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Zinc in PDB 1tb7: Catalytic Domain of Human Phosphodiesterase 4D in Complex with Amp

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

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

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Amp, PDB code: 1tb7 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 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.316, 78.958, 164.740, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.2

Other elements in 1tb7:

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Amp 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 Amp (pdb code 1tb7). 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 Amp, PDB code: 1tb7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1tb7

Go back to Zinc Binding Sites List in 1tb7
Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:13.6
occ:1.00
O A:HOH1190 2.1 12.3 1.0
OD2 A:ASP201 2.1 10.5 1.0
OD1 A:ASP318 2.1 9.7 1.0
O2P A:AMP1003 2.2 11.6 1.0
NE2 A:HIS164 2.2 9.1 1.0
NE2 A:HIS200 2.2 6.7 1.0
CD2 A:HIS200 3.1 8.9 1.0
CG A:ASP318 3.1 12.2 1.0
CG A:ASP201 3.1 10.3 1.0
CD2 A:HIS164 3.2 8.7 1.0
CE1 A:HIS164 3.2 9.8 1.0
CE1 A:HIS200 3.3 9.4 1.0
OD2 A:ASP318 3.3 11.3 1.0
P A:AMP1003 3.3 18.0 1.0
OD1 A:ASP201 3.6 9.6 1.0
MG A:MG1002 3.6 6.4 1.0
O1P A:AMP1003 3.7 14.3 1.0
O A:HOH1005 3.9 11.4 1.0
O5' A:AMP1003 4.2 19.2 1.0
CG A:HIS200 4.3 8.1 1.0
CB A:ASP201 4.3 9.6 1.0
ND1 A:HIS164 4.3 9.9 1.0
CG A:HIS164 4.3 9.5 1.0
ND1 A:HIS200 4.3 10.3 1.0
CB A:ASP318 4.4 11.2 1.0
O3P A:AMP1003 4.5 18.7 1.0
CD2 A:HIS160 4.6 13.4 1.0
O A:HOH1188 4.8 11.5 1.0
CG2 A:VAL168 4.8 11.0 1.0
C5' A:AMP1003 4.9 19.8 1.0
CA A:ASP318 4.9 11.0 1.0

Zinc binding site 2 out of 2 in 1tb7

Go back to Zinc Binding Sites List in 1tb7
Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:15.1
occ:1.00
O B:HOH1175 2.0 13.7 1.0
OD2 B:ASP201 2.1 6.8 1.0
O2P B:AMP1003 2.2 13.1 1.0
OD1 B:ASP318 2.2 8.1 1.0
NE2 B:HIS200 2.2 8.7 1.0
NE2 B:HIS164 2.2 8.6 1.0
CD2 B:HIS200 3.1 8.5 1.0
CG B:ASP201 3.1 8.0 1.0
CG B:ASP318 3.2 9.3 1.0
CD2 B:HIS164 3.2 8.5 1.0
CE1 B:HIS164 3.2 9.4 1.0
CE1 B:HIS200 3.3 8.8 1.0
P B:AMP1003 3.3 18.3 1.0
OD2 B:ASP318 3.4 10.1 1.0
OD1 B:ASP201 3.5 7.2 1.0
O1P B:AMP1003 3.6 15.4 1.0
MG B:MG1002 3.6 7.5 1.0
O B:HOH1004 3.9 11.9 1.0
O5' B:AMP1003 4.2 21.2 1.0
CG B:HIS200 4.3 7.4 1.0
CB B:ASP201 4.3 7.3 1.0
ND1 B:HIS164 4.3 7.4 1.0
CG B:HIS164 4.3 7.9 1.0
ND1 B:HIS200 4.3 8.7 1.0
CB B:ASP318 4.5 9.1 1.0
O3P B:AMP1003 4.5 20.4 1.0
CD2 B:HIS160 4.6 11.4 1.0
C5' B:AMP1003 4.8 22.9 1.0
CG2 B:VAL168 4.8 8.7 1.0
O B:HOH1173 4.8 10.9 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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