Atomistry » Zinc » PDB 1m2o-1ml2 » 1mkd
Atomistry »
  Zinc »
    PDB 1m2o-1ml2 »
      1mkd »

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

Go back to Zinc Binding Sites List in 1mkd
Zinc binding site 1 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 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

Go back to Zinc Binding Sites List in 1mkd
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

Go back to Zinc Binding Sites List in 1mkd
Zinc binding site 3 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 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

Go back to Zinc Binding Sites List in 1mkd
Zinc binding site 4 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 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

Go back to Zinc Binding Sites List in 1mkd
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

Go back to Zinc Binding Sites List in 1mkd
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

Go back to Zinc Binding Sites List in 1mkd
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

Go back to Zinc Binding Sites List in 1mkd
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

Go back to Zinc Binding Sites List in 1mkd
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

Go back to Zinc Binding Sites List in 1mkd
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 Oct 16 16:57:09 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy