Sodium in PDB 9ggi: Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)

Enzymatic activity of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)

All present enzymatic activity of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl):
4.3.2.1;

Protein crystallography data

The structure of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl), PDB code: 9ggi was solved by M.Nielipinski, A.J.Pietrzyk-Brzezinska, D.Krzeszewska, B.Sekula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.45 / 1.55
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	106.044, 229.542, 111.586, 90, 90.56, 90
*R / R_free (%)*	14.7 / 17.1

Other elements in 9ggi:

The structure of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) (pdb code 9ggi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl), PDB code: 9ggi:

Sodium binding site 1 out of 1 in 9ggi

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Sodium Binding Sites List in 9ggi

Sodium binding site 1 out of 1 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)

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 Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Na610 b:27.9 occ:1.00	NZ	C:LYS381	2.5	35.6	1.0
	OD2	C:ASP380	2.7	32.6	1.0
	OD1	C:ASP380	3.0	24.0	1.0
	NH2	C:ARG288	3.1	18.7	1.0
	O	C:HOH762	3.2	22.7	1.0
	CG	C:ASP380	3.3	23.2	1.0
	O	C:PHE377	3.3	22.2	1.0
	NE	C:ARG288	3.5	18.4	1.0
	CZ	C:ARG288	3.7	18.4	1.0
	CE	C:LYS381	3.8	33.1	1.0
	C	C:PHE377	4.0	20.9	1.0
	CG2	C:VAL169	4.0	18.6	1.0
	O	C:HOH712	4.2	46.4	1.0
	CB	C:PHE377	4.2	20.7	1.0
	CG1	C:VAL169	4.2	18.6	1.0
	CD	C:LYS381	4.4	27.8	1.0
	CD2	C:PHE173	4.6	18.4	1.0
	N	C:GLN378	4.6	20.2	1.0
	CA	C:GLN378	4.7	21.1	1.0
	CB	C:ASP380	4.7	21.2	1.0
	CA	C:PHE377	4.7	19.7	1.0
	CB	C:VAL169	4.8	18.6	1.0
	CD	C:ARG288	4.8	18.4	1.0
	CG	C:LYS381	4.8	24.0	1.0
	CE2	C:PHE173	4.9	18.4	1.0

Reference:

M.Nielipinski, D.Krzeszewska, A.J.Pietrzyk-Brzezinska, B.Sekula. Arabidopsis Thaliana Argininosuccinate Lyase Structure Uncovers the Role of Serine As the Catalytic Base. J.Struct.Biol. 08130 2024.
ISSN: ESSN 1095-8657
PubMed: 39384000
DOI: 10.1016/J.JSB.2024.108130

Page generated: Mon Aug 18 17:08:26 2025

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