Atomistry » Sodium » PDB 5txu-5u63 » 5u0i
Atomistry »
  Sodium »
    PDB 5txu-5u63 »
      5u0i »

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

Last articles

Na in 3V8F
Na in 3VBH
Na in 3VBO
Na in 3V7J
Na in 3VBF
Na in 3VA7
Na in 3V7K
Na in 3V7Z
Na in 3V7L
Na in 3V72
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy