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Zinc in PDB 1mkd: Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex

Enzymatic activity of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex, PDB code: 1mkd was solved by M.E.Lee, J.Markowitz, J.-O.Lee, H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.325, 164.572, 325.540, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 26

Other elements in 1mkd:

The structure of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex also contains other interesting chemical elements:

Fluorine (F) 24 atoms
Magnesium (Mg) 12 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex (pdb code 1mkd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex, PDB code: 1mkd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 1mkd

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Zinc binding site 1 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:30.6
occ:1.00
 OD2 A:ASP298 2.1 34.6 1.0
OD1 A:ASP415 2.2 34.5 1.0
NE2 A:HIS297 2.3 26.2 1.0
NE2 A:HIS261 2.4 33.0 1.0
CG A:ASP415 3.0 33.2 1.0
OD2 A:ASP415 3.0 33.9 1.0
O A:HOH1001 3.1 1.1 1.0
CD2 A:HIS297 3.2 28.1 1.0
CG A:ASP298 3.2 32.3 1.0
CD2 A:HIS261 3.3 32.6 1.0
CE1 A:HIS261 3.3 31.9 1.0
CE1 A:HIS297 3.4 26.1 1.0
OD1 A:ASP298 3.7 36.9 1.0
MG A:MG2002 4.0 21.8 1.0
CD2 A:HIS257 4.1 32.2 1.0
CG A:HIS297 4.4 27.1 1.0
CB A:ASP415 4.4 31.8 1.0
CB A:ASP298 4.4 29.5 1.0
ND1 A:HIS261 4.5 31.1 1.0
ND1 A:HIS297 4.5 26.0 1.0
CG A:HIS261 4.5 31.2 1.0
NE2 A:HIS257 4.5 32.2 1.0
O A:ASP415 4.9 33.0 1.0
CG2 A:VAL265 5.0 27.7 1.0

Zinc binding site 2 out of 12 in 1mkd

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Zinc binding site 2 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


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 PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2003

b:31.5
occ:1.00
 OD1 B:ASP415 2.1 36.0 1.0
OD2 B:ASP298 2.2 33.5 1.0
NE2 B:HIS297 2.3 19.1 1.0
NE2 B:HIS261 2.3 26.9 1.0
CG B:ASP415 2.9 32.4 1.0
OD2 B:ASP415 3.0 33.9 1.0
O B:HOH1002 3.1 1.1 1.0
CD2 B:HIS297 3.2 22.7 1.0
CE1 B:HIS261 3.3 27.7 1.0
CD2 B:HIS261 3.3 30.4 1.0
CG B:ASP298 3.3 31.1 1.0
CE1 B:HIS297 3.3 22.6 1.0
MG B:MG2004 3.5 21.8 1.0
OD1 B:ASP298 3.8 34.9 1.0
CD2 B:HIS257 4.2 31.4 1.0
CB B:ASP415 4.4 31.1 1.0
CG B:HIS297 4.4 23.0 1.0
ND1 B:HIS261 4.4 28.1 1.0
ND1 B:HIS297 4.4 22.3 1.0
CG B:HIS261 4.4 30.2 1.0
CB B:ASP298 4.5 29.3 1.0
NE2 B:HIS257 4.6 31.9 1.0
O B:ASP415 4.8 30.0 1.0
CG2 B:VAL265 4.9 26.1 1.0
CA B:ASP415 4.9 30.7 1.0

Zinc binding site 3 out of 12 in 1mkd

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Zinc binding site 3 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2005

b:39.4
occ:1.00
 OD2 C:ASP298 2.0 35.3 1.0
OD1 C:ASP415 2.2 30.7 1.0
NE2 C:HIS297 2.2 26.8 1.0
NE2 C:HIS261 2.4 30.3 1.0
CG C:ASP415 2.9 29.6 1.0
OD2 C:ASP415 3.0 31.5 1.0
CD2 C:HIS297 3.0 26.0 1.0
CG C:ASP298 3.2 34.2 1.0
CE1 C:HIS297 3.3 27.3 1.0
O C:HOH1003 3.4 1.1 1.0
CD2 C:HIS261 3.4 30.5 1.0
CE1 C:HIS261 3.4 30.7 1.0
OD1 C:ASP298 3.7 35.5 1.0
MG C:MG2006 3.9 16.5 1.0
CD2 C:HIS257 4.2 33.3 1.0
CG C:HIS297 4.3 25.7 1.0
ND1 C:HIS297 4.4 26.9 1.0
CB C:ASP298 4.4 32.4 1.0
CB C:ASP415 4.4 29.3 1.0
ND1 C:HIS261 4.5 29.7 1.0
CG C:HIS261 4.5 30.4 1.0
NE2 C:HIS257 4.6 32.4 1.0
O C:ASP415 5.0 32.2 1.0
CG2 C:VAL265 5.0 29.0 1.0

Zinc binding site 4 out of 12 in 1mkd

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Zinc binding site 4 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2007

b:38.3
occ:1.00
 OD2 D:ASP298 2.1 36.5 1.0
OD1 D:ASP415 2.2 33.5 1.0
NE2 D:HIS297 2.3 26.3 1.0
NE2 D:HIS261 2.4 33.6 1.0
CG D:ASP415 2.9 32.9 1.0
OD2 D:ASP415 3.0 34.0 1.0
CD2 D:HIS297 3.2 27.5 1.0
O D:HOH1004 3.2 1.1 1.0
CG D:ASP298 3.2 35.0 1.0
CE1 D:HIS261 3.3 34.8 1.0
CD2 D:HIS261 3.3 34.7 1.0
CE1 D:HIS297 3.4 28.9 1.0
MG D:MG2008 3.7 13.9 1.0
OD1 D:ASP298 3.8 37.0 1.0
CD2 D:HIS257 4.1 34.1 1.0
CG D:HIS297 4.4 28.3 1.0
CB D:ASP415 4.4 31.6 1.0
ND1 D:HIS261 4.4 34.2 1.0
ND1 D:HIS297 4.4 28.1 1.0
CB D:ASP298 4.4 32.2 1.0
CG D:HIS261 4.4 34.1 1.0
NE2 D:HIS257 4.5 33.1 1.0
O D:ASP415 4.8 29.7 1.0
CG2 D:VAL265 4.9 29.9 1.0

Zinc binding site 5 out of 12 in 1mkd

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Zinc binding site 5 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2009

b:39.1
occ:1.00
 OD2 E:ASP298 2.0 34.0 1.0
NE2 E:HIS297 2.1 24.0 1.0
NE2 E:HIS261 2.3 32.2 1.0
OD1 E:ASP415 2.3 29.8 1.0
CD2 E:HIS297 3.0 25.0 1.0
CG E:ASP415 3.1 28.0 1.0
CG E:ASP298 3.1 31.8 1.0
OD2 E:ASP415 3.2 29.3 1.0
CD2 E:HIS261 3.2 32.9 1.0
CE1 E:HIS297 3.2 25.6 1.0
CE1 E:HIS261 3.3 33.7 1.0
O E:HOH1005 3.3 1.1 1.0
OD1 E:ASP298 3.7 33.3 1.0
MG E:MG2010 4.1 31.0 1.0
CD2 E:HIS257 4.1 33.8 1.0
CG E:HIS297 4.2 24.8 1.0
ND1 E:HIS297 4.3 25.6 1.0
CB E:ASP298 4.3 30.1 1.0
CG E:HIS261 4.3 33.7 1.0
ND1 E:HIS261 4.4 33.7 1.0
CB E:ASP415 4.5 27.3 1.0
NE2 E:HIS257 4.6 35.6 1.0
CG2 E:VAL265 4.9 27.7 1.0
O E:ASP415 5.0 28.7 1.0

Zinc binding site 6 out of 12 in 1mkd

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Zinc binding site 6 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2011

b:41.7
occ:1.00
 OD2 F:ASP298 2.0 31.2 1.0
OD1 F:ASP415 2.2 34.5 1.0
NE2 F:HIS297 2.3 27.4 1.0
NE2 F:HIS261 2.4 32.0 1.0
CG F:ASP415 3.0 31.5 1.0
OD2 F:ASP415 3.1 33.5 1.0
CD2 F:HIS297 3.1 27.6 1.0
CG F:ASP298 3.2 31.0 1.0
O F:HOH1006 3.3 1.1 1.0
CD2 F:HIS261 3.3 32.5 1.0
CE1 F:HIS261 3.4 33.7 1.0
CE1 F:HIS297 3.4 28.2 1.0
OD1 F:ASP298 3.7 34.6 1.0
MG F:MG2012 3.8 25.9 1.0
CD2 F:HIS257 4.1 32.8 1.0
CG F:HIS297 4.3 26.8 1.0
CB F:ASP298 4.4 30.6 1.0
ND1 F:HIS297 4.4 27.1 1.0
CB F:ASP415 4.4 29.9 1.0
ND1 F:HIS261 4.5 32.5 1.0
CG F:HIS261 4.5 32.4 1.0
NE2 F:HIS257 4.5 32.2 1.0
O F:ASP415 5.0 31.6 1.0
CG2 F:VAL265 5.0 29.1 1.0

Zinc binding site 7 out of 12 in 1mkd

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Zinc binding site 7 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2013

b:36.8
occ:1.00
 OD2 G:ASP298 2.0 35.4 1.0
OD1 G:ASP415 2.3 33.5 1.0
NE2 G:HIS261 2.3 31.4 1.0
NE2 G:HIS297 2.3 28.6 1.0
CG G:ASP415 3.0 33.1 1.0
OD2 G:ASP415 3.1 35.7 1.0
CD2 G:HIS297 3.2 30.0 1.0
CG G:ASP298 3.2 33.4 1.0
CD2 G:HIS261 3.2 32.1 1.0
CE1 G:HIS261 3.3 32.1 1.0
O G:HOH1007 3.4 1.1 1.0
CE1 G:HIS297 3.4 29.3 1.0
OD1 G:ASP298 3.8 35.0 1.0
MG G:MG2014 3.8 17.7 1.0
CD2 G:HIS257 4.1 33.2 1.0
CG G:HIS297 4.4 29.3 1.0
CB G:ASP298 4.4 31.2 1.0
ND1 G:HIS261 4.4 31.1 1.0
CG G:HIS261 4.4 32.7 1.0
ND1 G:HIS297 4.4 28.8 1.0
CB G:ASP415 4.5 31.5 1.0
NE2 G:HIS257 4.5 33.5 1.0
O G:ASP415 4.9 34.0 1.0
CG2 G:VAL265 4.9 31.0 1.0

Zinc binding site 8 out of 12 in 1mkd

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Zinc binding site 8 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn2015

b:33.5
occ:1.00
 OD2 H:ASP298 2.0 30.2 1.0
OD1 H:ASP415 2.2 32.7 1.0
NE2 H:HIS297 2.3 27.9 1.0
NE2 H:HIS261 2.3 31.9 1.0
CG H:ASP415 3.0 30.5 1.0
OD2 H:ASP415 3.1 32.0 1.0
CD2 H:HIS297 3.1 27.7 1.0
CG H:ASP298 3.2 30.2 1.0
CD2 H:HIS261 3.3 31.1 1.0
O H:HOH1008 3.3 1.1 1.0
CE1 H:HIS261 3.3 31.2 1.0
CE1 H:HIS297 3.3 27.8 1.0
OD1 H:ASP298 3.7 31.9 1.0
MG H:MG2016 3.8 32.2 1.0
CD2 H:HIS257 4.1 35.0 1.0
CG H:HIS297 4.3 26.9 1.0
CB H:ASP298 4.4 30.4 1.0
ND1 H:HIS297 4.4 27.5 1.0
ND1 H:HIS261 4.4 31.1 1.0
CG H:HIS261 4.4 31.4 1.0
CB H:ASP415 4.4 29.7 1.0
NE2 H:HIS257 4.5 36.4 1.0
O H:ASP415 4.9 30.0 1.0
CG2 H:VAL265 4.9 29.7 1.0

Zinc binding site 9 out of 12 in 1mkd

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Zinc binding site 9 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2017

b:36.7
occ:1.00
 OD2 I:ASP298 2.1 35.9 1.0
OD1 I:ASP415 2.1 31.8 1.0
NE2 I:HIS297 2.2 27.5 1.0
NE2 I:HIS261 2.3 32.4 1.0
CG I:ASP415 2.9 32.7 1.0
OD2 I:ASP415 3.0 34.9 1.0
CD2 I:HIS297 3.0 27.8 1.0
CG I:ASP298 3.2 34.6 1.0
CE1 I:HIS297 3.2 27.3 1.0
CD2 I:HIS261 3.3 33.8 1.0
CE1 I:HIS261 3.3 33.2 1.0
O I:HOH1009 3.4 1.1 1.0
OD1 I:ASP298 3.8 38.0 1.0
MG I:MG2018 4.0 21.8 1.0
CG I:HIS297 4.2 25.2 1.0
CD2 I:HIS257 4.2 35.3 1.0
ND1 I:HIS297 4.3 26.4 1.0
CB I:ASP415 4.3 32.1 1.0
CB I:ASP298 4.4 32.1 1.0
ND1 I:HIS261 4.4 33.1 1.0
CG I:HIS261 4.4 33.9 1.0
NE2 I:HIS257 4.7 35.4 1.0
O I:ASP415 4.8 34.5 1.0
CG2 I:VAL265 4.8 30.2 1.0
CA I:ASP415 5.0 32.0 1.0

Zinc binding site 10 out of 12 in 1mkd

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Zinc binding site 10 out of 12 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2019

b:27.7
occ:1.00
 OD2 J:ASP298 2.0 29.9 1.0
NE2 J:HIS261 2.2 34.1 1.0
NE2 J:HIS297 2.2 21.5 1.0
OD1 J:ASP415 2.2 33.4 1.0
CG J:ASP415 3.1 31.1 1.0
CD2 J:HIS297 3.1 24.2 1.0
CD2 J:HIS261 3.1 34.0 1.0
CG J:ASP298 3.1 28.8 1.0
OD2 J:ASP415 3.2 32.4 1.0
CE1 J:HIS261 3.2 33.9 1.0
O J:HOH1010 3.2 1.1 1.0
CE1 J:HIS297 3.3 22.5 1.0
MG J:MG2020 3.7 11.0 1.0
OD1 J:ASP298 3.7 32.5 1.0
CD2 J:HIS257 4.1 32.8 1.0
CB J:ASP298 4.3 28.0 1.0
CG J:HIS297 4.3 22.8 1.0
CG J:HIS261 4.3 33.8 1.0
ND1 J:HIS261 4.3 34.2 1.0
ND1 J:HIS297 4.3 21.8 1.0
CB J:ASP415 4.5 29.9 1.0
NE2 J:HIS257 4.5 33.8 1.0
CG2 J:VAL265 4.9 27.2 1.0
O J:ASP415 5.0 30.9 1.0

Reference:

M.E.Lee, J.Markowitz, J.-O.Lee, H.Lee. Crystal Structure of Phosphodiesterase 4D and Inhibitor Complex Febs Lett. V. 530 53 2002.
ISSN: ISSN 0014-5793
PubMed: 12387865
DOI: 10.1016/S0014-5793(02)03396-3
Page generated: Wed Dec 16 02:57:08 2020

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