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 / Rfree (%) 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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 Dec 13 19:37:48 2020

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