Nickel in PDB 4odp: Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide

Enzymatic activity of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide

All present enzymatic activity of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide:
5.2.1.8;

Protein crystallography data

The structure of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide, PDB code: 4odp 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)*	29.63 / 1.75
*Space group*	P 4₁ 3 2
*Cell size a, b, c (Å), α, β, γ (°)*	93.690, 93.690, 93.690, 90.00, 90.00, 90.00
*R / R_free (%)*	18.4 / 20.2

Other elements in 4odp:

The structure of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide (pdb code 4odp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide, PDB code: 4odp:

Nickel binding site 1 out of 1 in 4odp

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Nickel Binding Sites List in 4odp

Nickel binding site 1 out of 1 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni206 b:28.6 occ:1.00	NE2	A:HIS110	2.1	28.0	1.0
	NE2	A:HIS101	2.1	23.8	1.0
	NE2	A:HIS108	2.2	26.2	1.0
	NE2	A:HIS99	2.2	27.2	1.0
	ND1	A:HIS97	2.2	24.9	1.0
	CD2	A:HIS101	3.0	31.1	1.0
	CE1	A:HIS97	3.1	34.3	1.0
	CD2	A:HIS110	3.1	31.6	1.0
	CE1	A:HIS108	3.1	28.2	1.0
	CE1	A:HIS110	3.1	27.6	1.0
	CE1	A:HIS99	3.1	35.4	1.0
	CE1	A:HIS101	3.2	25.5	1.0
	CD2	A:HIS108	3.2	26.8	1.0
	CD2	A:HIS99	3.2	25.4	1.0
	CG	A:HIS97	3.3	29.3	1.0
	CB	A:HIS97	3.8	25.7	1.0
	CG	A:HIS101	4.2	25.1	1.0
	ND1	A:HIS110	4.2	28.6	1.0
	CG	A:HIS110	4.2	27.0	1.0
	ND1	A:HIS101	4.2	26.1	1.0
	ND1	A:HIS108	4.2	30.6	1.0
	NE2	A:HIS97	4.2	39.3	1.0
	ND1	A:HIS99	4.3	26.2	1.0
	CG	A:HIS108	4.3	29.5	1.0
	CG	A:HIS99	4.3	26.7	1.0
	CD2	A:HIS97	4.4	30.4	1.0

Reference:

E.M.Quistgaard, C.Low, P.Nordlund. Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide To Be Published.

Page generated: Wed Oct 9 18:36:17 2024

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