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Zinc in PDB 1xm6: Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram, PDB code: 1xm6 was solved by G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.71 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.221, 94.062, 105.236, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22.7

Other elements in 1xm6:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram 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 4B in Complex with (R)- Mesopram (pdb code 1xm6). 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 4B in Complex with (R)- Mesopram, PDB code: 1xm6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1xm6

Go back to Zinc Binding Sites List in 1xm6
Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram


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 4B in Complex with (R)- Mesopram within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:31.1
occ:1.00
O A:HOH1008 2.0 28.2 1.0
OD2 A:ASP275 2.1 21.1 1.0
OD2 A:ASP392 2.2 20.5 1.0
O A:HOH1009 2.2 24.9 1.0
NE2 A:HIS238 2.2 25.3 1.0
NE2 A:HIS274 2.2 20.9 1.0
CD2 A:HIS274 3.1 22.2 1.0
CG A:ASP392 3.1 22.9 1.0
CG A:ASP275 3.1 21.4 1.0
CD2 A:HIS238 3.2 22.9 1.0
CE1 A:HIS238 3.2 24.5 1.0
CE1 A:HIS274 3.3 21.5 1.0
OD1 A:ASP392 3.3 23.9 1.0
OD1 A:ASP275 3.6 22.8 1.0
MG A:MG1002 3.7 21.3 1.0
O A:HOH1007 4.0 24.0 1.0
O A:HOH1012 4.0 25.5 1.0
CD2 A:HIS234 4.3 23.6 1.0
CG A:HIS274 4.3 20.5 1.0
ND1 A:HIS238 4.3 20.5 1.0
CG A:HIS238 4.3 21.8 1.0
O A:HOH1028 4.3 30.1 1.0
ND1 A:HIS274 4.4 21.6 1.0
CB A:ASP275 4.4 21.9 1.0
NE2 A:HIS234 4.5 23.2 1.0
CB A:ASP392 4.5 23.1 1.0
O A:HOH1005 4.7 24.8 1.0
CG2 A:VAL242 4.7 20.1 1.0

Zinc binding site 2 out of 2 in 1xm6

Go back to Zinc Binding Sites List in 1xm6
Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram


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 4B in Complex with (R)- Mesopram within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:31.2
occ:1.00
O B:HOH2007 2.0 25.5 1.0
OD2 B:ASP392 2.0 20.0 1.0
OD2 B:ASP275 2.1 20.1 1.0
NE2 B:HIS238 2.2 20.6 1.0
NE2 B:HIS274 2.2 20.3 1.0
O B:HOH2008 2.3 28.8 1.0
CG B:ASP392 3.0 23.3 1.0
CD2 B:HIS274 3.1 23.2 1.0
CG B:ASP275 3.1 20.5 1.0
CD2 B:HIS238 3.2 22.1 1.0
CE1 B:HIS238 3.2 22.4 1.0
OD1 B:ASP392 3.3 25.6 1.0
CE1 B:HIS274 3.3 21.7 1.0
OD1 B:ASP275 3.5 22.2 1.0
MG B:MG1002 3.6 22.7 1.0
O B:HOH2006 4.0 28.5 1.0
O B:HOH2009 4.1 27.4 1.0
CD2 B:HIS234 4.2 20.7 1.0
CG B:HIS274 4.3 19.7 1.0
ND1 B:HIS238 4.3 18.9 1.0
CG B:HIS238 4.3 20.8 1.0
O B:HOH2049 4.3 32.8 1.0
CB B:ASP392 4.4 22.9 1.0
CB B:ASP275 4.4 21.1 1.0
ND1 B:HIS274 4.4 22.2 1.0
NE2 B:HIS234 4.5 22.3 1.0
O B:HOH2004 4.8 26.9 1.0
CG2 B:VAL242 4.8 23.2 1.0
CA B:ASP392 5.0 22.2 1.0

Reference:

G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang. Structural Basis For the Activity of Drugs That Inhibit Phosphodiesterases. Structure V. 12 2233 2004.
ISSN: ISSN 0969-2126
PubMed: 15576036
DOI: 10.1016/J.STR.2004.10.004
Page generated: Wed Dec 16 03:12:33 2020

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