Atomistry » Sodium » PDB 8k1k-8oyf » 8k69
Atomistry »
  Sodium »
    PDB 8k1k-8oyf »
      8k69 »

Sodium in PDB 8k69: Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom

Sodium Binding Sites:

The binding sites of Sodium atom in the Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom (pdb code 8k69). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom, PDB code: 8k69:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8k69

Go back to Sodium Binding Sites List in 8k69
Sodium binding site 1 out of 6 in the Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:30.0
occ:1.00
 O A:HOH701 2.1 30.0 1.0
O A:SER87 2.3 50.2 1.0
O A:VAL468 2.4 49.8 1.0
O A:GLY243 2.6 50.0 1.0
O A:ASN242 2.9 50.1 1.0
O A:SER367 2.9 50.1 1.0
O A:ASN467 2.9 48.7 1.0
O A:VAL86 3.0 50.0 1.0
C A:SER87 3.1 50.2 1.0
C A:VAL468 3.1 49.8 1.0
O A:HIS366 3.2 49.9 1.0
C A:GLY243 3.4 50.0 1.0
NA A:NA608 3.5 30.0 1.0
C A:SER367 3.6 50.1 1.0
CA A:VAL468 3.7 49.8 1.0
CA A:SER87 3.7 50.2 1.0
C A:ASN467 3.7 48.7 1.0
C A:VAL86 3.8 50.0 1.0
C A:ASN242 3.9 50.1 1.0
CA A:GLY243 3.9 50.0 1.0
N A:GLY88 4.0 47.9 1.0
N A:VAL468 4.0 49.8 1.0
N A:GLY469 4.1 48.7 1.0
N A:SER87 4.1 50.2 1.0
N A:GLY368 4.3 50.5 1.0
CA A:SER367 4.3 50.1 1.0
N A:GLY243 4.3 50.0 1.0
CA A:GLY88 4.3 47.9 1.0
C A:HIS366 4.3 49.9 1.0
N A:GLY244 4.4 51.0 1.0
CA A:GLY469 4.4 48.7 1.0
CA A:GLY368 4.4 50.5 1.0
NA A:NA609 4.5 30.0 1.0
CA A:GLY244 4.7 51.0 1.0
N A:SER367 4.8 50.1 1.0
CA A:ASN467 4.9 48.7 1.0

Sodium binding site 2 out of 6 in 8k69

Go back to Sodium Binding Sites List in 8k69
Sodium binding site 2 out of 6 in the Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:30.0
occ:1.00
 O A:HOH735 2.2 30.0 1.0
O A:VAL468 3.0 49.8 1.0
O A:GLY243 3.0 50.0 1.0
O A:SER87 3.1 50.2 1.0
O A:GLY88 3.2 47.9 1.0
CA A:GLY469 3.2 48.7 1.0
CA A:GLY88 3.3 47.9 1.0
O A:SER367 3.3 50.1 1.0
O A:GLY368 3.4 50.5 1.0
CA A:GLY244 3.4 51.0 1.0
C A:GLY88 3.4 47.9 1.0
NA A:NA607 3.5 30.0 1.0
O A:GLY469 3.5 48.7 1.0
CA A:GLY368 3.6 50.5 1.0
C A:GLY469 3.6 48.7 1.0
C A:GLY368 3.6 50.5 1.0
O A:GLY244 3.7 51.0 1.0
C A:GLY244 3.7 51.0 1.0
C A:VAL468 3.9 49.8 1.0
C A:GLY243 4.0 50.0 1.0
C A:SER87 4.0 50.2 1.0
N A:GLY469 4.0 48.7 1.0
N A:GLY88 4.1 47.9 1.0
N A:GLY244 4.2 51.0 1.0
C A:SER367 4.2 50.1 1.0
N A:GLY368 4.4 50.5 1.0
N A:LEU89 4.4 49.6 1.0
N A:GLU369 4.5 52.9 1.0
N A:LEU470 4.5 49.8 1.0
N A:LEU245 4.6 51.4 1.0

Sodium binding site 3 out of 6 in 8k69

Go back to Sodium Binding Sites List in 8k69
Sodium binding site 3 out of 6 in the Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na609

b:30.0
occ:1.00
 O A:HOH701 2.4 30.0 1.0
O A:ASN467 3.1 48.7 1.0
O A:VAL86 3.3 50.0 1.0
O A:ASN242 3.4 50.1 1.0
CG2 A:VAL86 3.6 50.0 1.0
O A:HIS366 3.7 49.9 1.0
CB A:ASN242 3.8 50.1 1.0
CB A:ASN467 4.0 48.7 1.0
O A:HOH752 4.0 30.0 1.0
CB A:HIS366 4.0 49.9 1.0
C A:ASN467 4.2 48.7 1.0
C A:ASN242 4.3 50.1 1.0
C A:VAL86 4.4 50.0 1.0
O A:ALA241 4.4 50.7 1.0
CB A:VAL86 4.4 50.0 1.0
O A:HOH760 4.5 30.0 1.0
NA A:NA607 4.5 30.0 1.0
C A:HIS366 4.5 49.9 1.0
O A:HOH722 4.6 30.0 1.0
O A:HOH709 4.6 30.0 1.0
O A:GLY466 4.6 48.3 1.0
CA A:ASN242 4.7 50.1 1.0
CA A:ASN467 4.7 48.7 1.0
CA A:HIS366 4.9 49.9 1.0
CG A:ASN242 4.9 50.1 1.0

Sodium binding site 4 out of 6 in 8k69

Go back to Sodium Binding Sites List in 8k69
Sodium binding site 4 out of 6 in the Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na707

b:30.0
occ:1.00
 O B:HOH801 2.4 30.0 1.0
O B:ASN467 3.1 48.7 1.0
O B:VAL86 3.3 50.0 1.0
O B:ASN242 3.4 50.1 1.0
CG2 B:VAL86 3.6 50.0 1.0
O B:HIS366 3.7 49.9 1.0
CB B:ASN242 3.8 50.1 1.0
CB B:ASN467 4.0 48.7 1.0
O B:HOH852 4.0 30.0 1.0
CB B:HIS366 4.0 49.9 1.0
C B:ASN467 4.2 48.7 1.0
C B:ASN242 4.3 50.1 1.0
C B:VAL86 4.4 50.0 1.0
O B:ALA241 4.4 50.7 1.0
CB B:VAL86 4.4 50.0 1.0
O B:HOH860 4.5 30.0 1.0
NA B:NA708 4.5 30.0 1.0
C B:HIS366 4.5 49.9 1.0
O B:HOH810 4.6 30.0 1.0
O B:HOH820 4.6 30.0 1.0
O B:GLY466 4.6 48.3 1.0
CA B:ASN242 4.7 50.1 1.0
CA B:ASN467 4.7 48.7 1.0
CA B:HIS366 4.9 49.9 1.0
CG B:ASN242 4.9 50.1 1.0

Sodium binding site 5 out of 6 in 8k69

Go back to Sodium Binding Sites List in 8k69
Sodium binding site 5 out of 6 in the Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na708

b:30.0
occ:1.00
 O B:HOH801 2.1 30.0 1.0
O B:SER87 2.3 50.2 1.0
O B:VAL468 2.4 49.8 1.0
O B:GLY243 2.6 50.0 1.0
O B:ASN242 2.9 50.1 1.0
O B:SER367 2.9 50.1 1.0
O B:ASN467 2.9 48.7 1.0
O B:VAL86 3.0 50.0 1.0
C B:SER87 3.1 50.2 1.0
C B:VAL468 3.1 49.8 1.0
O B:HIS366 3.2 49.9 1.0
C B:GLY243 3.4 50.0 1.0
NA B:NA709 3.5 30.0 1.0
C B:SER367 3.6 50.1 1.0
CA B:VAL468 3.7 49.8 1.0
CA B:SER87 3.7 50.2 1.0
C B:ASN467 3.7 48.7 1.0
C B:VAL86 3.8 50.0 1.0
C B:ASN242 3.9 50.1 1.0
CA B:GLY243 3.9 50.0 1.0
N B:GLY88 4.0 47.9 1.0
N B:VAL468 4.0 49.8 1.0
N B:GLY469 4.1 48.7 1.0
N B:SER87 4.1 50.2 1.0
CA B:SER367 4.3 50.1 1.0
N B:GLY368 4.3 50.5 1.0
N B:GLY243 4.3 50.0 1.0
CA B:GLY88 4.3 47.9 1.0
C B:HIS366 4.3 49.9 1.0
N B:GLY244 4.4 51.0 1.0
CA B:GLY469 4.4 48.7 1.0
CA B:GLY368 4.5 50.5 1.0
NA B:NA707 4.5 30.0 1.0
CA B:GLY244 4.7 51.0 1.0
N B:SER367 4.8 50.1 1.0
CA B:ASN467 4.9 48.7 1.0

Sodium binding site 6 out of 6 in 8k69

Go back to Sodium Binding Sites List in 8k69
Sodium binding site 6 out of 6 in the Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cryo-Em Structure of Oryza Sativa HKT2;2/1 at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na709

b:30.0
occ:1.00
 O B:HOH836 2.2 30.0 1.0
O B:VAL468 3.0 49.8 1.0
O B:GLY243 3.0 50.0 1.0
O B:SER87 3.1 50.2 1.0
O B:GLY88 3.2 47.9 1.0
CA B:GLY469 3.2 48.7 1.0
CA B:GLY88 3.3 47.9 1.0
O B:SER367 3.3 50.1 1.0
O B:GLY368 3.4 50.5 1.0
CA B:GLY244 3.4 51.0 1.0
C B:GLY88 3.4 47.9 1.0
NA B:NA708 3.5 30.0 1.0
O B:GLY469 3.5 48.7 1.0
CA B:GLY368 3.5 50.5 1.0
C B:GLY469 3.6 48.7 1.0
C B:GLY368 3.6 50.5 1.0
O B:GLY244 3.7 51.0 1.0
C B:GLY244 3.7 51.0 1.0
C B:VAL468 3.9 49.8 1.0
C B:GLY243 4.0 50.0 1.0
C B:SER87 4.0 50.2 1.0
N B:GLY469 4.0 48.7 1.0
N B:GLY88 4.1 47.9 1.0
N B:GLY244 4.2 51.0 1.0
C B:SER367 4.2 50.1 1.0
N B:GLY368 4.4 50.5 1.0
N B:LEU89 4.4 49.6 1.0
N B:GLU369 4.5 52.9 1.0
N B:LEU470 4.5 49.8 1.0
N B:LEU245 4.6 51.4 1.0
O B:HOH828 5.0 30.0 1.0

Reference:

X.Wang, X.Shen, Y.Qu, H.Zhang, C.Wang, F.Yang, H.Shen. Structural Insights Into Ion Selectivity and Transport Mechanism of Plant Hkt Transporters To Be Published.
Page generated: Wed Oct 9 12:43:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy