Atomistry » Sodium » PDB 4n01-4nji » 4naw
Atomistry »
  Sodium »
    PDB 4n01-4nji »
      4naw »

Sodium in PDB 4naw: Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3

Protein crystallography data

The structure of Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3, PDB code: 4naw was solved by Z.Metlagel, C.Otomo, G.Takaesu, T.Otomo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.83 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.584, 120.097, 189.466, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3 (pdb code 4naw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3, PDB code: 4naw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4naw

Go back to Sodium Binding Sites List in 4naw
Sodium binding site 1 out of 4 in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:41.6
occ:1.00
 O B:PRO97 2.3 34.5 1.0
O B:HOH405 2.3 35.8 1.0
O B:HOH413 2.4 47.1 1.0
OD1 B:ASN99 2.4 43.5 1.0
O B:ALA95 2.4 38.4 1.0
O J:HOH410 2.6 51.9 1.0
CG B:ASN99 3.4 37.2 1.0
H B:ASN99 3.5 33.9 1.0
C B:PRO97 3.5 35.3 1.0
C B:ALA95 3.5 45.0 1.0
O B:HOH440 3.8 39.3 1.0
HA B:LEU96 3.8 42.5 1.0
C B:LEU96 3.9 32.2 1.0
HA B:TRP98 3.9 36.4 1.0
N B:ASN99 4.0 28.2 1.0
O B:LEU96 4.0 37.3 1.0
HB2 B:ASN99 4.0 39.1 1.0
O B:HOH431 4.0 43.7 1.0
N B:PRO97 4.1 35.9 1.0
HB3 B:ALA95 4.1 60.9 1.0
CA B:LEU96 4.2 35.4 1.0
CB B:ASN99 4.2 32.6 1.0
HD2 B:PRO97 4.2 52.8 1.0
HD21 B:ASN99 4.3 41.1 1.0
ND2 B:ASN99 4.3 34.3 1.0
N B:LEU96 4.3 34.7 1.0
N B:TRP98 4.4 29.1 1.0
HB3 B:SER94 4.4 49.0 1.0
CA B:TRP98 4.4 30.4 1.0
CA B:PRO97 4.4 42.8 1.0
C B:TRP98 4.5 27.8 1.0
O B:HOH462 4.5 39.6 1.0
CA B:ALA95 4.5 40.2 1.0
CA B:ASN99 4.7 25.4 1.0
CB B:ALA95 4.7 50.8 1.0
CD B:PRO97 4.7 44.0 1.0
N B:ALA95 4.7 49.6 1.0
H B:ALA95 4.8 59.5 1.0
HB1 B:ALA95 4.9 60.9 1.0

Sodium binding site 2 out of 4 in 4naw

Go back to Sodium Binding Sites List in 4naw
Sodium binding site 2 out of 4 in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:39.3
occ:1.00
 O F:PRO97 2.3 35.8 1.0
O F:ALA95 2.4 39.3 1.0
OD1 F:ASN99 2.4 49.0 1.0
O F:HOH412 2.4 42.5 1.0
O F:HOH401 2.5 33.8 1.0
O F:HOH407 2.5 44.6 1.0
CG F:ASN99 3.4 35.9 1.0
H F:ASN99 3.5 39.4 1.0
C F:ALA95 3.5 42.7 1.0
C F:PRO97 3.5 34.9 1.0
HA F:LEU96 3.8 43.1 1.0
HA F:TRP98 3.8 40.4 1.0
C F:LEU96 3.9 37.6 1.0
O F:HOH436 3.9 38.9 1.0
HB2 F:ASN99 3.9 43.5 1.0
N F:ASN99 4.0 32.9 1.0
O F:LEU96 4.0 37.6 1.0
HB3 F:ALA95 4.1 48.7 1.0
N F:PRO97 4.1 34.0 1.0
O F:HOH457 4.1 47.5 1.0
CA F:LEU96 4.2 35.9 1.0
CB F:ASN99 4.2 36.2 1.0
HB3 F:SER94 4.3 62.0 1.0
N F:LEU96 4.3 38.9 1.0
N F:TRP98 4.4 33.0 1.0
ND2 F:ASN99 4.4 40.2 1.0
HD21 F:ASN99 4.4 48.3 1.0
O C:HOH114 4.4 52.4 1.0
CA F:TRP98 4.4 33.7 1.0
CA F:PRO97 4.4 34.8 1.0
CA F:ALA95 4.5 43.8 1.0
HD2 F:PRO97 4.5 44.0 1.0
C F:TRP98 4.5 40.7 1.0
O C:HOH108 4.5 42.5 1.0
N F:ALA95 4.6 41.8 1.0
H F:ALA95 4.7 50.2 1.0
CA F:ASN99 4.7 35.2 1.0
CB F:ALA95 4.7 40.6 1.0
O2 F:SO4301 4.9 0.4 1.0
CD F:PRO97 4.9 36.6 1.0
HB1 F:ALA95 5.0 48.7 1.0

Sodium binding site 3 out of 4 in 4naw

Go back to Sodium Binding Sites List in 4naw
Sodium binding site 3 out of 4 in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na305

b:72.4
occ:1.00
 O J:PRO97 2.4 42.6 1.0
OD1 J:ASN99 2.5 51.8 1.0
O J:HOH514 2.6 56.0 1.0
O J:ALA95 2.8 52.9 1.0
O J:HOH458 3.2 43.4 1.0
CG J:ASN99 3.4 45.6 1.0
C J:PRO97 3.6 34.1 1.0
O J:HOH464 3.8 51.5 1.0
HD2 J:PRO97 3.8 56.8 1.0
HD21 J:ASN99 3.8 60.0 1.0
C J:LEU96 3.8 39.8 1.0
N J:PRO97 3.8 46.6 1.0
C J:ALA95 3.9 59.0 1.0
HA J:LEU96 4.0 52.3 1.0
ND2 J:ASN99 4.0 50.0 1.0
O J:LEU96 4.0 51.3 1.0
H J:ASN99 4.1 37.0 1.0
HB3 J:ALA95 4.2 58.0 1.0
CA J:PRO97 4.3 40.3 1.0
CD J:PRO97 4.3 47.4 1.0
CA J:LEU96 4.4 43.6 1.0
O J:HOH519 4.4 58.3 1.0
HB2 J:ASN99 4.5 44.9 1.0
HA J:TRP98 4.5 45.5 1.0
O J:HOH528 4.5 60.0 1.0
N J:ASN99 4.5 30.8 1.0
N J:LEU96 4.5 53.5 1.0
CB J:ASN99 4.5 37.4 1.0
N J:TRP98 4.7 35.0 1.0
HB2 J:PRO97 4.7 47.8 1.0
HD22 J:ASN99 4.8 60.0 1.0
CA J:ALA95 4.9 53.8 1.0
CB J:ALA95 4.9 48.4 1.0
HD3 J:PRO97 4.9 56.8 1.0
CA J:TRP98 4.9 37.9 1.0
HB1 J:ALA95 5.0 58.0 1.0

Sodium binding site 4 out of 4 in 4naw

Go back to Sodium Binding Sites List in 4naw
Sodium binding site 4 out of 4 in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na304

b:69.1
occ:1.00
 O N:PRO97 2.3 43.7 1.0
O N:ALA95 2.4 50.5 1.0
OD1 N:ASN99 2.4 63.2 1.0
O N:HOH405 2.7 44.0 1.0
CG N:ASN99 3.4 47.9 1.0
C N:PRO97 3.5 36.7 1.0
H N:ASN99 3.5 42.0 1.0
C N:ALA95 3.5 48.4 1.0
HA N:LEU96 3.8 51.6 1.0
C N:LEU96 3.8 40.2 1.0
HB2 N:ASN99 3.9 55.3 1.0
N N:PRO97 3.9 41.6 1.0
HA N:TRP98 4.0 49.7 1.0
N N:ASN99 4.0 35.0 1.0
HB3 N:ALA95 4.0 73.7 1.0
HD2 N:PRO97 4.0 53.9 1.0
O N:LEU96 4.0 51.6 1.0
O N:HOH435 4.0 48.0 1.0
CB N:ASN99 4.2 46.1 1.0
CA N:LEU96 4.2 43.0 1.0
N N:LEU96 4.3 57.1 1.0
ND2 N:ASN99 4.3 51.8 1.0
HD21 N:ASN99 4.3 62.2 1.0
O N:HOH455 4.3 52.4 1.0
CA N:PRO97 4.3 40.7 1.0
N N:TRP98 4.4 39.8 1.0
CA N:TRP98 4.5 41.5 1.0
CA N:ALA95 4.5 50.8 1.0
CD N:PRO97 4.5 44.9 1.0
C N:TRP98 4.5 43.5 1.0
CB N:ALA95 4.6 61.4 1.0
CA N:ASN99 4.7 35.3 1.0
HB3 N:SER94 4.7 69.1 1.0
N N:ALA95 4.8 56.8 1.0
HB1 N:ALA95 4.8 73.7 1.0
H N:ALA95 4.8 68.1 1.0
HA N:ASN99 5.0 42.4 1.0
HB2 N:PRO97 5.0 50.6 1.0

Reference:

Z.Metlagel, C.Otomo, G.Takaesu, T.Otomo. Structural Basis of ATG3 Recognition By the Autophagic Ubiquitin-Like Protein ATG12. Proc.Natl.Acad.Sci.Usa V. 110 18844 2013.
ISSN: ISSN 0027-8424
PubMed: 24191030
DOI: 10.1073/PNAS.1314755110
Page generated: Sun Aug 17 20:45:22 2025

Last articles

Na in 6T3Q
Na in 6T3M
Na in 6SYR
Na in 6SYC
Na in 6SYD
Na in 6SXF
Na in 6SXG
Na in 6SU0
Na in 6SXE
Na in 6SXC
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy