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Iodine in PDB 6ygb: Crystal Structure of the Natc Complex Bound to Coa

Enzymatic activity of Crystal Structure of the Natc Complex Bound to Coa

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

Protein crystallography data

The structure of Crystal Structure of the Natc Complex Bound to Coa, PDB code: 6ygb 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) 45.43 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.042, 139.789, 166.561, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23.6

Other elements in 6ygb:

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

Chlorine (Cl) 8 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the Natc Complex Bound to Coa (pdb code 6ygb). 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 Natc Complex Bound to Coa, PDB code: 6ygb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 6ygb

Go back to Iodine Binding Sites List in 6ygb
Iodine binding site 1 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I801

b:50.0
occ:1.00
 NH1 B:ARG408 3.5 31.6 1.0
CG B:GLN409 3.6 39.3 1.0
N A:ARG140 3.6 36.5 1.0
O B:HOH909 3.8 27.8 1.0
CD B:ARG408 3.8 30.4 1.0
NE2 B:GLN409 3.8 37.8 1.0
CG B:ARG408 4.0 29.1 1.0
CA A:LYS139 4.0 39.6 1.0
CB B:ARG408 4.1 26.1 1.0
O B:CYS405 4.2 46.0 1.0
CD1 B:LEU455 4.2 30.9 1.0
O A:ARG140 4.2 40.3 1.0
CG A:LYS139 4.3 46.6 1.0
CD B:GLN409 4.3 40.4 1.0
C A:LYS139 4.3 35.7 1.0
N B:GLN409 4.5 37.8 1.0
CZ B:ARG408 4.6 34.5 1.0
CA A:ARG140 4.6 40.0 1.0
CB A:ARG140 4.7 40.1 1.0
NE B:ARG408 4.7 33.9 1.0
CB A:LYS139 4.7 43.4 1.0
CD1 B:ILE457 4.7 39.8 1.0
CB B:GLN409 4.8 37.1 1.0
CA B:GLN409 4.8 37.6 1.0
CG1 B:ILE457 4.9 39.6 1.0
C A:ARG140 4.9 41.4 1.0
O A:MET138 4.9 44.6 1.0
C B:ARG408 4.9 35.8 1.0

Iodine binding site 2 out of 9 in 6ygb

Go back to Iodine Binding Sites List in 6ygb
Iodine binding site 2 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I802

b:46.6
occ:0.51
 CD B:PRO460 3.7 30.4 1.0
CD2 B:PHE461 3.7 46.4 1.0
N B:PHE461 3.8 42.7 1.0
CE B:LYS459 3.9 43.0 1.0
CB B:PRO460 4.0 35.7 1.0
CG B:PRO460 4.1 38.3 1.0
N B:PRO460 4.1 36.0 1.0
CB B:PHE461 4.2 43.7 1.0
NZ B:LYS459 4.3 42.5 1.0
CB B:LYS459 4.4 36.3 1.0
CG B:PHE461 4.4 45.1 1.0
CA B:PRO460 4.5 35.9 1.0
C B:PRO460 4.5 40.2 1.0
CA B:PHE461 4.6 43.5 1.0
CE2 B:PHE461 4.6 46.7 1.0
C B:LYS459 4.8 35.2 1.0

Iodine binding site 3 out of 9 in 6ygb

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Iodine binding site 3 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I803

b:92.6
occ:0.64
 OE2 B:GLU119 3.2 82.2 1.0
CD B:GLU119 3.8 81.2 1.0
CE1 B:TYR274 3.9 85.9 1.0
CB B:ARG279 3.9 70.7 1.0
N B:ARG279 4.0 70.8 1.0
CD1 B:TYR274 4.1 81.9 1.0
CA B:ILE275 4.2 67.7 1.0
CG1 B:ILE275 4.2 64.6 1.0
CB B:HIS278 4.2 72.8 1.0
CA B:ARG279 4.3 70.2 1.0
CG B:GLU119 4.4 76.7 1.0
C B:HIS278 4.5 72.4 1.0
OE1 B:GLU119 4.5 85.1 1.0
CG B:ARG279 4.6 75.6 1.0
CB B:ILE275 4.6 65.2 1.0
O B:ILE275 4.8 66.2 1.0
CA B:HIS278 4.9 72.6 1.0
O B:TYR274 4.9 71.4 1.0

Iodine binding site 4 out of 9 in 6ygb

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Iodine binding site 4 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I804

b:68.6
occ:0.60
 O B:HOH915 3.5 47.6 1.0
OG1 B:THR107 3.5 59.7 1.0
CG B:PRO109 3.7 56.5 1.0
CB B:THR107 3.7 56.0 1.0
CG2 B:THR107 3.9 53.0 1.0
O B:HOH938 3.9 53.2 1.0
CB B:PRO109 4.0 57.6 1.0
CD B:PRO109 4.1 53.2 1.0
CB B:ARG286 4.1 72.4 1.0
CD B:ARG286 4.2 76.4 1.0
ND2 B:ASN178 4.2 73.5 1.0
CG2 B:THR110 4.6 60.5 1.0
CG B:ARG286 4.7 75.0 1.0
OE1 B:GLN276 4.9 53.4 1.0
O B:PRO284 5.0 61.7 1.0

Iodine binding site 5 out of 9 in 6ygb

Go back to Iodine Binding Sites List in 6ygb
Iodine binding site 5 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I805

b:81.2
occ:0.63
 OG B:SER420 3.4 45.0 1.0
O B:SER420 3.7 38.5 1.0
CD1 B:LEU421 3.9 46.6 1.0
C B:SER420 3.9 39.4 1.0
CB B:GLN424 4.0 37.8 1.0
O B:HOH950 4.0 39.5 1.0
N B:LEU421 4.1 40.2 1.0
CA B:LEU421 4.1 42.5 1.0
CB B:SER420 4.3 40.5 1.0
CG B:GLN424 4.3 37.1 1.0
O B:HOH971 4.4 40.9 1.0
CA B:SER420 4.7 40.4 1.0
OE1 B:GLN424 4.9 41.0 1.0
CB B:LEU421 4.9 44.8 1.0
CD2 B:LEU385 5.0 40.8 1.0

Iodine binding site 6 out of 9 in 6ygb

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Iodine binding site 6 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I806

b:98.4
occ:0.66
 NE2 B:GLN282 3.4 97.7 1.0
CA C:GLY54 3.7 59.5 1.0
N C:GLY54 3.9 60.5 1.0
CA C:HIS41 4.1 75.9 1.0
CD B:GLN282 4.1 95.6 1.0
CB C:MET52 4.2 65.5 1.0
ND1 C:HIS41 4.5 89.9 1.0
C C:HIS41 4.7 73.5 1.0
CG C:MET52 4.7 70.1 1.0
CG B:GLN282 4.7 91.6 1.0
OE1 B:GLN282 4.7 97.4 1.0
CB C:HIS41 4.8 83.7 1.0
N C:VAL42 4.9 70.2 1.0
SD C:MET52 4.9 72.5 1.0
N C:HIS41 4.9 74.0 1.0
C C:GLY54 4.9 59.6 1.0

Iodine binding site 7 out of 9 in 6ygb

Go back to Iodine Binding Sites List in 6ygb
Iodine binding site 7 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I807

b:97.4
occ:0.53
 O B:HOH903 3.4 62.6 1.0
OG1 B:THR157 3.9 58.9 1.0
ND2 B:ASN179 4.3 70.8 1.0
CZ B:PHE177 4.4 68.6 1.0
CB B:PHE182 4.4 75.5 1.0
O B:PHE182 4.4 80.9 1.0
CB B:ASN179 4.5 68.2 1.0
CD2 B:LEU122 4.6 61.3 1.0
CD1 B:LEU122 4.7 58.5 1.0
CE2 B:PHE177 4.7 68.6 1.0
NE2 B:GLN161 4.9 65.7 1.0
CB B:THR157 5.0 54.4 1.0
CG B:ASN179 5.0 70.0 1.0

Iodine binding site 8 out of 9 in 6ygb

Go back to Iodine Binding Sites List in 6ygb
Iodine binding site 8 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I808

b:68.7
occ:0.35
 OG1 B:THR628 3.3 40.6 1.0
CG1 B:VAL691 3.7 44.3 1.0
CG2 B:THR628 3.8 35.2 1.0
CA B:GLU625 4.0 55.5 1.0
CB B:THR628 4.1 37.4 1.0
CG B:LEU624 4.2 49.1 1.0
CE B:LYS695 4.3 68.0 1.0
N B:GLU625 4.3 51.7 1.0
O B:LEU624 4.4 45.9 1.0
CB B:GLU625 4.4 64.9 1.0
CD2 B:LEU624 4.5 50.5 1.0
C B:LEU624 4.5 49.8 1.0
CG B:GLU625 4.6 73.4 1.0
CG2 B:VAL691 4.6 39.5 1.0
CB B:VAL691 4.7 43.3 1.0

Iodine binding site 9 out of 9 in 6ygb

Go back to Iodine Binding Sites List in 6ygb
Iodine binding site 9 out of 9 in the Crystal Structure of the Natc Complex Bound to 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 Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:0.0
occ:0.63
 OG C:SER7 3.4 85.7 1.0
N C:SER7 3.8 88.2 1.0
O B:HOH1018 4.0 65.2 1.0
N C:LEU6 4.0 87.8 1.0
CD C:LYS5 4.1 96.6 1.0
CB C:LYS5 4.1 97.0 1.0
CB C:SER7 4.2 87.8 1.0
CG2 B:VAL39 4.3 76.2 1.0
CB C:LEU6 4.4 81.2 1.0
NZ C:LYS5 4.5 97.3 1.0
CE C:LYS5 4.5 97.7 1.0
CG C:LYS5 4.6 98.2 1.0
CA C:LEU6 4.6 83.7 1.0
CG1 B:VAL39 4.6 77.7 1.0
CA C:SER7 4.6 89.8 1.0
C C:LEU6 4.6 83.6 1.0
C C:LYS5 4.8 92.7 1.0
CA C:LYS5 4.9 99.8 1.0
CD2 B:LEU33 5.0 0.0 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 00:37:30 2024

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