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Sodium in PDB 4z79: Leiomodin-1 Actin-Binding Site 2 (ABS2)

Protein crystallography data

The structure of Leiomodin-1 Actin-Binding Site 2 (ABS2), PDB code: 4z79 was solved by G.Rebowski, M.Boczkowska, R.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.18 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.019, 52.192, 75.890, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 17.7

Other elements in 4z79:

The structure of Leiomodin-1 Actin-Binding Site 2 (ABS2) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Leiomodin-1 Actin-Binding Site 2 (ABS2) (pdb code 4z79). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Leiomodin-1 Actin-Binding Site 2 (ABS2), PDB code: 4z79:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4z79

Go back to Sodium Binding Sites List in 4z79
Sodium binding site 1 out of 3 in the Leiomodin-1 Actin-Binding Site 2 (ABS2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Leiomodin-1 Actin-Binding Site 2 (ABS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:31.9
occ:1.00
O A:HOH770 2.6 30.5 1.0
HA A:ALA354 2.7 10.2 1.0
HG2 A:LYS326 3.3 13.8 1.0
CA A:ALA354 3.6 8.5 1.0
O A:GLU353 3.9 9.5 1.0
HA A:LYS326 4.1 11.0 1.0
O A:ALA354 4.2 8.8 1.0
CG A:LYS326 4.2 11.5 1.0
HB1 A:ALA354 4.2 11.3 1.0
HB2 A:ALA354 4.3 11.3 1.0
C A:ALA354 4.3 8.2 1.0
CB A:ALA354 4.3 9.4 1.0
N A:ALA354 4.4 8.3 1.0
HE3 A:LYS326 4.5 30.2 1.0
C A:GLU353 4.5 9.4 1.0
HG3 A:LYS326 4.6 13.8 1.0
HB3 A:LYS326 4.6 12.1 1.0
CB A:LYS326 4.8 10.1 1.0
CA A:LYS326 4.9 9.1 1.0
HD2 A:PHE357 4.9 11.3 1.0
O A:HOH684 5.0 16.8 1.0

Sodium binding site 2 out of 3 in 4z79

Go back to Sodium Binding Sites List in 4z79
Sodium binding site 2 out of 3 in the Leiomodin-1 Actin-Binding Site 2 (ABS2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Leiomodin-1 Actin-Binding Site 2 (ABS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:23.9
occ:1.00
HZ3 A:LYS387 2.1 10.8 0.5
HD3 A:LYS387 2.7 13.7 0.5
O A:LEU383 2.7 7.0 1.0
O A:HOH690 2.7 8.7 1.0
HZ2 A:LYS387 2.8 10.8 0.5
NZ A:LYS387 2.8 9.0 0.5
HA A:ASN414 3.0 10.6 1.0
O A:LYS384 3.2 8.0 1.0
HD22 A:ASN414 3.2 8.7 1.0
O A:ASN386 3.2 8.2 1.0
HG2 A:LYS387 3.2 13.5 0.5
HA A:LYS384 3.3 7.6 1.0
O A:GLN413 3.3 11.1 1.0
CD A:LYS387 3.4 11.4 0.5
HB2 A:ASN414 3.4 9.5 1.0
C A:LYS384 3.4 6.4 1.0
HZ2 A:LYS387 3.5 14.4 0.5
HZ1 A:LYS387 3.5 10.8 0.5
HD2 A:LYS387 3.5 13.7 0.5
CE A:LYS387 3.6 13.4 0.5
ND2 A:ASN414 3.6 7.2 1.0
C A:LEU383 3.8 7.2 1.0
CA A:LYS384 3.8 6.3 1.0
CA A:ASN414 3.8 8.8 1.0
CB A:ASN414 3.9 7.9 1.0
HG3 A:LYS387 3.9 13.5 0.5
HE2 A:LYS387 4.0 16.0 0.5
C A:ASN386 4.0 6.2 1.0
CG A:LYS387 4.0 11.3 0.5
N A:ALA385 4.0 6.9 1.0
H A:ASN386 4.0 7.8 1.0
CG A:ASN414 4.1 8.3 1.0
N A:ASN386 4.1 6.5 1.0
C A:ALA385 4.1 8.4 1.0
HD21 A:ASN414 4.1 8.7 1.0
HA A:LYS387 4.2 9.3 0.5
N A:LYS384 4.2 6.0 1.0
HA A:LYS387 4.2 12.9 0.5
NZ A:LYS387 4.3 12.0 0.5
C A:GLN413 4.3 11.3 1.0
H A:ASN415 4.3 10.5 1.0
HE3 A:LYS387 4.4 16.0 0.5
HZ3 A:LYS387 4.4 14.4 0.5
CA A:ALA385 4.5 9.7 1.0
HA A:ALA385 4.5 11.7 1.0
H A:ALA385 4.5 8.3 1.0
O A:ALA385 4.5 9.6 1.0
N A:ASN414 4.5 7.8 1.0
CA A:ASN386 4.7 6.7 1.0
N A:LYS387 4.7 9.6 1.0
CG A:LYS387 4.7 12.4 0.5
OG1 A:THR416 4.8 9.9 1.0
HZ1 A:LYS387 4.8 14.4 0.5
HB3 A:ASN414 4.8 9.5 1.0
HD2 A:LYS387 4.8 16.9 0.5
CA A:LYS387 4.9 10.8 0.5
CA A:LYS387 4.9 7.7 0.5
CD A:LYS387 4.9 14.1 0.5
HG1 A:THR416 4.9 11.9 1.0
HG2 A:LYS387 4.9 14.9 0.5
HA A:LEU383 4.9 9.4 1.0
N A:ASN415 4.9 8.8 1.0
C A:ASN414 4.9 8.2 1.0

Sodium binding site 3 out of 3 in 4z79

Go back to Sodium Binding Sites List in 4z79
Sodium binding site 3 out of 3 in the Leiomodin-1 Actin-Binding Site 2 (ABS2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Leiomodin-1 Actin-Binding Site 2 (ABS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:16.8
occ:1.00
HH21 A:ARG483 3.2 17.0 1.0
HH22 A:ARG483 3.3 17.0 1.0
NH2 A:ARG483 3.5 14.2 1.0
HD2 A:ARG483 4.4 19.2 1.0
CZ A:ARG483 4.7 13.5 1.0

Reference:

M.Boczkowska, G.Rebowski, E.Kremneva, P.Lappalainen, R.Dominguez. How Leiomodin and Tropomodulin Use A Common Fold For Different Actin Assembly Functions. Nat Commun V. 6 8314 2015.
ISSN: ESSN 2041-1723
PubMed: 26370058
DOI: 10.1038/NCOMMS9314
Page generated: Tue Dec 15 10:05:47 2020

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