Sodium in PDB 4odn: Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide

Enzymatic activity of Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide

All present enzymatic activity of Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide:
5.2.1.8;

Protein crystallography data

The structure of Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide, PDB code: 4odn was solved by E.M.Quistgaard, C.Low, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	28.41 / 1.60
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	39.830, 40.550, 53.220, 90.00, 91.24, 90.00
*R / R_free (%)*	17.6 / 19.8

Other elements in 4odn:

The structure of Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide (pdb code 4odn). 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 Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide, PDB code: 4odn:

Sodium binding site 1 out of 1 in 4odn

Go back to

Sodium Binding Sites List in 4odn

Sodium binding site 1 out of 1 in the Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na207 b:36.1 occ:1.00	OD1	A:ASN35	2.1	19.8	1.0
	O4	A:SO4201	2.2	20.3	1.0
	CG	A:ASN35	2.5	16.4	1.0
	CB	A:ASN35	2.7	11.9	1.0
	N	A:LEU30	2.7	7.8	1.0
	S	A:SO4201	2.7	32.0	1.0
	O1	A:SO4201	2.8	31.9	1.0
	O3	A:SO4201	3.0	33.4	1.0
	O	A:LEU30	3.3	11.6	1.0
	CB	A:TYR29	3.5	8.1	1.0
	CA	A:LEU30	3.6	7.4	1.0
	CA	A:TYR29	3.6	7.5	1.0
	C	A:TYR29	3.6	8.3	1.0
	ND2	A:ASN35	3.6	19.8	1.0
	CB	A:LEU30	3.7	9.5	1.0
	C	A:LEU30	3.8	9.2	1.0
	O	A:GLY146	4.1	11.1	1.0
	O	A:HOH301	4.1	8.7	1.0
	O2	A:SO4201	4.1	35.2	1.0
	ND1	A:HIS147	4.2	13.3	1.0
	CA	A:ASN35	4.2	10.3	1.0
	CA	A:HIS147	4.2	10.2	1.0
	N	A:ALA148	4.4	9.4	1.0
	CD2	A:TYR29	4.4	8.9	1.0
	CG	A:TYR29	4.5	8.2	1.0
	O	A:TYR29	4.8	8.5	1.0
	CB	A:HIS147	4.8	10.7	1.0
	CG	A:HIS147	4.8	11.3	1.0
	N	A:ASN35	4.8	8.9	1.0
	C	A:HIS147	4.8	10.0	1.0
	C	A:GLY146	5.0	10.4	1.0
	CE1	A:HIS147	5.0	13.3	1.0

Reference:

E.M.Quistgaard, C.Low, P.Nordlund. Structure of Slyd From Thermus Thermophilus in Complex with S2-Plus Peptide To Be Published.

Page generated: Mon Oct 7 17:26:55 2024

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