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 / R_free (%)*	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

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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

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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

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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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