00
O A:HOH531 2.1 23.1 1.0
O A:HOH530 2.2 17.7 1.0
OD2 A:ASP275 2.2 27.4 1.0
NE2 A:HIS274 2.3 27.8 1.0
OD2 A:ASP392 2.3 33.0 1.0
NE2 A:HIS238 2.4 30.6 1.0
CD2 A:HIS274 3.1 27.2 1.0
CG A:ASP392 3.1 34.1 1.0
CG A:ASP275 3.2 27.8 1.0
OD1 A:ASP392 3.2 34.1 1.0
CE1 A:HIS238 3.2 30.8 1.0
CE1 A:HIS274 3.3 27.9 1.0
CD2 A:HIS238 3.4 30.1 1.0
MG A:MG529 3.5 71.0 1.0
OD1 A:ASP275 3.7 28.8 1.0
O A:HOH8 3.8 36.3 1.0
O A:HOH5 4.0 29.2 1.0
CG A:HIS274 4.3 27.6 1.0
CB A:ASP275 4.3 27.3 1.0
ND1 A:HIS274 4.3 27.6 1.0
CD2 A:HIS234 4.4 23.9 1.0
O A:HOH7 4.4 29.5 1.0
ND1 A:HIS238 4.4 30.7 1.0
NE2 A:HIS234 4.4 23.3 1.0
CB A:ASP392 4.5 34.4 1.0
CG A:HIS238 4.5 30.3 1.0
CG2 A:VAL242 4.8 33.4 1.0

Zinc binding site 2 out of 2 in 3kkt

Go back to Zinc Binding Sites List in 3kkt
Zinc binding site 2 out of 2 in the Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509.


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 Human PDE4B with 5-[3-[(1S,2S,4R)- Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)- Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502- 509. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:31.2
occ:1.00
O B:HOH11 2.1 19.2 1.0
OD2 B:ASP392 2.1 31.9 1.0
OD2 B:ASP275 2.1 24.7 1.0
O B:HOH12 2.3 26.2 1.0
NE2 B:HIS238 2.4 22.3 1.0
NE2 B:HIS274 2.4 20.2 1.0
CG B:ASP392 3.0 31.6 1.0
CD2 B:HIS274 3.1 20.9 1.0
CG B:ASP275 3.2 24.4 1.0
OD1 B:ASP392 3.2 32.2 1.0
CE1 B:HIS238 3.3 22.0 1.0
CD2 B:HIS238 3.3 23.6 1.0
CE1 B:HIS274 3.5 20.8 1.0
OD1 B:ASP275 3.6 25.2 1.0
O B:HOH27 3.7 50.9 1.0
O B:HOH10 3.9 32.5 1.0
MG B:MG530 4.0 53.6 1.0
CD2 B:HIS234 4.2 26.2 1.0
NE2 B:HIS234 4.3 26.4 1.0
CG B:HIS274 4.3 21.9 1.0
CB B:ASP392 4.4 31.4 1.0
CB B:ASP275 4.4 24.3 1.0
ND1 B:HIS238 4.4 24.3 1.0
ND1 B:HIS274 4.5 20.7 1.0
CG B:HIS238 4.5 25.2 1.0
O B:HOH13 4.6 21.5 1.0
CG2 B:VAL242 4.8 29.4 1.0
CA B:ASP392 5.0 31.4 1.0

Reference:

R.K.Y.Cheng, L.Crawley, J.Barker, M.Whittaker. Crystal Structure of Human PDE4B with 5-[3-[(1S,2S,4R)-Bicyclo[2.2.1]Hept-2-Yloxy]-4-Methoxyp Henyl]Tetrahydro-2(1H)-Pyrimidinone Reveals Ordering of the C-Terminal Helix Residues 502-509. To Be Published.
Page generated: Wed Dec 16 04:30:18 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy