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Iodine in PDB 6ygd: Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa

Enzymatic activity of Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa

All present enzymatic activity of Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa:
2.3.1.256;

Protein crystallography data

The structure of Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa, PDB code: 6ygd was solved by S.Grunwald, L.Hopf, T.Bock-Bierbaum, C.C.Lally, C.M.T.Spahn, O.Daumke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.34 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.136, 134.927, 165.740, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.8

Other elements in 6ygd:

The structure of Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa (pdb code 6ygd). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa, PDB code: 6ygd:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 6ygd

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Iodine binding site 1 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I801

b:53.6
occ:0.91
 CG B:GLN409 3.6 59.3 1.0
NH1 B:ARG408 3.6 27.8 1.0
N A:ARG140 3.6 32.8 1.0
CD B:ARG408 3.7 27.0 1.0
CG B:ARG408 3.9 35.8 1.0
NE2 B:GLN409 4.0 72.0 1.0
CA A:LYS139 4.0 39.4 1.0
O B:HOH939 4.0 40.1 1.0
CB B:ARG408 4.0 38.2 1.0
O B:CYS405 4.1 49.9 1.0
O A:ARG140 4.2 43.0 1.0
CG A:LYS139 4.2 44.1 1.0
CD1 B:LEU455 4.2 28.6 1.0
C A:LYS139 4.3 39.9 1.0
CD B:GLN409 4.3 65.8 1.0
N B:GLN409 4.5 52.7 1.0
CZ B:ARG408 4.6 38.8 1.0
NE B:ARG408 4.6 35.7 1.0
CB A:LYS139 4.6 44.2 1.0
CA A:ARG140 4.6 36.2 1.0
CD1 B:ILE457 4.7 46.0 1.0
CB A:ARG140 4.8 39.9 1.0
O A:MET138 4.8 58.2 1.0
CB B:GLN409 4.8 55.8 1.0
C B:ARG408 4.9 49.1 1.0
C A:ARG140 4.9 41.8 1.0
CA B:GLN409 4.9 58.0 1.0
CG1 B:ILE457 5.0 50.6 1.0

Iodine binding site 2 out of 10 in 6ygd

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Iodine binding site 2 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I802

b:0.4
occ:0.99
 N B:PHE461 3.8 41.8 1.0
CD B:PRO460 3.9 37.1 1.0
CE B:LYS459 4.0 38.8 1.0
CB B:PHE461 4.0 42.1 1.0
CD2 B:PHE461 4.1 45.2 1.0
CB B:PRO460 4.1 36.1 1.0
NZ B:LYS459 4.3 34.2 1.0
CG B:PRO460 4.3 38.1 1.0
N B:PRO460 4.3 39.1 1.0
CA B:PHE461 4.5 44.0 1.0
CB B:LYS459 4.6 37.5 1.0
C B:PRO460 4.6 38.0 1.0
CG B:PHE461 4.6 45.4 1.0
CA B:PRO460 4.6 35.5 1.0
C B:LYS459 5.0 47.6 1.0

Iodine binding site 3 out of 10 in 6ygd

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Iodine binding site 3 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I803

b:77.4
occ:0.55
 CE1 B:TYR274 3.8 81.2 1.0
CB B:ARG279 3.9 0.0 1.0
CD1 B:TYR274 4.0 79.6 1.0
CD B:GLU119 4.1 0.9 1.0
CG B:GLU119 4.2 0.7 1.0
OE2 B:GLU119 4.2 0.2 1.0
N B:ARG279 4.2 91.0 1.0
C B:HIS278 4.3 86.6 1.0
NE B:ARG279 4.3 0.1 1.0
CA B:ILE275 4.3 74.0 1.0
CG1 B:ILE275 4.4 78.6 1.0
O B:HIS278 4.4 86.6 1.0
CB B:HIS278 4.5 92.0 1.0
OE1 B:GLU119 4.5 0.8 1.0
CA B:ARG279 4.5 95.9 1.0
CB B:ILE275 4.7 77.7 1.0
CD B:ARG279 4.8 0.0 1.0
O B:TYR274 4.8 75.6 1.0
O B:ILE275 4.9 77.5 1.0
CA B:HIS278 4.9 88.9 1.0
CG B:ARG279 4.9 0.5 1.0
NH2 B:ARG116 5.0 86.6 1.0

Iodine binding site 4 out of 10 in 6ygd

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Iodine binding site 4 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I804

b:79.7
occ:0.64
 O B:HOH959 3.6 52.0 1.0
OG1 B:THR107 3.7 80.5 1.0
CB B:THR107 3.8 72.2 1.0
CG B:PRO109 4.0 66.7 1.0
CG2 B:THR107 4.0 68.2 1.0
CD B:ARG286 4.0 86.9 1.0
CD B:PRO109 4.2 63.2 1.0
CB B:ARG286 4.2 80.6 1.0
CB B:PRO109 4.3 67.1 1.0
CG2 B:THR110 4.5 63.3 1.0
OE1 B:GLN276 4.7 72.7 1.0
O B:PRO284 4.7 86.1 1.0
CG B:ARG286 4.8 83.7 1.0
OD1 B:ASN178 4.8 95.5 1.0
CB B:PHE283 5.0 82.1 1.0

Iodine binding site 5 out of 10 in 6ygd

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Iodine binding site 5 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I805

b:99.0
occ:0.83
 O B:HOH911 3.6 51.0 1.0
OG B:SER420 3.8 61.8 1.0
CB B:GLN424 3.9 39.0 1.0
O B:SER420 4.0 41.3 1.0
CG B:GLN424 4.2 40.8 1.0
CA B:LEU421 4.2 43.2 1.0
C B:SER420 4.2 40.7 1.0
O B:HOH901 4.3 67.7 1.0
CD1 B:LEU421 4.3 51.5 1.0
N B:LEU421 4.3 40.1 1.0
OE1 B:GLN424 4.5 45.5 1.0
CB B:SER420 4.6 48.6 1.0
CD B:GLN424 4.7 45.0 1.0
CD2 B:LEU385 4.8 42.5 1.0
CB B:LEU421 4.9 45.9 1.0

Iodine binding site 6 out of 10 in 6ygd

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Iodine binding site 6 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I806

b:95.1
occ:0.45
 OG1 B:THR157 3.9 75.0 1.0
CZ B:PHE177 4.2 88.3 1.0
CD1 B:LEU122 4.3 62.6 1.0
CB B:THR157 4.5 61.0 1.0
CB B:PHE182 4.7 90.2 1.0
CE1 B:PHE177 4.8 88.9 1.0
CB B:ASN179 4.8 77.0 1.0
CD2 B:LEU122 5.0 64.7 1.0

Iodine binding site 7 out of 10 in 6ygd

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Iodine binding site 7 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I807

b:59.0
occ:0.31
 OG1 B:THR628 3.3 50.5 1.0
CG1 B:VAL691 3.8 49.8 1.0
CA B:GLU625 3.8 56.6 1.0
CB B:GLU625 4.1 59.1 1.0
CG2 B:THR628 4.1 35.7 1.0
CB B:THR628 4.2 46.3 1.0
N B:GLU625 4.2 54.3 1.0
CE B:LYS695 4.4 70.1 1.0
O B:LEU624 4.5 45.1 1.0
C B:LEU624 4.6 49.7 1.0
CG B:LEU624 4.6 40.2 1.0
CG B:GLU625 4.6 66.6 1.0
CG2 B:VAL691 4.7 38.9 1.0
CB B:VAL691 4.7 41.9 1.0
C B:GLU625 4.9 55.1 1.0
CD2 B:LEU624 5.0 37.3 1.0

Iodine binding site 8 out of 10 in 6ygd

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Iodine binding site 8 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I808

b:83.6
occ:0.56
 CA B:GLN431 3.9 58.2 1.0
CA B:ASN429 4.1 80.5 1.0
C B:ASN429 4.2 76.0 1.0
CG B:GLU426 4.2 60.7 1.0
N B:GLN431 4.2 62.7 1.0
CB B:GLN431 4.3 65.1 1.0
OD1 B:ASN429 4.3 90.2 1.0
CG B:GLN431 4.3 71.3 1.0
C B:SER430 4.4 63.8 1.0
CA B:GLU426 4.4 45.6 1.0
N B:SER430 4.4 71.6 1.0
O B:SER430 4.4 65.8 1.0
O B:GLU426 4.5 56.4 1.0
SG B:CYS434 4.5 47.6 1.0
CB B:CYS434 4.5 43.3 1.0
OE2 B:GLU426 4.6 81.7 1.0
O B:ASN429 4.7 74.5 1.0
CD B:GLU426 4.8 75.5 1.0
CB B:GLU426 4.8 50.4 1.0
CB B:ASN429 4.8 85.5 1.0
O B:PHE425 4.9 55.1 1.0
C B:GLU426 4.9 49.5 1.0
N B:ASN429 5.0 80.2 1.0

Iodine binding site 9 out of 10 in 6ygd

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Iodine binding site 9 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


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 Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:65.3
occ:0.45
 NE2 B:GLN282 3.6 0.2 1.0
CA C:GLY54 3.8 78.7 1.0
N C:GLY54 4.0 82.5 1.0
CA C:HIS41 4.0 88.3 1.0
ND1 C:HIS41 4.2 0.3 1.0
CD B:GLN282 4.4 1.0 1.0
CB C:MET52 4.4 75.5 1.0
CB C:HIS41 4.6 97.0 1.0
SD C:MET52 4.6 82.5 1.0
CG C:MET52 4.6 80.6 1.0
C C:HIS41 4.7 85.5 1.0
N C:HIS41 4.9 85.5 1.0
CG C:HIS41 4.9 0.6 1.0
C C:GLY54 5.0 75.1 1.0
N C:VAL42 5.0 85.3 1.0
OE1 B:GLN282 5.0 0.6 1.0

Iodine binding site 10 out of 10 in 6ygd

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Iodine binding site 10 out of 10 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I102

b:0.8
occ:0.69
 OG C:SER7 3.3 99.5 1.0
N C:LEU6 3.5 92.6 1.0
N C:SER7 3.6 99.3 1.0
CB C:LEU6 3.6 95.5 1.0
CB C:LYS5 3.7 97.9 1.0
CE C:LYS5 3.7 0.9 1.0
NZ C:LYS5 3.9 97.4 1.0
CA C:LEU6 3.9 89.5 1.0
C C:LEU6 4.1 96.5 1.0
CG2 B:VAL39 4.3 97.5 1.0
CD C:LYS5 4.3 0.6 1.0
CB C:SER7 4.4 0.3 1.0
CD2 B:LEU29 4.4 96.5 1.0
CA C:SER7 4.4 0.1 1.0
C C:LYS5 4.5 95.6 1.0
CG C:LYS5 4.6 0.4 1.0
CA C:LYS5 4.7 0.9 1.0
CG C:LEU6 5.0 94.2 1.0
CG1 B:VAL39 5.0 98.6 1.0

Reference:

S.Grunwald, L.V.M.Hopf, T.Bock-Bierbaum, C.C.M.Lally, C.M.T.Spahn, O.Daumke. Divergent Architecture of the Heterotrimeric Natc Complex Explains N-Terminal Acetylation of Cognate Substrates. Nat Commun V. 11 5506 2020.
ISSN: ESSN 2041-1723
PubMed: 33139728
DOI: 10.1038/S41467-020-19321-8
Page generated: Mon Aug 12 00:40:35 2024

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