Atomistry » Sodium » PDB 4khu-4kxx » 4kvo
Atomistry »
  Sodium »
    PDB 4khu-4kxx »
      4kvo »

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

Last articles

Mn in 4WIU
Mn in 4WIE
Mn in 4WFO
Mn in 4WFA
Mn in 4UXA
Mn in 4W8Y
Mn in 4W9S
Mn in 4V15
Mn in 4V0U
Mn in 4V0W
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy