Sodium in PDB 1uxj: Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

Enzymatic activity of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

All present enzymatic activity of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface:
1.1.1.37;

Protein crystallography data

The structure of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface, PDB code: 1uxj was solved by A.Bjork, B.Dalhus, D.Mantzilas, V.G.H.Eijsink, R.Sirevag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.00 / 1.75
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	105.247, 105.247, 102.196, 90.00, 90.00, 120.00
*R / R_free (%)*	17.7 / 21.1

Other elements in 1uxj:

The structure of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface also contains other interesting chemical elements:

Cadmium	(Cd)	9 atoms
Chlorine	(Cl)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface (pdb code 1uxj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface, PDB code: 1uxj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1uxj

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Sodium Binding Sites List in 1uxj

Sodium binding site 1 out of 3 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1314 b:30.7 occ:0.50	ND1	A:HIS19	2.7	16.0	1.0
	O	A:HOH2017	2.7	15.5	1.0
	CE1	A:HIS19	3.4	15.7	1.0
	CG	A:HIS19	3.7	16.3	1.0
	CE1	A:TYR227	3.8	14.1	1.0
	CG2	A:THR16	4.1	12.7	1.0
	CB	A:HIS19	4.1	14.8	1.0
	CD1	A:TYR227	4.4	12.8	1.0
	OG1	A:THR16	4.5	13.2	1.0
	NE2	A:HIS19	4.5	18.3	1.0
	CB	A:THR16	4.7	13.2	1.0
	CA	A:THR16	4.7	11.9	1.0
	CD2	A:HIS19	4.7	18.5	1.0
	CZ	A:TYR227	4.7	13.1	1.0
	OH	A:TYR227	4.8	13.9	1.0
	NA	A:NA1315	4.8	24.6	0.5

Sodium binding site 2 out of 3 in 1uxj

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Sodium Binding Sites List in 1uxj

Sodium binding site 2 out of 3 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1315 b:24.6 occ:0.50	O	A:HOH2251	2.8	22.9	1.0
	O	A:HOH2017	3.2	15.5	1.0
	CE2	A:TYR226	3.7	13.9	1.0
	CD1	A:PHE12	4.2	18.7	1.0
	CE1	A:PHE12	4.3	21.6	1.0
	OH	A:TYR227	4.4	13.9	1.0
	CZ	A:TYR226	4.4	17.1	1.0
	OH	A:TYR226	4.4	19.0	1.0
	CD2	A:TYR226	4.4	14.2	1.0
	OG1	A:THR16	4.5	13.2	1.0
	NA	A:NA1314	4.8	30.7	0.5
	O	A:HOH2055	5.0	23.4	1.0

Sodium binding site 3 out of 3 in 1uxj

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Sodium Binding Sites List in 1uxj

Sodium binding site 3 out of 3 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Na1315 b:14.2 occ:1.00	OE2	C:GLU238	2.2	28.6	1.0
	OE1	C:GLU238	2.7	28.9	1.0
	CD	C:GLU238	2.8	25.5	1.0
	NZ	A:LYS165	4.0	29.3	1.0
	O	A:HOH2186	4.2	33.6	1.0
	NZ	C:LYS24	4.2	36.2	1.0
	CG	C:GLU238	4.3	21.3	1.0
	CE	C:LYS244	4.5	26.6	1.0
	NZ	C:LYS242	4.9	28.5	1.0
	NZ	C:LYS244	4.9	24.7	1.0

Reference:

A.Bjork, B.Dalhus, D.Mantzilas, R.Sirevag, V.G.H.Eijsink. Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface. J.Mol.Biol. V. 341 1215 2004.
ISSN: ISSN 0022-2836
PubMed: 15321717
DOI: 10.1016/J.JMB.2004.06.079

Page generated: Sun Oct 6 22:47:41 2024

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