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Zinc in PDB 2qfp: Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Fluoride

Enzymatic activity of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Fluoride

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

Protein crystallography data

The structure of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Fluoride, PDB code: 2qfp was solved by L.W.Guddat, G.S.Schenk, L.R.Gahan, T.W.Elliot, E.Leung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.719, 188.466, 192.398, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 25.4

Other elements in 2qfp:

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

Fluorine (F) 4 atoms
Iron (Fe) 4 atoms
Sodium (Na) 11 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 2qfp

Go back to Zinc Binding Sites List in 2qfp
Zinc binding site 1 out of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Fluoride


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 Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn434

b:32.1
occ:1.00
 NE2 A:HIS286 1.9 26.9 1.0
OD1 A:ASN201 2.1 30.2 1.0
ND1 A:HIS323 2.1 26.7 1.0
F A:F436 2.2 40.1 1.0
OD2 A:ASP164 2.5 36.1 1.0
CE1 A:HIS286 2.8 24.4 1.0
CE1 A:HIS323 3.0 28.8 1.0
CD2 A:HIS286 3.1 22.7 1.0
CG A:ASN201 3.2 27.7 1.0
CG A:HIS323 3.2 26.2 1.0
CA A:HIS323 3.3 25.5 1.0
CG A:ASP164 3.3 33.0 1.0
FE A:FE433 3.5 47.2 1.0
OD1 A:ASP164 3.6 28.3 1.0
CB A:HIS323 3.6 24.6 1.0
OD2 A:ASP135 3.7 25.4 1.0
ND2 A:ASN201 3.9 25.5 1.0
NA A:NA442 3.9 69.4 1.0
ND1 A:HIS286 3.9 22.1 1.0
O A:HIS323 3.9 27.3 1.0
CG A:HIS286 4.1 21.8 1.0
C A:HIS323 4.1 25.1 1.0
NE2 A:HIS323 4.1 28.7 1.0
N A:HIS323 4.1 23.3 1.0
CD2 A:HIS323 4.3 24.7 1.0
N A:ASN201 4.3 26.6 1.0
CB A:ASN201 4.3 27.0 1.0
CD2 A:HIS202 4.5 22.6 1.0
CB A:ASP164 4.5 29.5 1.0
CG A:ASP135 4.8 24.8 1.0
OH A:TYR253 4.8 21.5 1.0
O A:HOH594 4.8 43.6 1.0
CA A:ASN201 4.9 26.6 1.0

Zinc binding site 2 out of 4 in 2qfp

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


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 Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn434

b:34.0
occ:1.00
 NE2 B:HIS286 1.9 26.4 1.0
OD1 B:ASN201 2.0 30.5 1.0
ND1 B:HIS323 2.1 22.9 1.0
F B:F436 2.2 38.9 1.0
OD2 B:ASP164 2.2 31.0 1.0
CE1 B:HIS286 2.9 24.7 1.0
CD2 B:HIS286 3.0 21.9 1.0
CE1 B:HIS323 3.0 24.2 1.0
CG B:ASN201 3.1 24.6 1.0
CG B:HIS323 3.2 22.4 1.0
CG B:ASP164 3.2 30.5 1.0
CA B:HIS323 3.3 24.7 1.0
OD2 B:ASP135 3.6 25.1 1.0
OD1 B:ASP164 3.6 29.1 1.0
CB B:HIS323 3.6 24.2 1.0
FE B:FE433 3.6 46.3 1.0
ND2 B:ASN201 3.7 23.4 1.0
ND1 B:HIS286 4.0 26.4 1.0
O B:HIS323 4.1 27.4 1.0
CG B:HIS286 4.1 23.9 1.0
NE2 B:HIS323 4.1 25.3 1.0
N B:HIS323 4.2 24.3 1.0
C B:HIS323 4.2 25.4 1.0
CD2 B:HIS323 4.3 21.2 1.0
N B:ASN201 4.3 20.2 1.0
NA B:NA442 4.3 90.7 1.0
CB B:ASN201 4.4 22.9 1.0
CB B:ASP164 4.5 29.6 1.0
CD2 B:HIS202 4.5 21.9 1.0
CG B:ASP135 4.7 26.8 1.0
OH B:TYR253 4.7 25.5 1.0
CA B:ASN201 4.9 22.1 1.0
O2 B:SO4435 5.0 92.3 1.0

Zinc binding site 3 out of 4 in 2qfp

Go back to Zinc Binding Sites List in 2qfp
Zinc binding site 3 out of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Fluoride


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 Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn434

b:33.6
occ:1.00
 F C:F436 1.8 38.0 1.0
NE2 C:HIS286 1.9 22.4 1.0
OD1 C:ASN201 2.2 33.7 1.0
OD2 C:ASP164 2.3 30.9 1.0
ND1 C:HIS323 2.3 29.1 1.0
CE1 C:HIS286 2.9 23.6 1.0
CD2 C:HIS286 2.9 23.0 1.0
CE1 C:HIS323 3.2 30.7 1.0
CG C:ASN201 3.2 30.1 1.0
CG C:ASP164 3.3 33.6 1.0
CG C:HIS323 3.3 30.7 1.0
CA C:HIS323 3.3 30.2 1.0
FE C:FE433 3.6 51.3 1.0
CB C:HIS323 3.6 28.6 1.0
OD1 C:ASP164 3.7 33.6 1.0
OD2 C:ASP135 3.7 26.7 1.0
ND2 C:ASN201 3.9 29.7 1.0
ND1 C:HIS286 4.0 24.7 1.0
CG C:HIS286 4.1 23.4 1.0
O C:HIS323 4.2 31.1 1.0
N C:HIS323 4.2 28.9 1.0
C C:HIS323 4.3 31.2 1.0
N C:ASN201 4.3 28.1 1.0
NE2 C:HIS323 4.3 28.1 1.0
NA C:NA443 4.3 89.4 1.0
CB C:ASN201 4.4 30.9 1.0
CD2 C:HIS323 4.4 27.9 1.0
CD2 C:HIS202 4.5 30.1 1.0
CB C:ASP164 4.5 31.2 1.0
OH C:TYR253 4.8 31.0 1.0
CG C:ASP135 4.8 31.1 1.0
CA C:ASN201 4.9 29.4 1.0

Zinc binding site 4 out of 4 in 2qfp

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


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 Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn434

b:33.7
occ:1.00
 NE2 D:HIS286 1.9 19.5 1.0
ND1 D:HIS323 2.1 28.1 1.0
F D:F436 2.2 39.2 1.0
OD1 D:ASN201 2.2 31.1 1.0
OD2 D:ASP164 2.4 38.5 1.0
CE1 D:HIS286 2.6 19.4 1.0
CE1 D:HIS323 3.0 28.7 1.0
CG D:HIS323 3.1 26.6 1.0
CD2 D:HIS286 3.2 19.2 1.0
CA D:HIS323 3.3 29.2 1.0
CG D:ASP164 3.3 36.9 1.0
CG D:ASN201 3.3 29.8 1.0
FE D:FE433 3.5 50.0 1.0
CB D:HIS323 3.5 28.6 1.0
OD1 D:ASP164 3.5 36.7 1.0
OD2 D:ASP135 3.6 25.0 1.0
ND1 D:HIS286 3.8 20.2 1.0
ND2 D:ASN201 3.9 25.0 1.0
O D:HIS323 4.1 30.8 1.0
CG D:HIS286 4.1 17.4 1.0
N D:HIS323 4.1 29.5 1.0
C D:HIS323 4.2 30.1 1.0
NE2 D:HIS323 4.2 28.6 1.0
NA D:NA443 4.2 95.1 1.0
CD2 D:HIS323 4.2 26.4 1.0
N D:ASN201 4.4 29.9 1.0
CB D:ASN201 4.5 28.6 1.0
CD2 D:HIS202 4.5 31.1 1.0
CB D:ASP164 4.6 33.5 1.0
O D:HOH567 4.6 94.5 1.0
CG D:ASP135 4.7 26.7 1.0
OH D:TYR253 4.8 30.5 1.0
CA D:ASN201 5.0 29.3 1.0

Reference:

G.Schenk, T.W.Elliott, E.Leung, L.E.Carrington, N.Mitic, L.R.Gahan, L.W.Guddat. Crystal Structures of A Purple Acid Phosphatase, Representing Different Steps of This Enzyme'S Catalytic Cycle. Bmc Struct.Biol. V. 8 6 2008.
ISSN: ESSN 1472-6807
PubMed: 18234116
DOI: 10.1186/1472-6807-8-6
Page generated: Thu Oct 17 03:25:13 2024

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