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Iodine in PDB 6yga: Crystal Structure of the Apo Natc Complex

Enzymatic activity of Crystal Structure of the Apo Natc Complex

All present enzymatic activity of Crystal Structure of the Apo Natc Complex:
2.3.1.256;

Protein crystallography data

The structure of Crystal Structure of the Apo Natc Complex, PDB code: 6yga 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) 46.23 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.124, 140.421, 166.409, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.5

Other elements in 6yga:

The structure of Crystal Structure of the Apo Natc Complex also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Apo Natc Complex (pdb code 6yga). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of the Apo Natc Complex, PDB code: 6yga:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 1 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:65.5
occ:0.43
 O A:HOH318 3.5 52.7 1.0
CB A:ALA96 3.8 51.3 1.0
N A:GLY92 3.9 71.3 1.0
N A:ALA96 3.9 57.1 1.0
CA A:ARG91 4.0 73.1 1.0
O A:HOH315 4.1 68.5 1.0
CG1 A:VAL86 4.1 55.7 1.0
CG2 A:VAL86 4.3 53.1 1.0
CB A:VAL86 4.3 55.9 1.0
CB A:ARG91 4.4 74.9 1.0
N A:ILE95 4.5 62.9 1.0
CA A:ALA96 4.5 53.5 1.0
C A:ARG91 4.5 73.3 1.0
CG A:ARG91 4.7 75.3 1.0
O A:TYR90 4.9 71.1 1.0
CA A:GLY92 4.9 72.7 1.0
N A:GLY94 4.9 64.8 1.0
N A:HIS93 4.9 69.5 1.0
C A:ILE95 5.0 58.2 1.0

Iodine binding site 2 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 2 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:0.5
occ:0.72
 NZ A:LYS139 3.4 56.3 1.0
NZ A:LYS153 3.6 61.9 1.0
O A:HOH320 4.0 67.9 1.0
CE A:LYS139 4.7 53.7 1.0
O A:HOH323 4.9 70.3 1.0
CD A:LYS139 5.0 50.6 1.0

Iodine binding site 3 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 3 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I801

b:43.2
occ:1.00
 NH1 B:ARG408 3.6 39.7 1.0
N A:ARG140 3.6 35.1 1.0
O B:HOH922 3.7 40.2 1.0
CG B:GLN409 3.7 40.4 1.0
CD B:ARG408 3.9 34.6 1.0
NE2 B:GLN409 3.9 40.4 1.0
CA A:LYS139 4.1 38.5 1.0
CG B:ARG408 4.1 31.2 1.0
CD1 B:LEU455 4.1 32.7 1.0
O B:CYS405 4.1 42.3 1.0
CB B:ARG408 4.2 30.6 1.0
O A:ARG140 4.2 41.3 1.0
CG A:LYS139 4.3 48.1 1.0
CD B:GLN409 4.3 41.5 1.0
C A:LYS139 4.3 36.4 1.0
CA A:ARG140 4.6 36.6 1.0
N B:GLN409 4.6 36.1 1.0
CB A:ARG140 4.6 37.8 1.0
CZ B:ARG408 4.6 40.5 1.0
CD1 B:ILE457 4.6 47.6 1.0
NE B:ARG408 4.7 37.5 1.0
CB A:LYS139 4.7 43.8 1.0
CG1 B:ILE457 4.8 45.8 1.0
C A:ARG140 4.9 39.4 1.0
CB B:GLN409 4.9 37.7 1.0
C B:ARG408 4.9 37.3 1.0
O A:MSE138 4.9 41.7 1.0
CA B:GLN409 4.9 36.8 1.0

Iodine binding site 4 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 4 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I802

b:53.1
occ:0.61
 CD2 B:PHE461 3.6 47.9 1.0
CD B:PRO460 3.7 37.9 1.0
N B:PHE461 3.8 41.8 1.0
CE B:LYS459 3.9 51.9 1.0
CB B:PRO460 3.9 39.4 1.0
NZ B:LYS459 4.0 53.3 1.0
CG B:PRO460 4.0 40.1 1.0
N B:PRO460 4.1 39.7 1.0
CB B:PHE461 4.2 44.1 1.0
CG B:PHE461 4.4 46.9 1.0
CB B:LYS459 4.4 41.0 1.0
CA B:PRO460 4.4 39.2 1.0
C B:PRO460 4.5 41.7 1.0
CE2 B:PHE461 4.6 46.5 1.0
CA B:PHE461 4.6 41.0 1.0
C B:LYS459 4.8 38.5 1.0

Iodine binding site 5 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 5 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I803

b:73.8
occ:0.65
 OE2 B:GLU119 3.3 83.1 1.0
CE1 B:TYR274 3.7 83.9 1.0
CD B:GLU119 3.9 80.1 1.0
N B:ARG279 3.9 72.6 1.0
CD1 B:TYR274 4.0 79.8 1.0
CB B:ARG279 4.0 70.0 1.0
CA B:ILE275 4.1 66.6 1.0
CG1 B:ILE275 4.1 65.0 1.0
CB B:HIS278 4.1 80.5 1.0
CG B:GLU119 4.4 72.3 1.0
CA B:ARG279 4.4 71.1 1.0
CB B:ILE275 4.5 64.3 1.0
C B:HIS278 4.5 73.9 1.0
OE1 B:GLU119 4.6 83.7 1.0
O B:ILE275 4.7 69.1 1.0
O B:TYR274 4.8 70.7 1.0
CZ B:TYR274 4.8 88.9 1.0
CA B:HIS278 4.8 76.3 1.0
N B:ILE275 4.9 66.8 1.0
C B:ILE275 4.9 67.2 1.0

Iodine binding site 6 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 6 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I804

b:66.6
occ:0.74
 O B:HOH1019 3.3 50.4 1.0
OG1 B:THR107 3.7 58.1 1.0
CB B:THR107 3.8 53.1 1.0
CG2 B:THR107 3.9 48.8 1.0
CG B:PRO109 3.9 57.1 1.0
CD B:ARG286 4.0 86.2 1.0
O B:HOH914 4.0 50.7 1.0
CG B:ARG286 4.1 82.3 1.0
CB B:PRO109 4.1 58.6 1.0
NE B:ARG286 4.2 90.5 1.0
CD B:PRO109 4.2 55.3 1.0
CB B:ARG286 4.4 74.7 1.0
ND2 B:ASN178 4.6 69.8 1.0
CG2 B:THR110 4.7 56.2 1.0
O B:PRO284 4.8 53.4 1.0
CZ B:ARG286 5.0 93.7 1.0
OE1 B:GLN276 5.0 53.4 1.0

Iodine binding site 7 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 7 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I805

b:61.1
occ:0.61
 OG B:SER420 3.6 42.9 1.0
O B:SER420 3.8 41.1 1.0
O B:HOH919 3.9 37.2 1.0
CB B:GLN424 4.0 42.6 1.0
C B:SER420 4.0 41.9 1.0
CA B:LEU421 4.1 43.9 1.0
CD1 B:LEU421 4.1 51.4 1.0
N B:LEU421 4.2 42.6 1.0
CG B:GLN424 4.3 43.8 1.0
CB B:SER420 4.4 39.2 1.0
OE1 B:GLN424 4.8 46.2 1.0
CB B:LEU421 4.8 44.2 1.0
CA B:SER420 4.9 41.4 1.0
OE2 B:GLU388 4.9 73.8 1.0
CD B:GLN424 5.0 46.5 1.0

Iodine binding site 8 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 8 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I806

b:85.2
occ:0.49
 NE2 B:GLN282 3.3 98.5 1.0
CA C:GLY54 3.7 61.5 1.0
N C:GLY54 3.8 62.3 1.0
CA C:HIS41 3.9 76.7 1.0
CB C:MSE52 4.0 69.0 1.0
CD B:GLN282 4.3 94.7 1.0
C C:HIS41 4.4 75.3 1.0
ND1 C:HIS41 4.4 88.4 1.0
CG C:MSE52 4.5 72.8 1.0
CB C:HIS41 4.6 83.8 1.0
N C:VAL42 4.7 73.1 1.0
O C:VAL42 4.8 69.7 1.0
N C:MSE53 4.8 67.6 1.0
N C:HIS41 4.8 72.6 1.0
SE C:MSE52 4.8 80.2 0.6
C C:GLY54 4.9 62.8 1.0
OE1 B:GLN282 4.9 95.9 1.0
C C:MSE53 5.0 62.7 1.0
CG B:GLN282 5.0 89.1 1.0
CA C:MSE52 5.0 70.2 1.0

Iodine binding site 9 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 9 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I807

b:68.7
occ:0.43
 OG1 B:THR157 3.6 63.0 1.0
O B:HOH931 3.7 61.4 1.0
CB B:ASN179 4.3 63.3 1.0
CZ B:PHE177 4.3 55.6 1.0
ND2 B:ASN179 4.4 70.0 1.0
CD1 B:LEU122 4.4 71.3 1.0
CB B:THR157 4.5 57.9 1.0
CB B:PHE182 4.6 66.3 1.0
CD2 B:LEU122 4.6 71.9 1.0
CE2 B:PHE177 4.7 56.2 1.0
CG B:ASN179 4.9 68.7 1.0
N B:LYS158 5.0 56.9 1.0
C B:THR157 5.0 57.9 1.0

Iodine binding site 10 out of 11 in 6yga

Go back to Iodine Binding Sites List in 6yga
Iodine binding site 10 out of 11 in the Crystal Structure of the Apo Natc Complex


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 Apo Natc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I808

b:65.8
occ:0.34
 OG1 B:THR628 3.4 45.2 1.0
CG1 B:VAL691 3.7 54.7 1.0
CG2 B:THR628 3.9 41.5 1.0
CA B:GLU625 4.1 57.9 1.0
CE B:LYS695 4.1 70.3 1.0
CB B:THR628 4.1 43.8 1.0
CG B:LEU624 4.2 51.5 1.0
CD2 B:LEU624 4.4 53.3 1.0
N B:GLU625 4.4 55.1 1.0
O B:LEU624 4.4 46.4 1.0
CB B:GLU625 4.5 64.8 1.0
C B:LEU624 4.5 52.2 1.0
CG2 B:VAL691 4.6 47.7 1.0
CB B:VAL691 4.7 51.7 1.0
CG B:GLU625 4.7 72.4 1.0
NZ B:LYS695 4.8 71.5 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 00:37:19 2024

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