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Zinc in PDB 1ro9: Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp

Enzymatic activity of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp

All present enzymatic activity of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp, PDB code: 1ro9 was solved by R.X.Xu, W.J.Rocque, M.H.Lambert, D.E.Vanderwall, R.T.Nolte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.13
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 104.332, 159.211, 108.651, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.4

Other elements in 1ro9:

The structure of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp (pdb code 1ro9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp, PDB code: 1ro9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ro9

Go back to Zinc Binding Sites List in 1ro9
Zinc binding site 1 out of 4 in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn529

b:35.3
occ:1.00
 NE2 A:HIS238 2.0 20.3 1.0
NE2 A:HIS274 2.1 19.8 1.0
OD1 A:ASP392 2.2 23.9 1.0
OD2 A:ASP275 2.2 21.1 1.0
O3P A:8BR531 2.9 66.3 1.0
CE1 A:HIS238 2.9 20.2 1.0
CD2 A:HIS238 3.0 19.1 1.0
CG A:ASP392 3.1 25.6 1.0
CD2 A:HIS274 3.1 17.6 1.0
CE1 A:HIS274 3.1 19.6 1.0
CG A:ASP275 3.3 20.5 1.0
OD2 A:ASP392 3.3 24.8 1.0
OD1 A:ASP275 3.8 20.7 1.0
P A:8BR531 3.9 65.7 1.0
O1P A:8BR531 3.9 67.3 1.0
ZN A:ZN530 4.0 58.8 1.0
ND1 A:HIS238 4.1 19.6 1.0
CG A:HIS238 4.2 20.3 1.0
ND1 A:HIS274 4.3 18.6 1.0
CG A:HIS274 4.3 18.4 1.0
O2P A:8BR531 4.3 67.1 1.0
CD2 A:HIS234 4.3 22.6 1.0
CB A:ASP392 4.4 24.3 1.0
CB A:ASP275 4.4 19.9 1.0
CG2 A:VAL242 4.6 25.6 1.0
NE2 A:HIS234 4.8 23.6 1.0
O A:HOH549 4.9 22.7 1.0
CA A:ASP392 4.9 24.8 1.0

Zinc binding site 2 out of 4 in 1ro9

Go back to Zinc Binding Sites List in 1ro9
Zinc binding site 2 out of 4 in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn530

b:58.8
occ:1.00
 O A:HOH549 2.3 22.7 1.0
O A:HOH658 2.4 27.0 1.0
OD1 A:ASP275 2.4 20.7 1.0
O A:HOH553 2.5 21.6 1.0
O3P A:8BR531 3.3 66.3 1.0
CG A:ASP275 3.4 20.5 1.0
OD2 A:ASP275 3.5 21.1 1.0
O A:HOH572 3.6 36.9 1.0
ZN A:ZN529 4.0 35.3 1.0
O A:HOH651 4.3 43.5 1.0
CD2 A:HIS234 4.4 22.6 1.0
NE2 A:HIS307 4.4 22.7 1.0
OE2 A:GLU304 4.4 24.6 1.0
NE2 A:HIS234 4.4 23.6 1.0
CD2 A:HIS274 4.5 17.6 1.0
O A:HIS274 4.5 19.9 1.0
P A:8BR531 4.5 65.7 1.0
CD2 A:HIS278 4.5 20.1 1.0
OG1 A:THR345 4.6 24.4 1.0
O A:HOH669 4.6 33.2 1.0
O A:THR345 4.6 26.9 1.0
OD2 A:ASP392 4.7 24.8 1.0
CD2 A:HIS307 4.7 21.3 1.0
O2P A:8BR531 4.8 67.1 1.0
CB A:ASP275 4.8 19.9 1.0
NE2 A:HIS278 4.8 20.1 1.0
NE2 A:HIS274 4.8 19.8 1.0
CB A:THR345 4.9 26.7 1.0

Zinc binding site 3 out of 4 in 1ro9

Go back to Zinc Binding Sites List in 1ro9
Zinc binding site 3 out of 4 in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn529

b:39.5
occ:1.00
 NE2 B:HIS238 2.0 24.6 1.0
NE2 B:HIS274 2.2 21.8 1.0
OD1 B:ASP392 2.2 29.5 1.0
OD2 B:ASP275 2.2 27.5 1.0
CE1 B:HIS238 3.0 24.9 1.0
CD2 B:HIS238 3.0 25.8 1.0
O2P B:8BR531 3.0 84.2 1.0
CD2 B:HIS274 3.1 21.0 1.0
CG B:ASP392 3.1 31.5 1.0
CG B:ASP275 3.1 25.3 1.0
CE1 B:HIS274 3.2 21.5 1.0
OD2 B:ASP392 3.3 32.4 1.0
O3P B:8BR531 3.4 84.7 1.0
OD1 B:ASP275 3.6 26.8 1.0
P B:8BR531 3.6 84.0 1.0
O1P B:8BR531 3.9 84.8 1.0
ZN B:ZN530 4.0 61.3 1.0
ND1 B:HIS238 4.1 24.5 1.0
CD2 B:HIS234 4.1 31.6 1.0
CG B:HIS238 4.2 25.2 1.0
CG B:HIS274 4.3 21.3 1.0
ND1 B:HIS274 4.3 21.2 1.0
CB B:ASP275 4.3 25.3 1.0
CB B:ASP392 4.5 30.4 1.0
NE2 B:HIS234 4.5 32.2 1.0
CG2 B:VAL242 4.6 33.0 1.0
O B:HOH588 4.6 49.7 1.0
CA B:ASP392 5.0 31.1 1.0

Zinc binding site 4 out of 4 in 1ro9

Go back to Zinc Binding Sites List in 1ro9
Zinc binding site 4 out of 4 in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with 8-Br-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn530

b:61.3
occ:1.00
 O B:HOH545 2.3 23.5 1.0
O B:HOH533 2.4 28.2 1.0
OD1 B:ASP275 2.5 26.8 1.0
O B:HOH550 2.6 27.5 1.0
O3P B:8BR531 2.8 84.7 1.0
CG B:ASP275 3.5 25.3 1.0
OD2 B:ASP275 3.8 27.5 1.0
ZN B:ZN529 4.0 39.5 1.0
O B:HOH590 4.1 41.0 1.0
P B:8BR531 4.2 84.0 1.0
OE2 B:GLU304 4.2 31.1 1.0
NE2 B:HIS307 4.2 24.9 1.0
OG1 B:THR345 4.4 31.5 1.0
O B:HIS274 4.5 24.8 1.0
O B:THR345 4.5 29.7 1.0
O1P B:8BR531 4.5 84.8 1.0
O B:HOH592 4.5 39.1 1.0
CD2 B:HIS274 4.5 21.0 1.0
CD2 B:HIS307 4.6 24.4 1.0
CD2 B:HIS278 4.6 29.3 1.0
NE2 B:HIS234 4.6 32.2 1.0
CD2 B:HIS234 4.6 31.6 1.0
OD2 B:ASP392 4.7 32.4 1.0
CB B:THR345 4.8 30.3 1.0
NE2 B:HIS278 4.8 29.9 1.0
CB B:ASP275 4.9 25.3 1.0
O2P B:8BR531 4.9 84.2 1.0
NE2 B:HIS274 4.9 21.8 1.0

Reference:

R.X.Xu, W.J.Rocque, M.H.Lambert, D.E.Vanderwall, M.A.Luther, R.T.Nolte. Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B Complexed with Amp, 8-Br-Amp, and Rolipram. J.Mol.Biol. V. 337 355 2004.
ISSN: ISSN 0022-2836
PubMed: 15003452
DOI: 10.1016/J.JMB.2004.01.040
Page generated: Wed Oct 16 18:38:08 2024

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