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Calcium in PDB 3g4g: Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871, PDB code: 3g4g was solved by B.L.Staker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.80 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.129, 75.311, 162.559, 90.00, 92.43, 90.00
R / Rfree (%) 18.8 / 25.7

Other elements in 3g4g:

The structure of Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871 (pdb code 3g4g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871, PDB code: 3g4g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3g4g

Go back to Calcium Binding Sites List in 3g4g
Calcium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:53.2
occ:1.00
 CB A:HIS271 3.4 23.5 1.0
CA A:HIS271 3.5 22.9 1.0
CD2 A:LEU494 3.7 17.9 1.0
CG A:HIS271 3.8 27.1 1.0
C A:HIS271 3.8 21.7 1.0
CD2 A:HIS271 3.9 32.4 1.0
CB A:PHE273 4.0 19.9 1.0
N A:ARG274 4.0 22.6 1.0
N A:PHE273 4.1 19.6 1.0
O A:HIS271 4.2 20.6 1.0
CB A:ARG274 4.3 24.3 1.0
CD2 A:PHE273 4.3 20.0 1.0
N A:VAL272 4.3 20.2 1.0
CA A:PHE273 4.4 20.1 1.0
NE2 A:GLN497 4.5 26.2 1.0
C A:PHE273 4.6 20.9 1.0
CG A:PHE273 4.6 18.9 1.0
CA A:ARG274 4.7 24.0 1.0
CG A:LEU494 4.7 15.7 1.0
NE2 A:GLN493 4.7 19.9 1.0
ND1 A:HIS271 4.9 30.3 1.0
N A:HIS271 4.9 23.3 1.0

Calcium binding site 2 out of 4 in 3g4g

Go back to Calcium Binding Sites List in 3g4g
Calcium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:41.5
occ:1.00
 CB B:HIS271 3.8 36.0 1.0
CA B:HIS271 3.9 35.7 1.0
CD2 B:PHE273 4.0 32.1 1.0
CD2 B:LEU494 4.0 26.9 1.0
CB B:PHE273 4.0 32.9 1.0
N B:ARG274 4.0 35.0 1.0
C B:HIS271 4.1 34.9 1.0
CG B:HIS271 4.2 38.6 1.0
N B:PHE273 4.2 32.4 1.0
NE2 B:GLN497 4.3 25.0 1.0
ND1 B:HIS271 4.3 41.1 1.0
CG B:ARG274 4.4 41.1 1.0
N B:VAL272 4.5 34.1 1.0
CG B:PHE273 4.5 32.5 1.0
CA B:PHE273 4.5 32.9 1.0
O B:HIS271 4.6 35.0 1.0
CB B:ARG274 4.7 37.2 1.0
C B:PHE273 4.8 33.8 1.0
CG B:LEU494 5.0 24.1 1.0
CA B:ARG274 5.0 36.2 1.0
NE B:ARG274 5.0 49.0 1.0

Calcium binding site 3 out of 4 in 3g4g

Go back to Calcium Binding Sites List in 3g4g
Calcium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2

b:52.0
occ:1.00
 ND1 C:HIS271 3.0 36.4 1.0
CB C:HIS271 3.3 26.5 1.0
CA C:HIS271 3.5 25.4 1.0
N C:ARG274 3.6 26.0 1.0
CG C:HIS271 3.6 30.7 1.0
CB C:PHE273 3.7 23.0 1.0
CG C:ARG274 3.7 34.5 1.0
C C:HIS271 3.7 24.1 1.0
CD2 C:LEU494 3.9 23.8 1.0
N C:PHE273 3.9 23.4 1.0
O C:HIS271 4.1 24.4 1.0
CA C:PHE273 4.2 23.7 1.0
N C:VAL272 4.2 22.8 1.0
CE1 C:HIS271 4.2 36.9 1.0
CD2 C:PHE273 4.3 22.8 1.0
C C:PHE273 4.3 24.6 1.0
CB C:ARG274 4.3 28.7 1.0
CA C:ARG274 4.5 27.6 1.0
CG C:PHE273 4.5 22.8 1.0
NE2 C:GLN493 4.9 35.1 1.0
CD2 C:HIS271 4.9 34.8 1.0
NE2 C:GLN497 4.9 27.2 1.0
C C:VAL272 5.0 22.7 1.0
N C:HIS271 5.0 24.8 1.0
CD C:ARG274 5.0 40.3 1.0

Calcium binding site 4 out of 4 in 3g4g

Go back to Calcium Binding Sites List in 3g4g
Calcium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Phosphodiesterase 4D with Regulatory Domain and D155871 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca3

b:35.4
occ:1.00
 CB D:HIS271 3.6 27.7 1.0
CD2 D:LEU494 3.7 19.5 1.0
CG D:ARG274 3.7 36.2 1.0
CA D:HIS271 3.8 27.2 1.0
NE D:ARG274 3.8 47.3 1.0
ND1 D:HIS271 3.9 35.5 1.0
N D:ARG274 3.9 28.1 1.0
CG D:HIS271 4.0 32.3 1.0
CB D:PHE273 4.0 24.8 1.0
C D:HIS271 4.1 25.6 1.0
NE2 D:GLN493 4.1 32.4 1.0
CZ D:ARG274 4.1 50.8 1.0
N D:PHE273 4.2 24.8 1.0
CD2 D:PHE273 4.3 23.8 1.0
CD D:ARG274 4.3 42.3 1.0
NH2 D:ARG274 4.4 50.3 1.0
N D:VAL272 4.4 24.8 1.0
O D:HIS271 4.4 25.6 1.0
CB D:ARG274 4.5 30.7 1.0
CA D:PHE273 4.5 25.2 1.0
OE1 D:GLN497 4.5 18.6 1.0
C D:PHE273 4.6 26.1 1.0
CG D:PHE273 4.7 24.8 1.0
CA D:ARG274 4.8 30.1 1.0
NH1 D:ARG274 4.8 51.3 1.0
CD D:GLN493 4.9 31.5 1.0
CG D:LEU494 4.9 19.0 1.0
CE1 D:HIS271 4.9 36.4 1.0
NE2 D:GLN497 4.9 22.6 1.0
OE1 D:GLN493 5.0 35.7 1.0

Reference:

A.B.Burgin, O.T.Magnusson, J.Singh, P.Witte, B.L.Staker, J.M.Bjornsson, M.Thorsteinsdottir, S.Hrafnsdottir, T.Hagen, A.S.Kiselyov, L.J.Stewart, M.E.Gurney. Design of Phosphodiesterase 4D (PDE4D) Allosteric Modulators For Enhancing Cognition with Improved Safety. Nat.Biotechnol. V. 28 63 2010.
ISSN: ISSN 1087-0156
PubMed: 20037581
DOI: 10.1038/NBT.1598
Page generated: Tue Jul 8 12:36:10 2025

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