Zinc in PDB 5lbo: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001, PDB code: 5lbo was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.40 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.223, 111.092, 160.798, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21

Other elements in 5lbo:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 (pdb code 5lbo). 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 Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001, PDB code: 5lbo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5lbo

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:35.6
occ:1.00
 OD2 A:ASP201 2.1 26.7 1.0
OD1 A:ASP318 2.1 29.7 1.0
NE2 A:HIS164 2.2 29.4 1.0
NE2 A:HIS200 2.3 30.4 1.0
O A:HOH1124 2.4 32.2 1.0
O A:HOH1108 2.5 30.6 1.0
CG A:ASP318 3.0 31.6 1.0
CD2 A:HIS200 3.1 28.2 1.0
CG A:ASP201 3.1 30.0 1.0
CE1 A:HIS164 3.2 28.9 1.0
CD2 A:HIS164 3.2 30.2 1.0
OD2 A:ASP318 3.3 31.6 1.0
CE1 A:HIS200 3.3 31.4 1.0
OD1 A:ASP201 3.5 30.6 1.0
MG A:MG1002 3.8 23.6 1.0
O A:HOH1191 4.0 28.1 1.0
O A:HOH1135 4.0 36.0 1.0
CD2 A:HIS160 4.1 32.6 1.0
CG A:HIS200 4.3 30.7 1.0
ND1 A:HIS164 4.3 30.5 1.0
NE2 A:HIS160 4.3 34.3 1.0
CB A:ASP201 4.3 29.4 1.0
ND1 A:HIS200 4.4 31.0 1.0
CG A:HIS164 4.4 27.9 1.0
CB A:ASP318 4.4 29.3 1.0
O A:HOH1110 4.7 28.5 1.0
CG2 A:VAL168 4.8 35.6 1.0
CA A:ASP318 5.0 29.9 1.0
C29 A:6M51011 5.0 41.1 1.0

Zinc binding site 2 out of 4 in 5lbo

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:39.3
occ:1.00
 OD2 B:ASP201 2.1 30.5 1.0
O B:HOH1108 2.1 25.5 1.0
OD1 B:ASP318 2.2 33.4 1.0
NE2 B:HIS164 2.2 29.9 1.0
O B:HOH1149 2.3 26.8 1.0
NE2 B:HIS200 2.3 36.0 1.0
CG B:ASP201 3.1 28.4 1.0
CG B:ASP318 3.1 34.9 1.0
CD2 B:HIS200 3.2 32.4 1.0
CE1 B:HIS164 3.2 32.0 1.0
CD2 B:HIS164 3.2 30.0 1.0
OD2 B:ASP318 3.3 38.5 1.0
CE1 B:HIS200 3.3 30.0 1.0
OD1 B:ASP201 3.5 25.8 1.0
MG B:MG1002 3.8 24.2 1.0
O B:HOH1182 3.9 23.6 1.0
CD2 B:HIS160 4.0 34.0 1.0
O B:HOH1123 4.2 31.9 1.0
CB B:ASP201 4.2 29.1 1.0
NE2 B:HIS160 4.3 33.9 1.0
ND1 B:HIS164 4.3 33.3 1.0
CG B:HIS200 4.3 32.5 1.0
CG B:HIS164 4.4 29.9 1.0
ND1 B:HIS200 4.4 35.5 1.0
CB B:ASP318 4.5 37.7 1.0
CG2 B:VAL168 4.8 35.4 1.0
O B:HOH1116 4.8 28.1 1.0
C29 B:6M51011 4.9 38.2 1.0
CA B:ASP318 5.0 39.7 1.0

Zinc binding site 3 out of 4 in 5lbo

Go back to Zinc Binding Sites List in 5lbo
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:38.8
occ:1.00
 OD2 C:ASP201 2.1 30.9 1.0
OD1 C:ASP318 2.1 33.8 1.0
O C:HOH1126 2.2 34.5 1.0
NE2 C:HIS200 2.3 27.3 1.0
NE2 C:HIS164 2.3 33.0 1.0
O C:HOH1105 2.3 28.3 1.0
CG C:ASP318 3.0 37.6 1.0
CD2 C:HIS200 3.1 28.6 1.0
CG C:ASP201 3.1 32.1 1.0
CE1 C:HIS164 3.2 29.4 1.0
OD2 C:ASP318 3.2 37.9 1.0
CD2 C:HIS164 3.3 29.8 1.0
CE1 C:HIS200 3.3 28.3 1.0
OD1 C:ASP201 3.5 29.1 1.0
MG C:MG1002 3.8 22.6 1.0
O C:HOH1167 4.0 24.7 1.0
CD2 C:HIS160 4.1 29.0 1.0
O C:HOH1116 4.2 35.4 1.0
CG C:HIS200 4.3 27.1 1.0
NE2 C:HIS160 4.3 28.6 1.0
CB C:ASP201 4.3 31.0 1.0
ND1 C:HIS164 4.3 32.0 1.0
ND1 C:HIS200 4.3 29.1 1.0
CG C:HIS164 4.4 28.0 1.0
CB C:ASP318 4.4 36.4 1.0
O C:HOH1114 4.5 27.5 1.0
CG2 C:VAL168 4.8 33.7 1.0
C29 C:6M51008 4.9 38.8 1.0
CA C:ASP318 5.0 35.1 1.0

Zinc binding site 4 out of 4 in 5lbo

Go back to Zinc Binding Sites List in 5lbo
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:32.2
occ:1.00
 OD2 D:ASP201 2.1 26.6 1.0
OD1 D:ASP318 2.1 26.5 1.0
NE2 D:HIS164 2.3 23.3 1.0
O D:HOH1122 2.3 22.9 1.0
NE2 D:HIS200 2.3 28.1 1.0
O D:HOH1174 2.3 28.1 1.0
CG D:ASP318 3.0 29.6 1.0
CG D:ASP201 3.1 27.2 1.0
CD2 D:HIS200 3.1 25.1 1.0
CE1 D:HIS164 3.2 22.1 1.0
CD2 D:HIS164 3.3 22.6 1.0
OD2 D:ASP318 3.3 27.7 1.0
CE1 D:HIS200 3.4 26.9 1.0
OD1 D:ASP201 3.5 25.1 1.0
MG D:MG1002 3.9 20.5 1.0
O D:HOH1206 3.9 24.2 1.0
CD2 D:HIS160 4.1 37.0 1.0
O D:HOH1171 4.2 27.9 1.0
NE2 D:HIS160 4.3 40.4 1.0
ND1 D:HIS164 4.3 22.9 1.0
CB D:ASP201 4.3 26.3 1.0
CG D:HIS200 4.3 26.4 1.0
CG D:HIS164 4.4 22.1 1.0
ND1 D:HIS200 4.4 25.8 1.0
CB D:ASP318 4.4 27.8 1.0
O D:HOH1124 4.6 21.9 1.0
CG2 D:VAL168 4.8 27.2 1.0
CA D:ASP318 5.0 27.5 1.0

Reference:

A.R.Blaazer, A.K.Singh, E.De Heuvel, E.Edink, K.M.Orrling, J.J.N.Veerman, T.Van Den Bergh, C.Jansen, E.Balasubramaniam, W.J.Mooij, H.Custers, M.Sijm, D.N.A.Tagoe, T.D.Kalejaiye, J.C.Munday, H.Tenor, A.Matheeussen, M.Wijtmans, M.Siderius, C.De Graaf, L.Maes, H.P.De Koning, D.S.Bailey, G.J.Sterk, I.J.P.De Esch, D.G.Brown, R.Leurs. Targeting A Subpocket in Trypanosoma Brucei Phosphodiesterase B1 (TBRPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J. Med. Chem. V. 61 3870 2018.
ISSN: ISSN 1520-4804
PubMed: 29672041
DOI: 10.1021/ACS.JMEDCHEM.7B01670
Page generated: Wed Dec 16 06:28:40 2020

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