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Zinc in PDB 1tbb: Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram, PDB code: 1tbb was solved by K.Y.J.Zhang, G.L.Card, Y.Suzuki, D.R.Artis, D.Fong, S.Gillette, D.Hsieh, J.Neiman, B.L.West, C.Zhang, M.V.Milburn, S.-H.Kim, J.Schlessinger, G.Bollag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.65 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.106, 79.019, 164.548, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 20.4

Other elements in 1tbb:

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram (pdb code 1tbb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram, PDB code: 1tbb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1tbb

Go back to Zinc Binding Sites List in 1tbb
Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:20.6
occ:1.00
O A:HOH1225 1.9 19.5 1.0
OD1 A:ASP318 2.1 6.6 1.0
OD2 A:ASP201 2.2 7.6 1.0
O A:HOH1226 2.2 16.3 1.0
NE2 A:HIS200 2.2 2.8 1.0
NE2 A:HIS164 2.3 10.2 1.0
CD2 A:HIS200 3.0 4.8 1.0
CG A:ASP318 3.1 8.3 1.0
CE1 A:HIS164 3.1 6.0 1.0
CG A:ASP201 3.2 8.8 1.0
CD2 A:HIS164 3.3 10.6 1.0
OD2 A:ASP318 3.3 11.8 1.0
CE1 A:HIS200 3.4 6.4 1.0
OD1 A:ASP201 3.6 6.8 1.0
MG A:MG1002 3.6 15.7 1.0
O A:HOH1224 3.9 18.2 1.0
O A:HOH1019 4.0 24.8 1.0
CG A:HIS200 4.2 5.8 1.0
ND1 A:HIS164 4.3 8.7 1.0
CD2 A:HIS160 4.3 10.1 1.0
CG A:HIS164 4.3 7.5 1.0
CB A:ASP201 4.4 7.4 1.0
ND1 A:HIS200 4.4 6.3 1.0
CB A:ASP318 4.5 8.5 1.0
NE2 A:HIS160 4.6 10.9 1.0
CG2 A:VAL168 4.7 6.0 1.0
O A:HOH1222 4.8 17.0 1.0
CA A:ASP318 5.0 8.4 1.0

Zinc binding site 2 out of 2 in 1tbb

Go back to Zinc Binding Sites List in 1tbb
Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:22.2
occ:1.00
O B:HOH1220 2.0 18.9 1.0
OD2 B:ASP201 2.1 6.5 1.0
O B:HOH1221 2.2 17.9 1.0
NE2 B:HIS200 2.2 4.7 1.0
OD1 B:ASP318 2.2 8.2 1.0
NE2 B:HIS164 2.3 4.5 1.0
CD2 B:HIS200 3.0 5.5 1.0
CG B:ASP201 3.1 6.5 1.0
CG B:ASP318 3.2 8.3 1.0
CD2 B:HIS164 3.2 5.1 1.0
CE1 B:HIS164 3.2 6.0 1.0
CE1 B:HIS200 3.3 6.5 1.0
OD2 B:ASP318 3.4 11.4 1.0
OD1 B:ASP201 3.6 4.8 1.0
MG B:MG1002 3.7 16.3 1.0
O B:HOH1219 3.9 18.9 1.0
O B:HOH1018 4.1 23.8 1.0
ND1 B:HIS160 4.2 10.8 1.0
CG B:HIS200 4.2 6.2 1.0
O B:HOH1072 4.3 39.0 1.0
CB B:ASP201 4.3 5.8 1.0
ND1 B:HIS200 4.3 6.5 1.0
ND1 B:HIS164 4.4 5.5 1.0
CG B:HIS164 4.4 5.8 1.0
CE1 B:HIS160 4.4 6.1 1.0
CB B:ASP318 4.5 7.2 1.0
CG2 B:VAL168 4.8 5.7 1.0
O B:HOH1217 4.8 17.8 1.0
CA B:ASP318 5.0 7.6 1.0

Reference:

K.Y.J.Zhang, G.L.Card, Y.Suzuki, D.R.Artis, D.Fong, S.Gillette, D.Hsieh, J.Neiman, B.L.West, C.Zhang, M.V.Milburn, S.-H.Kim, J.Schlessinger, G.Bollag. A Glutamine Switch Mechanism For Nucleotide Selectivity By Phosphodiesterases Mol.Cell V. 15 279 2004.
ISSN: ISSN 1097-2765
PubMed: 15260978
DOI: 10.1016/J.MOLCEL.2004.07.005
Page generated: Mon Jan 25 16:13:53 2021

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