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Chlorine 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:

Iodine (I) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa, PDB code: 6ygd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6ygd

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Chlorine binding site 1 out of 6 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
A:Cl202

b:80.6
occ:1.00
 O A:TYR5 3.8 55.6 1.0
CE2 A:TYR48 4.2 46.5 1.0
C A:TYR5 4.4 52.9 1.0
CD A:PRO7 4.5 50.1 1.0
CA A:LYS6 4.5 51.4 1.0
CD2 A:TYR48 4.7 49.0 1.0
N A:LYS6 4.7 46.7 1.0
CG A:PRO7 4.9 53.4 1.0
CB A:TYR5 5.0 42.0 1.0

Chlorine binding site 2 out of 6 in 6ygd

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Chlorine binding site 2 out of 6 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl809

b:59.0
occ:1.00
 ND2 B:ASN383 3.8 72.8 1.0
OG B:SER430 3.8 55.2 1.0
CD2 B:TYR433 4.0 47.3 1.0
CB B:SER430 4.1 55.3 1.0
CE2 B:TYR433 4.1 45.4 1.0
CG B:ASN383 4.3 71.7 1.0
CE1 B:PHE425 4.3 38.0 1.0
OD1 B:ASN383 4.4 76.0 1.0
CD1 B:PHE425 4.5 39.8 1.0
CD1 B:LEU385 4.8 42.4 1.0
CG2 B:VAL428 4.8 54.1 1.0

Chlorine binding site 3 out of 6 in 6ygd

Go back to Chlorine Binding Sites List in 6ygd
Chlorine binding site 3 out of 6 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl810

b:78.9
occ:1.00
 CB B:GLU368 3.7 47.1 1.0
O B:GLU368 3.9 55.8 1.0
NE2 B:GLN528 3.9 49.3 1.0
OE1 B:GLU368 4.0 51.0 1.0
CG B:GLU368 4.2 49.2 1.0
CB B:ALA531 4.2 33.3 1.0
CD2 B:LEU318 4.3 51.1 1.0
O B:ALA531 4.3 34.5 1.0
CD B:GLU368 4.4 51.4 1.0
C B:ALA531 4.4 34.5 1.0
CA B:GLU368 4.4 50.2 1.0
CB B:PHE535 4.5 46.7 1.0
C B:GLU368 4.6 52.5 1.0
N B:THR532 4.6 29.8 1.0
OG1 B:THR532 4.7 37.3 1.0
CB B:LEU318 4.7 41.6 1.0
CA B:THR532 4.7 29.3 1.0
CG1 B:VAL659 4.8 23.1 1.0
CG B:PHE535 4.9 44.0 1.0
CD2 B:PHE535 4.9 45.4 1.0
CD B:GLN528 4.9 46.3 1.0
CA B:ALA531 5.0 35.6 1.0

Chlorine binding site 4 out of 6 in 6ygd

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Chlorine binding site 4 out of 6 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl811

b:61.8
occ:1.00
 NE1 B:TRP396 3.4 33.4 1.0
OG B:SER444 3.7 43.5 1.0
CE1 B:PHE411 3.9 51.0 1.0
CZ2 B:TRP396 4.0 35.4 1.0
CA B:SER444 4.1 34.4 1.0
CE2 B:TRP396 4.1 32.2 1.0
N B:SER444 4.1 38.4 1.0
CZ B:PHE411 4.1 45.7 1.0
C B:SER443 4.2 40.6 1.0
O B:SER443 4.2 45.7 1.0
CB B:SER443 4.3 35.4 1.0
CB B:SER444 4.5 38.4 1.0
CB B:GLU447 4.5 28.8 1.0
OH B:TYR321 4.6 46.4 1.0
CD1 B:TRP396 4.6 35.5 1.0
CG B:GLU447 4.8 27.7 1.0
CD B:LYS325 4.9 57.8 1.0
CA B:SER443 4.9 34.5 1.0
O B:MET440 5.0 41.5 1.0

Chlorine binding site 5 out of 6 in 6ygd

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Chlorine binding site 5 out of 6 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl812

b:67.8
occ:1.00
 NE1 B:TRP436 3.8 36.3 1.0
O B:HIS365 3.9 41.5 1.0
CD2 B:HIS365 4.0 36.2 1.0
CB B:HIS365 4.0 37.3 1.0
CA B:HIS365 4.2 38.0 1.0
CG B:HIS365 4.3 38.1 1.0
C B:HIS365 4.4 37.4 1.0
CD1 B:TYR321 4.5 42.1 1.0
CB B:PHE369 4.5 56.2 1.0
CG B:TYR321 4.6 44.9 1.0
CE2 B:TRP436 4.7 40.9 1.0
CD1 B:TRP436 4.8 39.7 1.0
CE2 B:PHE535 4.8 48.4 1.0
CE2 B:PHE439 4.8 45.0 1.0
CE1 B:TYR321 4.8 44.7 1.0
CZ2 B:TRP436 4.9 42.5 1.0
CD1 B:PHE369 4.9 60.8 1.0
CB B:TYR321 5.0 43.5 1.0
CZ B:PHE535 5.0 41.5 1.0

Chlorine binding site 6 out of 6 in 6ygd

Go back to Chlorine Binding Sites List in 6ygd
Chlorine binding site 6 out of 6 in the Crystal Structure of the Natc Complex Bound to Gag Peptide and Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl813

b:0.7
occ:1.00
 CD1 B:ILE582 3.9 34.5 1.0
CB B:ASN570 4.0 52.4 1.0
N B:GLU579 4.0 63.4 1.0
OG B:SER574 4.1 87.5 1.0
O B:ASN570 4.2 55.9 1.0
CA B:GLU579 4.2 58.5 1.0
C B:ASN578 4.3 50.8 1.0
CB B:GLU579 4.3 66.4 1.0
N B:ASN570 4.4 40.5 1.0
O B:ASN578 4.7 38.3 1.0
CA B:ASN570 4.7 46.4 1.0
ND2 B:ASN570 4.7 65.7 1.0
CA B:ASN578 4.7 52.0 1.0
O B:SER577 4.9 68.3 1.0
C B:ASN570 4.9 55.2 1.0
CB B:LYS569 4.9 44.7 1.0
CG B:ASN570 4.9 57.3 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: Sat Jul 12 22:04:32 2025

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