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Sodium 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
Zinc (Zn) 4 atoms
Iron (Fe) 4 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 11 binding sites of Sodium where determined in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Fluoride, PDB code: 2qfp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in 2qfp

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Sodium binding site 1 out of 11 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 Sodium with other atoms in the Na 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:Na442

b:69.4
occ:1.00
 F A:F436 2.3 40.1 1.0
O4 A:SO4435 2.3 83.0 1.0
O2 A:SO4435 2.5 82.4 1.0
O A:HOH594 2.5 43.6 1.0
S A:SO4435 2.9 82.1 1.0
ND2 A:ASN201 3.2 25.5 1.0
O3 B:SO4441 3.2 87.8 1.0
NE2 A:HIS296 3.5 26.1 1.0
NE2 A:HIS202 3.6 24.0 1.0
O3 A:SO4435 3.7 82.6 1.0
NA A:NA444 3.8 68.3 1.0
CE1 A:HIS296 3.9 26.2 1.0
ZN A:ZN434 3.9 32.1 1.0
OD1 A:ASN201 3.9 30.2 1.0
CE1 A:HIS323 3.9 28.8 1.0
CG A:ASN201 4.0 27.7 1.0
CD2 A:HIS202 4.1 22.6 1.0
O1 A:SO4435 4.1 82.8 1.0
ND1 A:HIS323 4.2 26.7 1.0
FE A:FE433 4.4 47.2 1.0
OD2 A:ASP164 4.6 36.1 1.0
CE1 A:HIS202 4.6 22.5 1.0
CD2 A:HIS296 4.7 26.8 1.0
S B:SO4441 4.7 88.0 1.0
CE1 A:HIS295 4.7 31.8 1.0
O A:HIS323 4.8 27.3 1.0
NE2 A:HIS325 4.8 32.6 1.0
NE2 A:HIS323 4.9 28.7 1.0
CE1 A:HIS325 4.9 30.9 1.0

Sodium binding site 2 out of 11 in 2qfp

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Sodium binding site 2 out of 11 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 Sodium with other atoms in the Na 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
A:Na443

b:0.8
occ:1.00
 O1 B:SO4441 2.6 87.8 1.0
NA A:NA444 3.4 68.3 1.0
O4 B:SO4441 3.4 87.4 1.0
NE2 A:HIS295 3.5 31.8 1.0
O A:HOH497 3.5 39.7 1.0
S B:SO4441 3.5 88.0 1.0
NH1 B:ARG258 3.6 48.6 1.0
CD2 A:HIS295 3.8 31.1 1.0
CE1 A:HIS296 4.1 26.2 1.0
NH2 B:ARG258 4.1 43.1 1.0
O3 B:SO4441 4.1 87.8 1.0
CZ B:ARG258 4.2 43.8 1.0
ND1 A:HIS296 4.3 24.9 1.0
CE1 A:HIS295 4.7 31.8 1.0
O2 B:SO4441 4.8 88.0 1.0

Sodium binding site 3 out of 11 in 2qfp

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Sodium binding site 3 out of 11 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 Sodium with other atoms in the Na 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
A:Na444

b:68.3
occ:1.00
 O4 A:SO4435 2.6 83.0 1.0
O3 B:SO4441 2.7 87.8 1.0
NE2 A:HIS295 2.9 31.8 1.0
O1 B:SO4441 3.0 87.8 1.0
O3 A:SO4435 3.1 82.6 1.0
CE1 A:HIS295 3.3 31.8 1.0
NA A:NA443 3.4 0.8 1.0
S B:SO4441 3.4 88.0 1.0
S A:SO4435 3.4 82.1 1.0
O A:HOH594 3.8 43.6 1.0
CE1 A:HIS296 3.8 26.2 1.0
NA A:NA442 3.8 69.4 1.0
NE2 A:HIS296 4.1 26.1 1.0
O4 B:SO4441 4.2 87.4 1.0
CD2 A:HIS295 4.2 31.1 1.0
O1 A:SO4435 4.4 82.8 1.0
O2 A:SO4435 4.5 82.4 1.0
ND1 A:HIS295 4.6 32.0 1.0
O2 B:SO4441 4.6 88.0 1.0
ND1 A:HIS296 4.9 24.9 1.0

Sodium binding site 4 out of 11 in 2qfp

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Sodium binding site 4 out of 11 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 Sodium with other atoms in the Na 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
B:Na442

b:90.7
occ:1.00
 O1 B:SO4435 2.4 93.0 1.0
O2 B:SO4435 2.5 92.3 1.0
ND2 B:ASN201 2.9 23.4 1.0
S B:SO4435 3.0 92.9 1.0
F B:F436 3.0 38.9 1.0
O1 A:SO4441 3.0 94.5 1.0
NE2 B:HIS296 3.5 26.6 1.0
CE1 B:HIS296 3.5 25.9 1.0
NE2 B:HIS202 3.8 23.6 1.0
CE1 B:HIS323 3.8 24.2 1.0
O B:HOH612 3.9 55.8 1.0
O3 B:SO4435 3.9 92.2 1.0
CG B:ASN201 4.0 24.6 1.0
O4 B:SO4435 4.1 92.9 1.0
OD1 B:ASN201 4.2 30.5 1.0
S A:SO4441 4.2 95.2 1.0
ZN B:ZN434 4.3 34.0 1.0
ND1 B:HIS323 4.3 22.9 1.0
CD2 B:HIS202 4.3 21.9 1.0
O4 A:SO4441 4.3 94.9 1.0
NA B:NA444 4.4 98.7 1.0
CD2 B:HIS296 4.8 25.5 1.0
ND1 B:HIS296 4.8 25.8 1.0
CE1 B:HIS202 4.8 24.2 1.0
NE2 B:HIS323 4.8 25.3 1.0
CE1 B:HIS295 4.8 27.2 1.0
O2 A:SO4441 5.0 94.9 1.0
FE B:FE433 5.0 46.3 1.0

Sodium binding site 5 out of 11 in 2qfp

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Sodium binding site 5 out of 11 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 Sodium with other atoms in the Na binding site number 5 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:Na443

b:81.8
occ:1.00
 O2 A:SO4441 2.5 94.9 1.0
NA B:NA444 3.0 98.7 1.0
NE2 B:HIS295 3.3 27.5 1.0
CD2 B:HIS295 3.6 24.7 1.0
S A:SO4441 3.7 95.2 1.0
O4 A:SO4441 3.7 94.9 1.0
NH2 A:ARG258 4.2 38.2 1.0
CE1 B:HIS296 4.4 25.9 1.0
O1 A:SO4441 4.5 94.5 1.0
CE1 B:HIS295 4.6 27.2 1.0
ND1 B:HIS296 4.7 25.8 1.0
O3 A:SO4441 4.7 95.1 1.0
CG B:HIS295 4.9 27.0 1.0
NE A:ARG258 5.0 36.4 1.0
CZ A:ARG258 5.0 41.2 1.0

Sodium binding site 6 out of 11 in 2qfp

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Sodium binding site 6 out of 11 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 Sodium with other atoms in the Na binding site number 6 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:Na444

b:98.7
occ:1.00
 O2 A:SO4441 2.5 94.9 1.0
O1 B:SO4435 2.7 93.0 1.0
NA B:NA443 3.0 81.8 1.0
NE2 B:HIS295 3.0 27.5 1.0
O1 A:SO4441 3.1 94.5 1.0
S A:SO4441 3.4 95.2 1.0
CE1 B:HIS295 3.6 27.2 1.0
S B:SO4435 4.0 92.9 1.0
O4 B:SO4435 4.1 92.9 1.0
CD2 B:HIS295 4.2 24.7 1.0
O4 A:SO4441 4.2 94.9 1.0
NA B:NA442 4.4 90.7 1.0
CE1 B:HIS296 4.5 25.9 1.0
O3 A:SO4441 4.6 95.1 1.0
O3 B:SO4435 4.8 92.2 1.0
ND1 B:HIS295 4.8 26.5 1.0
NE2 B:HIS296 4.9 26.6 1.0

Sodium binding site 7 out of 11 in 2qfp

Go back to Sodium Binding Sites List in 2qfp
Sodium binding site 7 out of 11 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 Sodium with other atoms in the Na binding site number 7 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:Na442

b:76.0
occ:1.00
 O1 D:SO4441 2.5 94.6 1.0
O2 D:SO4441 3.1 94.3 1.0
S D:SO4441 3.3 95.1 1.0
NA C:NA444 3.3 0.0 1.0
NE2 C:HIS295 3.3 37.5 1.0
CD2 C:HIS295 3.6 36.7 1.0
O3 D:SO4441 3.8 95.0 1.0
NH1 D:ARG258 4.2 42.0 1.0
CE1 C:HIS296 4.2 31.0 1.0
NH2 D:ARG258 4.4 37.4 1.0
ND1 C:HIS296 4.4 30.9 1.0
CZ D:ARG258 4.5 38.5 1.0
O4 D:SO4441 4.6 94.5 1.0
CE1 C:HIS295 4.6 37.4 1.0
CG C:HIS295 4.9 36.2 1.0

Sodium binding site 8 out of 11 in 2qfp

Go back to Sodium Binding Sites List in 2qfp
Sodium binding site 8 out of 11 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 Sodium with other atoms in the Na binding site number 8 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:Na443

b:89.4
occ:1.00
 O3 C:SO4435 2.4 87.6 1.0
O4 C:SO4435 2.7 87.0 1.0
F C:F436 2.8 38.0 1.0
S C:SO4435 3.0 87.0 1.0
ND2 C:ASN201 3.2 29.7 1.0
NE2 C:HIS296 3.2 32.8 1.0
CE1 C:HIS296 3.3 31.0 1.0
CE1 C:HIS323 3.8 30.7 1.0
NE2 C:HIS202 3.9 29.5 1.0
O1 D:SO4441 3.9 94.6 1.0
O2 C:SO4435 4.0 87.8 1.0
NA C:NA444 4.1 0.0 1.0
CG C:ASN201 4.1 30.1 1.0
O1 C:SO4435 4.2 87.3 1.0
O3 D:SO4441 4.2 95.0 1.0
ND1 C:HIS323 4.2 29.1 1.0
OD1 C:ASN201 4.3 33.7 1.0
O4 D:SO4441 4.3 94.5 1.0
ZN C:ZN434 4.3 33.6 1.0
O C:HOH548 4.3 36.1 1.0
S D:SO4441 4.4 95.1 1.0
CD2 C:HIS202 4.4 30.1 1.0
CD2 C:HIS296 4.5 31.4 1.0
CE1 C:HIS295 4.6 37.4 1.0
ND1 C:HIS296 4.6 30.9 1.0
NE2 C:HIS295 4.7 37.5 1.0
FE C:FE433 4.8 51.3 1.0
NE2 C:HIS323 4.8 28.1 1.0
CE1 C:HIS202 4.9 31.3 1.0

Sodium binding site 9 out of 11 in 2qfp

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Sodium binding site 9 out of 11 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 Sodium with other atoms in the Na binding site number 9 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:Na444

b:0.0
occ:1.00
 O3 D:SO4441 2.5 95.0 1.0
O3 C:SO4435 2.6 87.6 1.0
NE2 C:HIS295 2.8 37.5 1.0
O1 D:SO4441 3.1 94.6 1.0
CE1 C:HIS295 3.3 37.4 1.0
S D:SO4441 3.3 95.1 1.0
NA C:NA442 3.3 76.0 1.0
O2 C:SO4435 3.4 87.8 1.0
S C:SO4435 3.6 87.0 1.0
CD2 C:HIS295 4.1 36.7 1.0
NA C:NA443 4.1 89.4 1.0
O2 D:SO4441 4.1 94.3 1.0
CE1 C:HIS296 4.4 31.0 1.0
O1 C:SO4435 4.4 87.3 1.0
O4 D:SO4441 4.5 94.5 1.0
ND1 C:HIS295 4.6 36.3 1.0
NE2 C:HIS296 4.6 32.8 1.0
O4 C:SO4435 4.7 87.0 1.0
CG C:HIS295 5.0 36.2 1.0

Sodium binding site 10 out of 11 in 2qfp

Go back to Sodium Binding Sites List in 2qfp
Sodium binding site 10 out of 11 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 Sodium with other atoms in the Na binding site number 10 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:Na442

b:73.5
occ:1.00
 O4 C:SO4441 2.6 88.1 1.0
NE2 D:HIS295 3.6 35.6 1.0
S C:SO4441 3.6 88.4 1.0
O3 C:SO4441 3.6 87.5 1.0
O D:HOH557 3.6 33.5 1.0
CD2 D:HIS295 3.9 36.4 1.0
O1 C:SO4441 4.0 88.3 1.0
NH2 C:ARG258 4.6 51.5 1.0
CE1 D:HIS296 4.6 35.1 1.0
CE1 D:HIS295 4.8 36.8 1.0
O2 C:SO4441 4.9 88.5 1.0
ND1 D:HIS296 4.9 33.1 1.0
CZ C:ARG258 5.0 50.6 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: Mon Oct 7 04:01:21 2024

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