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Iodine in PDB 4bvx: Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C

Enzymatic activity of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C

All present enzymatic activity of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C:
6.1.1.10;

Protein crystallography data

The structure of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C, PDB code: 4bvx was solved by H.Y.Cho, W.W.Seo, H.J.Cho, B.S.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.49 / 1.60
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.284, 71.584, 116.381, 90.00, 90.00, 90.00
R / Rfree (%) 21.681 / 24.657

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C (pdb code 4bvx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C, PDB code: 4bvx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 4bvx

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Iodine binding site 1 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


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 AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1204

b:20.7
occ:0.75
 I3 A:I3C1204 0.0 20.7 0.8
C6 A:I3C1204 2.1 19.1 0.8
C1 A:I3C1204 3.0 19.9 0.8
C5 A:I3C1204 3.1 18.9 0.8
OG A:SER31 3.1 13.6 0.5
C7 A:I3C1204 3.3 19.4 0.8
N13 A:I3C1204 3.3 18.3 0.8
O9 A:I3C1204 3.5 18.6 0.8
O8 A:I3C1204 3.8 19.0 0.8
CB A:LEU29 3.9 12.0 1.0
CD1 A:LEU29 4.0 12.9 1.0
O A:ILE30 4.2 14.6 1.0
CB A:SER31 4.4 13.5 0.5
CB A:SER31 4.4 14.3 0.5
C2 A:I3C1204 4.4 20.0 0.8
C4 A:I3C1204 4.4 18.9 0.8
C A:ILE30 4.5 13.2 1.0
OG A:SER31 4.6 15.7 0.5
CG A:LEU29 4.6 11.9 1.0
CA A:SER31 4.6 13.8 0.5
CA A:SER31 4.6 13.5 0.5
N A:SER31 4.7 12.9 1.0
NE A:ARG2 4.8 20.0 1.0
C A:LEU29 4.8 11.8 1.0
CG A:ARG2 4.8 20.0 1.0
N A:ILE30 4.9 12.2 1.0
C3 A:I3C1204 5.0 19.7 0.8
CA A:LEU29 5.0 11.8 1.0

Iodine binding site 2 out of 9 in 4bvx

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Iodine binding site 2 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1204

b:17.3
occ:0.75
 I2 A:I3C1204 0.0 17.3 0.8
C4 A:I3C1204 2.1 18.9 0.8
C3 A:I3C1204 3.1 19.7 0.8
C5 A:I3C1204 3.1 18.9 0.8
N13 A:I3C1204 3.2 18.3 0.8
C10 A:I3C1204 3.2 19.8 0.8
O12 A:I3C1204 3.5 19.1 0.8
NH1 A:ARG2 3.8 20.0 1.0
O11 A:I3C1204 3.8 20.8 0.8
O A:HOH2003 4.1 16.4 1.0
C6 A:I3C1204 4.4 19.1 0.8
C2 A:I3C1204 4.5 20.0 0.8
CZ A:ARG2 4.7 20.0 1.0

Iodine binding site 3 out of 9 in 4bvx

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Iodine binding site 3 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


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 AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1204

b:25.7
occ:0.75
 I1 A:I3C1204 0.0 25.7 0.8
C2 A:I3C1204 2.1 20.0 0.8
C3 A:I3C1204 3.1 19.7 0.8
C1 A:I3C1204 3.1 19.9 0.8
C10 A:I3C1204 3.3 19.8 0.8
C7 A:I3C1204 3.3 19.4 0.8
O11 A:I3C1204 3.6 20.8 0.8
O8 A:I3C1204 3.6 19.0 0.8
NH2 A:ARG2 3.8 20.0 1.0
O12 A:I3C1204 3.8 19.1 0.8
O9 A:I3C1204 3.9 18.6 0.8
C4 A:I3C1204 4.4 18.9 0.8
C6 A:I3C1204 4.4 19.1 0.8
CZ A:ARG2 4.7 20.0 1.0
NH1 A:ARG2 5.0 20.0 1.0

Iodine binding site 4 out of 9 in 4bvx

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Iodine binding site 4 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


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 AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1205

b:47.4
occ:0.50
 I3 A:I3C1205 0.0 47.4 0.5
C6 A:I3C1205 2.1 36.1 0.5
C5 A:I3C1205 3.1 33.0 0.5
C1 A:I3C1205 3.1 35.8 0.5
N13 A:I3C1205 3.2 33.5 0.5
C7 A:I3C1205 3.4 35.0 0.5
O9 A:I3C1205 3.6 35.2 0.5
O8 A:I3C1205 4.0 35.3 0.5
C4 A:I3C1205 4.4 30.5 0.5
NH1 A:ARG25 4.5 41.2 1.0
C2 A:I3C1205 4.5 34.3 0.5

Iodine binding site 5 out of 9 in 4bvx

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Iodine binding site 5 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1205

b:22.8
occ:0.50
 I2 A:I3C1205 0.0 22.8 0.5
C4 A:I3C1205 2.1 30.5 0.5
C3 A:I3C1205 3.1 31.3 0.5
O A:LEU71 3.1 14.9 1.0
C5 A:I3C1205 3.1 33.0 0.5
N13 A:I3C1205 3.3 33.5 0.5
C10 A:I3C1205 3.3 29.7 0.5
O12 A:I3C1205 3.7 26.2 0.5
O11 A:I3C1205 3.7 29.6 0.5
NH2 A:ARG25 3.8 42.1 1.0
O A:HOH2046 3.9 18.8 1.0
C A:LEU71 4.0 13.8 1.0
O A:LEU72 4.1 18.8 1.0
CA A:LEU72 4.1 15.6 1.0
O A:HOH2084 4.2 23.4 1.0
CZ A:ARG25 4.3 40.0 1.0
NE A:ARG25 4.3 37.5 1.0
C A:LEU72 4.3 16.8 1.0
CB B:ALA65 4.4 13.0 1.0
C2 A:I3C1205 4.4 34.3 0.5
C6 A:I3C1205 4.5 36.1 0.5
N A:LEU72 4.5 14.3 1.0
N A:GLY74 4.7 19.9 1.0
CA A:GLY74 4.8 20.5 1.0

Iodine binding site 6 out of 9 in 4bvx

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Iodine binding site 6 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1205

b:39.3
occ:0.50
 I1 A:I3C1205 0.0 39.3 0.5
C2 A:I3C1205 2.1 34.3 0.5
O A:HOH2085 2.8 30.5 1.0
C3 A:I3C1205 3.1 31.3 0.5
C1 A:I3C1205 3.1 35.8 0.5
C10 A:I3C1205 3.2 29.7 0.5
C7 A:I3C1205 3.4 35.0 0.5
O8 A:I3C1205 3.6 35.3 0.5
O12 A:I3C1205 3.6 26.2 0.5
O11 A:I3C1205 3.6 29.6 0.5
O9 A:I3C1205 4.0 35.2 0.5
O B:SER63 4.1 17.4 1.0
CG2 B:THR64 4.3 14.9 1.0
C4 A:I3C1205 4.4 30.5 0.5
C6 A:I3C1205 4.5 36.1 0.5
CA B:THR64 4.7 14.4 1.0
CB B:THR64 4.8 14.8 1.0

Iodine binding site 7 out of 9 in 4bvx

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Iodine binding site 7 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1169

b:17.7
occ:0.75
 I3 B:I3C1169 0.0 17.7 0.8
C6 B:I3C1169 2.1 16.7 0.8
C5 B:I3C1169 3.0 16.3 0.8
C1 B:I3C1169 3.1 18.1 0.8
N13 B:I3C1169 3.2 14.8 0.8
C7 B:I3C1169 3.3 17.8 0.8
NE2 B:HIS148 3.5 19.5 1.0
O9 B:I3C1169 3.7 17.5 0.8
CD2 B:HIS148 3.7 18.1 1.0
O8 B:I3C1169 3.8 18.3 0.8
SG B:CYS147 4.0 11.5 1.0
CB B:CYS147 4.2 10.5 1.0
CE1 B:HIS148 4.3 18.4 1.0
C4 B:I3C1169 4.4 16.2 0.8
C2 B:I3C1169 4.4 18.1 0.8
O B:ARG144 4.6 8.3 1.0
CG B:HIS148 4.6 16.0 1.0
CG B:ARG144 4.8 10.1 1.0
ND1 B:HIS148 4.9 18.3 1.0
C3 B:I3C1169 5.0 17.6 0.8
N B:HIS148 5.0 11.2 1.0

Iodine binding site 8 out of 9 in 4bvx

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Iodine binding site 8 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1169

b:14.8
occ:0.75
 I2 B:I3C1169 0.0 14.8 0.8
C4 B:I3C1169 2.1 16.2 0.8
C5 B:I3C1169 3.0 16.3 0.8
C3 B:I3C1169 3.1 17.6 0.8
O B:HOH2071 3.1 20.9 1.0
N13 B:I3C1169 3.2 14.8 0.8
C10 B:I3C1169 3.3 17.7 0.8
CD1 B:LEU140 3.6 19.7 1.0
O11 B:I3C1169 3.6 18.2 0.8
O B:HOH2091 3.9 19.4 1.0
O12 B:I3C1169 4.0 18.0 0.8
O B:LEU140 4.1 12.8 1.0
N B:ARG144 4.1 8.5 1.0
CB B:SER143 4.2 9.5 1.0
CA B:ARG144 4.3 8.7 1.0
CG B:LYS166 4.3 26.5 1.0
CB B:ARG144 4.3 9.5 1.0
C6 B:I3C1169 4.4 16.7 0.8
C2 B:I3C1169 4.4 18.1 0.8
C B:SER143 4.5 8.7 1.0
O B:HOH2093 4.5 25.2 1.0
CA B:LYS166 4.8 26.8 1.0
CG B:LEU140 4.8 18.9 1.0
O B:HOH2090 4.8 19.6 1.0
CB B:PHE164 4.8 13.4 1.0
N B:LYS166 5.0 24.6 1.0
C1 B:I3C1169 5.0 18.1 0.8
O B:ILE165 5.0 24.1 1.0

Iodine binding site 9 out of 9 in 4bvx

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Iodine binding site 9 out of 9 in the Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1169

b:25.3
occ:0.75
 I1 B:I3C1169 0.0 25.3 0.8
C2 B:I3C1169 2.1 18.1 0.8
C3 B:I3C1169 3.1 17.6 0.8
C1 B:I3C1169 3.1 18.1 0.8
C10 B:I3C1169 3.2 17.7 0.8
C7 B:I3C1169 3.3 17.8 0.8
O12 B:I3C1169 3.4 18.0 0.8
O8 B:I3C1169 3.6 18.3 0.8
CE B:LYS166 3.6 26.6 1.0
NZ B:LYS166 3.7 26.6 1.0
O9 B:I3C1169 3.8 17.5 0.8
O11 B:I3C1169 3.8 18.2 0.8
CD B:ARG144 3.9 11.1 1.0
NH1 B:ARG168 3.9 40.7 1.0
CZ B:ARG168 3.9 40.3 1.0
NE B:ARG168 4.2 41.5 1.0
NH2 B:ARG168 4.3 36.6 1.0
C4 B:I3C1169 4.4 16.2 0.8
C6 B:I3C1169 4.5 16.7 0.8
CD B:ARG168 4.6 43.2 1.0
CD B:LYS166 4.8 26.5 1.0
NE B:ARG144 4.8 12.3 1.0
NH1 B:ARG144 4.9 13.8 1.0
CG B:ARG144 4.9 10.1 1.0

Reference:

H.Y.Cho, W.W.Seo, H.J.Cho, B.S.Kang. Crystal Structure of the AIMP3-Mrs N-Terminal Domain Complex with I3C To Be Published.
Page generated: Sun Aug 11 17:28:17 2024

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