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Sodium in PDB 5u0j: C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form

Enzymatic activity of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form

All present enzymatic activity of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form:
3.5.1.2;

Protein crystallography data

The structure of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form, PDB code: 5u0j was solved by C.C.Pasquali, A.Gonzalez, S.M.G.Dias, A.L.B.Ambrosio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.10 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.490, 47.180, 115.698, 90.00, 90.09, 90.00
R / Rfree (%) 18.4 / 22.2

Sodium Binding Sites:

The binding sites of Sodium atom in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form (pdb code 5u0j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form, PDB code: 5u0j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5u0j

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Sodium binding site 1 out of 6 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:41.3
occ:1.00
 O A:HOH830 2.4 35.9 1.0
OH A:TYR562 2.4 42.7 1.0
O A:HOH889 2.4 55.9 1.0
O A:HOH899 2.5 61.6 1.0
O A:HOH946 2.5 51.9 1.0
O A:HOH841 2.5 42.4 1.0
CZ A:TYR562 3.4 45.2 1.0
CE1 A:TYR562 3.7 33.0 1.0
O A:HOH937 3.7 49.7 1.0
O A:HOH939 4.3 60.7 1.0
O A:HOH816 4.3 52.3 1.0
OE2 A:GLU596 4.4 33.9 1.0
OE1 A:GLU596 4.5 32.6 1.0
O B:HOH783 4.5 42.1 1.0
O A:HOH872 4.5 36.7 1.0
CE2 A:TYR562 4.6 39.7 1.0
CD A:GLU596 4.8 33.3 1.0
O A:HOH921 4.9 55.6 1.0

Sodium binding site 2 out of 6 in 5u0j

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Sodium binding site 2 out of 6 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:81.6
occ:1.00
 O A:HOH922 2.4 52.8 1.0
O A:HOH867 2.6 57.9 1.0
O A:HOH871 2.8 56.4 1.0
O A:HOH862 2.8 52.2 1.0
O A:HOH893 2.9 42.1 1.0
O A:GLY597 2.9 29.0 1.0
O A:HOH818 3.7 48.3 1.0
C A:GLY597 4.0 38.2 1.0
CA A:GLY597 4.7 28.2 1.0
CG2 A:VAL599 4.8 33.4 1.0
O A:HOH886 4.9 25.8 1.0

Sodium binding site 3 out of 6 in 5u0j

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Sodium binding site 3 out of 6 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:49.0
occ:1.00
 O A:HOH938 2.3 50.6 1.0
O A:HOH854 2.6 43.9 1.0
O A:HOH852 2.6 42.5 1.0
O A:HOH905 3.9 50.5 1.0
O A:HOH858 4.1 40.2 1.0
O A:HIS629 4.2 30.4 1.0
O A:HOH878 4.5 41.7 1.0

Sodium binding site 4 out of 6 in 5u0j

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Sodium binding site 4 out of 6 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na701

b:46.7
occ:1.00
 O C:HOH858 2.3 41.2 1.0
OH C:TYR562 2.4 37.8 1.0
O C:HOH900 2.5 52.3 1.0
O C:HOH953 2.5 52.1 1.0
O C:HOH902 2.5 61.2 1.0
O C:HOH854 2.7 40.2 1.0
CZ C:TYR562 3.4 41.0 1.0
CE1 C:TYR562 3.7 30.7 1.0
O C:HOH920 3.8 61.0 1.0
O C:HOH815 4.1 52.7 1.0
OE2 C:GLU596 4.3 31.9 1.0
O C:HOH846 4.3 45.5 1.0
O C:HOH934 4.3 50.8 1.0
O D:HOH875 4.6 45.2 1.0
OE1 C:GLU596 4.6 33.1 1.0
O C:HOH877 4.6 36.2 1.0
CE2 C:TYR562 4.7 35.5 1.0
CD C:GLU596 4.8 33.5 1.0

Sodium binding site 5 out of 6 in 5u0j

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Sodium binding site 5 out of 6 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na701

b:43.7
occ:1.00
 O D:HOH836 2.3 34.3 1.0
O D:HOH896 2.4 56.2 1.0
OH D:TYR562 2.4 40.6 1.0
O D:HOH956 2.5 54.5 1.0
O D:HOH856 2.7 37.1 1.0
CZ D:TYR562 3.4 38.4 1.0
CE1 D:TYR562 3.7 32.9 1.0
O D:HOH807 4.2 50.4 1.0
O D:HOH945 4.2 60.1 1.0
O C:HOH848 4.3 41.0 1.0
OE2 D:GLU596 4.4 33.1 1.0
CE2 D:TYR562 4.6 37.8 1.0
OE1 D:GLU596 4.6 32.9 1.0
O D:HOH865 4.7 37.7 1.0
CD D:GLU596 4.9 33.2 1.0
O D:HOH926 4.9 56.4 1.0

Sodium binding site 6 out of 6 in 5u0j

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Sodium binding site 6 out of 6 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na702

b:47.3
occ:1.00
 O D:HOH947 2.4 53.0 1.0
O D:HOH847 2.5 41.9 1.0
O D:HOH855 2.7 41.7 1.0
O D:HOH846 4.1 39.9 1.0
O D:HIS629 4.2 28.3 1.0
O D:HOH891 4.4 40.8 1.0
O D:HOH906 4.6 54.7 1.0

Reference:

C.C.Pasquali, Z.Islam, D.Adamoski, I.M.Ferreira, R.D.Righeto, J.Bettini, R.V.Portugal, W.W.Yue, A.Gonzalez, S.M.G.Dias, A.L.B.Ambrosio. The Origin and Evolution of Human Glutaminases and Their Atypical C-Terminal Ankyrin Repeats. J. Biol. Chem. V. 292 11572 2017.
ISSN: ESSN 1083-351X
PubMed: 28526749
DOI: 10.1074/JBC.M117.787291
Page generated: Tue Oct 8 00:20:01 2024

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