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Sodium in PDB 4kvo: The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa

Enzymatic activity of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa

All present enzymatic activity of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa:
2.3.1.88;

Protein crystallography data

The structure of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa, PDB code: 4kvo was solved by G.P.Liszczak, R.Q.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.05 / 3.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.739, 119.692, 132.024, 80.28, 76.85, 70.65
R / Rfree (%) 21.7 / 24.6

Other elements in 4kvo:

The structure of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa also contains other interesting chemical elements:

Chlorine (Cl) 63 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa (pdb code 4kvo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa, PDB code: 4kvo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4kvo

Go back to Sodium Binding Sites List in 4kvo
Sodium binding site 1 out of 5 in the The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:38.1
occ:1.00
 CG A:PHE536 4.3 49.7 1.0
CD2 A:PHE536 4.4 49.4 1.0
CD1 E:TYR33 4.5 40.8 1.0
CL E:CL204 4.5 47.2 1.0
CD1 A:PHE536 4.5 51.2 1.0
CB A:PHE536 4.5 49.2 1.0
CB A:ASP532 4.6 47.2 1.0
CE1 A:PHE533 4.7 44.9 1.0
CZ A:PHE533 4.8 44.4 1.0
CE E:LYS29 4.8 46.8 1.0
CE2 A:PHE536 4.8 50.3 1.0
CE1 A:PHE536 4.9 51.9 1.0
CE1 E:TYR33 4.9 43.1 1.0
OD2 A:ASP532 4.9 51.2 1.0

Sodium binding site 2 out of 5 in 4kvo

Go back to Sodium Binding Sites List in 4kvo
Sodium binding site 2 out of 5 in the The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na801

b:60.9
occ:1.00
 OD2 D:ASP529 2.3 60.8 1.0
CG D:ASP529 3.0 58.9 1.0
N H:LYS29 3.0 36.0 1.0
OD1 D:ASP529 3.1 60.0 1.0
CB H:LYS29 3.3 36.8 1.0
NE2 D:GLN491 3.4 39.0 1.0
CG H:GLN27 3.6 51.2 1.0
CG2 D:THR525 3.7 41.5 1.0
CA H:LYS29 3.7 41.5 1.0
N H:LEU28 3.8 49.8 1.0
C H:LEU28 4.0 38.6 1.0
CD H:GLN27 4.0 54.9 1.0
NE2 H:GLN27 4.1 58.8 1.0
CA H:LEU28 4.2 36.1 1.0
CB H:LEU28 4.3 44.8 1.0
CB D:ASP529 4.3 54.2 1.0
CD D:GLN491 4.3 38.5 1.0
OE1 D:GLN491 4.4 41.2 1.0
C H:GLN27 4.4 49.1 1.0
CG H:LYS29 4.6 37.0 1.0
CB H:GLN27 4.7 49.6 1.0
O H:GLN27 4.8 49.8 1.0
OE1 H:GLN27 4.8 54.2 1.0
CD1 D:TRP526 4.9 38.2 1.0
CD H:LYS29 4.9 43.4 1.0

Sodium binding site 3 out of 5 in 4kvo

Go back to Sodium Binding Sites List in 4kvo
Sodium binding site 3 out of 5 in the The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:72.1
occ:1.00
 O E:TYR26 2.7 39.6 1.0
OD1 E:ASN18 2.7 45.1 1.0
N E:TYR26 3.0 49.8 1.0
CB E:ASN25 3.2 55.3 1.0
OH E:TYR31 3.3 40.4 1.0
CG E:GLN15 3.5 38.8 1.0
CA E:ASN25 3.6 53.6 1.0
C E:TYR26 3.7 48.6 1.0
CG E:ASN18 3.7 44.5 1.0
C E:ASN25 3.8 52.0 1.0
CE1 E:TYR31 3.9 37.1 1.0
O E:GLN15 3.9 45.8 1.0
CG E:LEU19 3.9 45.5 1.0
CA E:TYR26 3.9 48.4 1.0
CZ E:TYR31 4.0 39.1 1.0
CB E:ASN18 4.2 42.6 1.0
CD1 E:LEU19 4.3 45.5 1.0
CG E:ASN25 4.3 59.3 1.0
CA E:GLN15 4.4 42.9 1.0
NE2 E:GLN15 4.5 39.4 1.0
CB E:GLN15 4.5 42.7 1.0
CD E:GLN15 4.5 39.2 1.0
CD2 E:LEU19 4.6 46.7 1.0
ND2 E:ASN25 4.6 59.5 1.0
C E:GLN15 4.6 44.4 1.0
CB E:TYR26 4.7 45.9 1.0
N E:LEU19 4.7 47.9 1.0
O A:MET490 4.7 39.3 1.0
CD2 E:TYR26 4.7 43.1 1.0
ND2 E:ASN18 4.9 45.2 1.0
N E:GLN27 4.9 39.9 1.0
O E:ASN25 4.9 53.6 1.0
CB E:LEU19 5.0 43.2 1.0
C E:ASN18 5.0 47.1 1.0
N E:ASN25 5.0 56.4 1.0

Sodium binding site 4 out of 5 in 4kvo

Go back to Sodium Binding Sites List in 4kvo
Sodium binding site 4 out of 5 in the The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na203

b:39.5
occ:1.00
 OD2 E:ASP141 3.3 82.7 1.0
O A:LEU473 3.8 63.6 1.0
CG E:ASP141 4.1 81.7 1.0
CB E:ASP141 4.2 83.0 1.0
NH1 E:ARG113 4.5 67.5 1.0
CA A:PHE474 4.6 59.7 1.0
CB E:PRO23 4.6 59.4 1.0
C A:PHE474 4.8 63.3 1.0
O A:PHE474 4.9 63.6 1.0
C A:LEU473 4.9 62.1 1.0
CD1 A:PHE474 4.9 54.5 1.0

Sodium binding site 5 out of 5 in 4kvo

Go back to Sodium Binding Sites List in 4kvo
Sodium binding site 5 out of 5 in the The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Nata (NAA10P/NAA15P) Amino-Terminal Acetyltrasferase Complex Bound to Accoa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na202

b:65.2
occ:1.00
 OD2 G:ASP125 3.2 0.4 1.0
CG2 G:ILE120 3.3 0.2 1.0
NH1 G:ARG124 3.8 0.6 1.0
CG G:ASP125 4.1 0.4 1.0
CD G:ARG124 4.2 0.8 1.0
OD1 G:ASP125 4.3 0.8 1.0
CA G:HIS121 4.4 0.6 1.0
N G:HIS121 4.5 0.9 1.0
C G:ILE120 4.6 0.3 1.0
O G:ILE120 4.7 0.1 1.0
CB G:ILE120 4.7 0.8 1.0
CZ G:ARG124 4.8 0.8 1.0
CB G:HIS121 4.9 0.1 1.0
CG G:HIS121 4.9 0.4 1.0
NE G:ARG124 4.9 0.0 1.0
ND1 G:HIS121 5.0 0.6 1.0

Reference:

G.Liszczak, J.M.Goldberg, H.Foyn, E.J.Petersson, T.Arnesen, R.Marmorstein. Molecular Basis For N-Terminal Acetylation By the Heterodimeric Nata Complex. Nat.Struct.Mol.Biol. V. 20 1098 2013.
ISSN: ISSN 1545-9993
PubMed: 23912279
DOI: 10.1038/NSMB.2636
Page generated: Mon Oct 7 16:36:55 2024

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