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Sodium in PDB 5u0i: C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Tetragonal Crystal Form

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

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

Protein crystallography data

The structure of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Tetragonal Crystal Form, PDB code: 5u0i 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) 38.09 / 1.42
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 75.290, 75.290, 88.310, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18

Other elements in 5u0i:

The structure of C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Tetragonal Crystal Form also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Tetragonal Crystal Form (pdb code 5u0i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Tetragonal Crystal Form, PDB code: 5u0i:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5u0i

Go back to Sodium Binding Sites List in 5u0i
Sodium binding site 1 out of 3 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Tetragonal 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) - Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:33.2
occ:1.00
 O B:HOH929 2.4 40.1 1.0
OG B:SER586 2.9 16.1 1.0
O B:HOH911 3.3 42.6 1.0
O B:TYR584 3.4 15.1 1.0
C B:ASP585 3.5 10.9 1.0
CB B:ARG618 3.6 15.9 1.0
N B:SER586 3.6 10.5 1.0
CB B:SER586 3.6 13.1 1.0
CA B:ASP585 3.8 10.7 1.0
CZ B:ARG618 3.8 17.2 1.0
O A:HOH811 3.8 34.4 1.0
NH2 B:ARG618 3.9 18.6 1.0
CA B:ARG618 3.9 13.3 1.0
NE B:ARG618 4.0 16.9 1.0
O B:ASP585 4.0 11.9 1.0
CG B:ARG618 4.0 19.3 1.0
C B:TYR584 4.1 12.5 1.0
CA B:SER586 4.2 11.2 1.0
NH1 B:ARG618 4.2 18.6 1.0
N B:ASP585 4.3 11.3 1.0
O B:HOH845 4.3 41.0 1.0
N B:ARG618 4.4 12.2 1.0
CD B:ARG618 4.6 19.0 1.0
O B:HOH819 4.7 34.6 1.0
CE1 A:TYR562 4.9 20.1 1.0
O A:HOH802 4.9 36.9 1.0

Sodium binding site 2 out of 3 in 5u0i

Go back to Sodium Binding Sites List in 5u0i
Sodium binding site 2 out of 3 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Tetragonal 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) - Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:31.9
occ:1.00
 O B:HOH909 2.4 39.4 1.0
OG1 B:THR563 2.7 15.2 1.0
CB B:THR563 3.4 13.3 1.0
CG2 B:THR563 3.7 15.2 1.0
OD2 B:ASP565 3.8 16.3 1.0
CB B:ASP565 4.1 14.0 1.0
O B:HOH850 4.3 44.0 1.0
CG B:ASP565 4.4 14.3 1.0
O B:HOH895 4.6 44.5 1.0
O B:PHE559 4.9 11.7 1.0
CA B:THR563 4.9 11.7 1.0

Sodium binding site 3 out of 3 in 5u0i

Go back to Sodium Binding Sites List in 5u0i
Sodium binding site 3 out of 3 in the C-Terminal Ankyrin Repeats From Human Kidney-Type Glutaminase (Kga) - Tetragonal 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) - Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na703

b:20.0
occ:1.00
 O B:HOH835 2.9 35.3 1.0
O B:HOH969 3.0 42.8 1.0
CD2 B:PHE614 4.1 39.6 1.0
O B:HOH897 4.3 22.6 1.0
CG2 B:THR622 4.4 12.5 1.0
CE2 B:PHE614 4.4 40.0 1.0
O B:HOH875 4.6 16.9 1.0
O B:HOH906 4.8 36.9 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 00:20:00 2024

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