Iodine in PDB 4xkz: Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa

Enzymatic activity of Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa:
6.1.1.9;

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa, PDB code: 4xkz was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 1.95
*Space group*	P 4 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	103.360, 103.360, 79.140, 90.00, 90.00, 90.00
*R / R_free (%)*	15.6 / 19.3

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa (pdb code 4xkz). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa, PDB code: 4xkz:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 4xkz

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Iodine Binding Sites List in 4xkz

Iodine binding site 1 out of 4 in the Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:I901 b:46.7 occ:0.80	C	A:LYS718	4.0	25.7	1.0
	N	A:PRO719	4.1	26.9	1.0
	O	A:LYS718	4.1	26.0	1.0
	CB	A:LYS718	4.1	25.7	1.0
	CA	A:PRO719	4.2	28.5	1.0
	CD2	A:LEU846	4.2	39.1	1.0
	CE3	A:TRP722	4.3	33.7	1.0
	CB	A:LYS845	4.3	32.2	1.0
	CG	A:PRO719	4.4	29.7	1.0
	CD	A:PRO719	4.5	27.5	1.0
	O	A:HOH1153	4.7	39.8	1.0
	CA	A:LYS718	4.7	23.9	1.0
	CB	A:PRO719	4.8	28.3	1.0
	CB	A:TRP722	4.9	32.0	1.0
	CZ3	A:TRP722	4.9	35.4	1.0

Iodine binding site 2 out of 4 in 4xkz

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Iodine Binding Sites List in 4xkz

Iodine binding site 2 out of 4 in the Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:I902 b:46.2 occ:0.40	I	A:IOD903	2.8	47.7	0.4
	O	A:HOH1040	3.0	25.8	1.0
	NH1	A:ARG740	3.2	29.9	1.0
	O	A:HOH1029	3.3	20.6	1.0
	CD	A:ARG740	3.7	28.6	1.0
	CD1	A:ILE675	3.9	21.0	1.0
	CG1	A:ILE675	4.1	20.1	1.0
	NE	A:ARG787	4.2	49.1	1.0
	CZ	A:ARG740	4.3	30.9	1.0
	CG2	A:ILE675	4.4	21.5	1.0
	NE	A:ARG740	4.5	31.0	1.0
	NH1	A:ARG787	4.5	60.2	1.0
	O	A:HOH1026	4.6	20.5	1.0
	CB	A:ARG740	4.7	23.8	1.0
	CZ	A:ARG787	4.8	56.5	1.0
	CB	A:ILE675	4.9	20.4	1.0
	CG	A:ARG740	4.9	26.7	1.0
	CD	A:ARG787	5.0	39.7	1.0

Iodine binding site 3 out of 4 in 4xkz

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Iodine Binding Sites List in 4xkz

Iodine binding site 3 out of 4 in the Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:I903 b:47.7 occ:0.40	I	A:IOD902	2.8	46.2	0.4
	O	A:HOH1169	2.8	39.8	1.0
	CD2	A:LEU678	4.0	20.7	1.0
	NE2	A:GLN679	4.2	22.8	1.0
	CG2	A:ILE675	4.2	21.5	1.0
	CG1	A:ILE675	4.5	20.1	1.0
	CB	A:ARG740	4.6	23.8	1.0
	O	A:HOH1114	4.6	40.1	1.0
	CD	A:ARG740	4.7	28.6	1.0
	NE	A:ARG787	4.8	49.1	1.0
	CG2	A:VAL741	4.9	22.2	1.0
	CB	A:ILE675	4.9	20.4	1.0
	CD	A:ARG787	5.0	39.7	1.0

Iodine binding site 4 out of 4 in 4xkz

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Iodine Binding Sites List in 4xkz

Iodine binding site 4 out of 4 in the Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:I904 b:27.1 occ:0.50	O	A:HOH1045	2.5	38.9	1.0
	CG2	A:ILE756	3.5	33.8	1.0
	N	A:ILE756	3.5	24.2	1.0
	CB	A:ILE756	3.8	34.0	1.0
	CB	A:MET753	3.9	26.9	1.0
	C	A:MET753	3.9	22.2	1.0
	CA	A:MET753	4.0	25.0	1.0
	N	A:PHE755	4.0	22.5	1.0
	O	A:MET753	4.2	20.7	1.0
	CB	A:PHE755	4.3	26.7	1.0
	CA	A:ILE756	4.3	26.3	1.0
	N	A:PRO754	4.4	22.6	1.0
	CA	A:PHE755	4.4	24.4	1.0
	C	A:PHE755	4.5	23.8	1.0
	CG	A:MET753	4.6	32.0	1.0
	SG	A:CYS639	4.6	31.0	1.0
	CD2	A:PHE755	4.8	37.6	1.0
	SD	A:MET753	4.9	39.7	1.0
	CD	A:PRO754	4.9	24.9	1.0
	C	A:PRO754	4.9	22.6	1.0

Reference:

T.E.Edwards, D.Fox Iii, C.Manoil. Crystal Structure of the C-Terminal Anticodon Loop Binding Domain of A Valyl-Trna Synthetase From Pseudomonas Aeruginosa. To Be Published.

Page generated: Sun Aug 11 20:20:09 2024

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