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Sodium in PDB 5t77: Crystal Structure of the Mop Flippase Murj

Protein crystallography data

The structure of Crystal Structure of the Mop Flippase Murj, PDB code: 5t77 was solved by A.C.Y.Kuk, S.-Y.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.19 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.163, 99.573, 74.660, 90.00, 112.91, 90.00
R / Rfree (%) 18.9 / 21.4

Other elements in 5t77:

The structure of Crystal Structure of the Mop Flippase Murj also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 3 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Mop Flippase Murj (pdb code 5t77). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Mop Flippase Murj, PDB code: 5t77:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5t77

Go back to Sodium Binding Sites List in 5t77
Sodium binding site 1 out of 2 in the Crystal Structure of the Mop Flippase Murj


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 the Mop Flippase Murj within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:57.6
occ:1.00
O A:HOH670 2.3 49.0 1.0
O A:HOH686 2.4 57.3 1.0
O A:HOH739 2.4 63.3 1.0
O A:HOH629 2.4 39.9 1.0
O A:HOH749 2.4 63.4 1.0
O A:PHE241 2.7 33.0 1.0
O A:HOH688 3.5 67.9 1.0
O A:TYR242 3.6 34.9 1.0
C A:PHE241 3.7 33.1 1.0
O A:HOH713 4.0 57.2 1.0
C A:TYR242 4.1 32.2 1.0
HA A:PHE241 4.1 39.6 1.0
HA A:TYR242 4.2 36.0 1.0
O A:HOH714 4.3 52.4 1.0
O A:HOH736 4.3 51.7 1.0
N A:TYR242 4.5 29.8 1.0
CA A:TYR242 4.5 30.0 1.0
CA A:PHE241 4.5 33.0 1.0
HA A:ASP243 4.6 43.8 1.0
O A:GLY112 4.6 28.4 1.0
N A:ASP243 4.8 34.2 1.0
HB3 A:PHE241 4.9 39.9 1.0

Sodium binding site 2 out of 2 in 5t77

Go back to Sodium Binding Sites List in 5t77
Sodium binding site 2 out of 2 in the Crystal Structure of the Mop Flippase Murj


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 the Mop Flippase Murj within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na511

b:35.3
occ:1.00
OH7 A:1PE514 2.3 50.6 1.0
O A:HOH606 2.4 56.9 1.0
O A:HOH724 2.5 34.0 1.0
O A:HOH634 2.6 37.8 1.0
O A:HOH699 2.6 27.6 1.0
HB2 A:SER35 3.4 36.2 1.0
C16 A:1PE514 3.7 56.0 1.0
HG A:SER35 3.9 41.2 1.0
H162 A:1PE514 4.1 67.2 1.0
CB A:SER35 4.2 30.1 1.0
O A:PHE32 4.2 25.9 1.0
H161 A:1PE514 4.2 67.2 1.0
H261 A:1PE514 4.2 77.0 1.0
CA A:CA508 4.3 42.0 1.0
OG A:SER35 4.3 34.4 1.0
O A:HOH656 4.4 40.3 1.0
C26 A:1PE514 4.5 64.2 1.0
HB1 A:ALA321 4.5 33.7 1.0
HB3 A:SER35 4.5 36.2 1.0
H262 A:1PE514 4.6 77.0 1.0
OE2 A:GLU37 4.7 35.4 1.0
O A:HOH684 4.8 41.0 1.0
O A:VAL34 4.9 28.8 1.0
O A:HOH635 5.0 41.5 1.0

Reference:

A.C.Kuk, E.H.Mashalidis, S.Y.Lee. Crystal Structure of the Mop Flippase Murj in An Inward-Facing Conformation. Nat. Struct. Mol. Biol. V. 24 171 2017.
ISSN: ESSN 1545-9985
PubMed: 28024149
DOI: 10.1038/NSMB.3346
Page generated: Tue Dec 15 11:36:04 2020

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