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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

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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

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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

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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

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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

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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

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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

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