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Zinc in PDB 4dt2: Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209

Enzymatic activity of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209

All present enzymatic activity of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209, PDB code: 4dt2 was solved by D.Feder, W.M.Hussein, D.J.Clayton, M.Kan, G.Schenk, R.P.Mcgeary, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.72 / 2.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.760, 126.760, 298.954, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 22.8

Other elements in 4dt2:

The structure of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 (pdb code 4dt2). 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 Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209, PDB code: 4dt2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4dt2

Go back to Zinc Binding Sites List in 4dt2
Zinc binding site 1 out of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209


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 Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:44.3
occ:0.98
 OD1 A:ASN201 2.1 45.7 1.0
NE2 A:HIS286 2.1 35.3 1.0
ND1 A:HIS323 2.2 39.9 1.0
OD2 A:ASP164 2.4 38.3 1.0
CAD A:0LV504 2.7 35.4 1.0
CE1 A:HIS286 3.0 35.9 1.0
CD2 A:HIS286 3.1 34.7 1.0
CAF A:0LV504 3.1 49.5 1.0
CE1 A:HIS323 3.1 39.0 1.0
CG A:ASN201 3.2 44.5 1.0
CG A:ASP164 3.2 37.4 1.0
FE A:FE502 3.2 45.9 0.8
CG A:HIS323 3.3 39.9 1.0
CA A:HIS323 3.4 35.2 1.0
OD1 A:ASP164 3.4 34.9 1.0
OD2 A:ASP135 3.6 34.7 1.0
CB A:HIS323 3.7 32.1 1.0
ND2 A:ASN201 3.7 44.0 1.0
CAE A:0LV504 4.0 44.2 1.0
O A:HIS323 4.1 42.4 1.0
ND1 A:HIS286 4.2 33.7 1.0
N A:ASN201 4.2 36.6 1.0
CG A:HIS286 4.2 33.6 1.0
C A:HIS323 4.2 38.7 1.0
N A:HIS323 4.3 33.4 1.0
NE2 A:HIS323 4.3 41.1 1.0
CB A:ASN201 4.4 38.1 1.0
CD2 A:HIS202 4.4 37.3 1.0
CD2 A:HIS323 4.4 38.0 1.0
CB A:ASP164 4.5 34.1 1.0
CAK A:0LV504 4.6 59.5 1.0
CG A:ASP135 4.8 35.9 1.0
CA A:ASN201 4.8 38.4 1.0
NE2 A:HIS202 4.9 41.8 1.0
OH A:TYR253 5.0 31.7 1.0
OH A:TYR167 5.0 37.4 1.0

Zinc binding site 2 out of 4 in 4dt2

Go back to Zinc Binding Sites List in 4dt2
Zinc binding site 2 out of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209


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 Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:51.0
occ:1.00
 NE2 B:HIS286 2.1 41.3 1.0
OD1 B:ASN201 2.1 41.1 1.0
OD2 B:ASP164 2.2 41.9 1.0
ND1 B:HIS323 2.4 45.9 1.0
CAD B:0LV504 2.7 46.6 1.0
CAF B:0LV504 2.9 55.4 1.0
CE1 B:HIS286 3.0 40.2 1.0
CD2 B:HIS286 3.1 44.0 1.0
CE1 B:HIS323 3.2 43.2 1.0
FE B:FE502 3.2 48.9 0.9
CG B:ASP164 3.3 41.3 1.0
CG B:ASN201 3.3 42.6 1.0
CA B:HIS323 3.3 41.5 1.0
CG B:HIS323 3.3 42.5 1.0
OD2 B:ASP135 3.6 40.3 1.0
OD1 B:ASP164 3.7 41.5 1.0
CB B:HIS323 3.7 42.0 1.0
ND2 B:ASN201 3.9 47.9 1.0
CAE B:0LV504 4.0 53.1 1.0
O B:HIS323 4.0 43.3 1.0
C B:HIS323 4.2 38.7 1.0
ND1 B:HIS286 4.2 39.2 1.0
N B:HIS323 4.2 39.1 1.0
CG B:HIS286 4.3 40.7 1.0
NE2 B:HIS323 4.3 41.6 1.0
CD2 B:HIS202 4.3 48.6 1.0
CAK B:0LV504 4.3 64.0 1.0
CD2 B:HIS323 4.3 43.5 1.0
N B:ASN201 4.4 37.6 1.0
CB B:ASN201 4.5 42.1 1.0
CB B:ASP164 4.5 36.0 1.0
CG B:ASP135 4.8 42.6 1.0
NE2 B:HIS202 4.9 52.0 1.0
CA B:ASN201 5.0 41.3 1.0

Zinc binding site 3 out of 4 in 4dt2

Go back to Zinc Binding Sites List in 4dt2
Zinc binding site 3 out of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209


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 Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:42.4
occ:0.98
 OD1 C:ASN201 2.2 49.2 1.0
OD2 C:ASP164 2.2 42.5 1.0
NE2 C:HIS286 2.2 40.0 1.0
ND1 C:HIS323 2.3 37.9 1.0
CE1 C:HIS286 3.1 40.9 1.0
CAD C:0LV512 3.1 48.8 1.0
CAF C:0LV512 3.1 57.5 1.0
FE C:FE506 3.1 56.0 1.0
CE1 C:HIS323 3.2 39.8 1.0
CG C:ASN201 3.2 45.6 1.0
CG C:ASP164 3.2 44.2 1.0
CA C:HIS323 3.3 36.8 1.0
CD2 C:HIS286 3.4 37.2 1.0
CG C:HIS323 3.4 39.7 1.0
OD2 C:ASP135 3.6 44.3 1.0
ND2 C:ASN201 3.6 44.1 1.0
OD1 C:ASP164 3.7 44.0 1.0
CB C:HIS323 3.7 35.6 1.0
O C:HIS323 3.9 41.0 1.0
C C:HIS323 4.1 37.1 1.0
N C:HIS323 4.2 38.9 1.0
ND1 C:HIS286 4.3 38.9 1.0
NE2 C:HIS323 4.3 39.9 1.0
CD2 C:HIS202 4.4 50.1 1.0
CG C:HIS286 4.4 40.1 1.0
CAE C:0LV512 4.4 61.1 1.0
CB C:ASN201 4.5 39.2 1.0
CD2 C:HIS323 4.5 39.0 1.0
CAK C:0LV512 4.5 65.1 1.0
N C:ASN201 4.5 38.4 1.0
CB C:ASP164 4.5 40.3 1.0
CG C:ASP135 4.8 44.7 1.0
OH C:TYR167 4.9 44.5 1.0
OH C:TYR253 4.9 37.4 1.0
NE2 C:HIS202 5.0 52.0 1.0

Zinc binding site 4 out of 4 in 4dt2

Go back to Zinc Binding Sites List in 4dt2
Zinc binding site 4 out of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209


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 Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn508

b:41.5
occ:0.93
 NE2 D:HIS286 2.0 35.8 1.0
ND1 D:HIS323 2.2 34.5 1.0
OD1 D:ASN201 2.2 44.4 1.0
OD2 D:ASP164 2.3 36.8 1.0
CAF D:0LV511 2.9 50.9 1.0
CAD D:0LV511 2.9 38.4 1.0
CE1 D:HIS286 3.0 34.8 1.0
CE1 D:HIS323 3.1 34.7 1.0
CD2 D:HIS286 3.1 33.4 1.0
FE D:FE509 3.2 48.2 0.8
CG D:HIS323 3.2 34.6 1.0
CA D:HIS323 3.3 32.7 1.0
CG D:ASP164 3.3 37.5 1.0
CG D:ASN201 3.5 45.2 1.0
CB D:HIS323 3.6 29.8 1.0
OD1 D:ASP135 3.6 37.1 1.0
OD1 D:ASP164 3.7 38.1 1.0
O D:HIS323 4.0 38.3 1.0
ND1 D:HIS286 4.1 34.5 1.0
N D:HIS323 4.1 30.4 1.0
C D:HIS323 4.1 35.0 1.0
NE2 D:HIS323 4.2 35.9 1.0
CG D:HIS286 4.2 34.4 1.0
CD2 D:HIS202 4.2 47.4 1.0
CAE D:0LV511 4.2 53.8 1.0
ND2 D:ASN201 4.2 47.0 1.0
CAK D:0LV511 4.2 59.9 1.0
CD2 D:HIS323 4.3 38.6 1.0
N D:ASN201 4.4 37.7 1.0
CB D:ASN201 4.5 37.2 1.0
CB D:ASP164 4.6 33.9 1.0
CG D:ASP135 4.6 36.5 1.0
OD2 D:ASP135 4.8 31.6 1.0
NE2 D:HIS202 4.8 51.0 1.0
OH D:TYR253 4.9 37.4 1.0
OH D:TYR167 4.9 32.9 1.0
CA D:ASN201 5.0 37.2 1.0

Reference:

D.Feder, W.M.Hussein, D.J.Clayton, M.W.Kan, G.Schenk, R.P.Mcgeary, L.W.Guddat. Identification of Purple Acid Phosphatase Inhibitors By Fragment-Based Screening: Promising New Leads For Osteoporosis Therapeutics. Chem.Biol.Drug Des. V. 80 665 2012.
ISSN: ISSN 1747-0277
PubMed: 22943065
DOI: 10.1111/CBDD.12001
Page generated: Sat Oct 26 21:37:12 2024

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