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Barium in PDB 8ayp: Nak C-Di Mutant with Rb+ and BA2+

Protein crystallography data

The structure of Nak C-Di Mutant with Rb+ and BA2+, PDB code: 8ayp was solved by S.Minniberger, A.J.R.Plested, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.68 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 68.171, 177.495, 68.042, 90, 90, 90
R / Rfree (%) 22.6 / 26.7

Other elements in 8ayp:

The structure of Nak C-Di Mutant with Rb+ and BA2+ also contains other interesting chemical elements:

Rubidium (Rb) 4 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Nak C-Di Mutant with Rb+ and BA2+ (pdb code 8ayp). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 4 binding sites of Barium where determined in the Nak C-Di Mutant with Rb+ and BA2+, PDB code: 8ayp:
Jump to Barium binding site number: 1; 2; 3; 4;

Barium binding site 1 out of 4 in 8ayp

Go back to Barium Binding Sites List in 8ayp
Barium binding site 1 out of 4 in the Nak C-Di Mutant with Rb+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Nak C-Di Mutant with Rb+ and BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba205

b:89.0
occ:0.30
O B:HOH302 2.8 65.2 1.0
O B:VAL64 4.3 26.1 1.0
C A:GLY65 4.3 41.8 1.0
O A:VAL64 4.4 26.8 1.0
C B:GLY65 4.4 43.5 1.0
O A:CYS66 4.4 65.5 1.0
N A:CYS66 4.5 53.2 1.0
N B:CYS66 4.5 52.0 1.0
O A:GLY65 4.5 48.8 1.0
CA B:GLY65 4.6 37.8 1.0
O B:CYS66 4.6 65.7 1.0
CA A:GLY65 4.7 36.9 1.0
C A:CYS66 4.7 66.5 1.0
O B:GLY65 4.7 46.7 1.0
RB A:RB204 4.8 26.3 0.6
CA A:CYS66 4.8 61.4 1.0
C B:CYS66 4.9 66.4 1.0
CA B:CYS66 4.9 59.7 1.0

Barium binding site 2 out of 4 in 8ayp

Go back to Barium Binding Sites List in 8ayp
Barium binding site 2 out of 4 in the Nak C-Di Mutant with Rb+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Nak C-Di Mutant with Rb+ and BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba206

b:84.3
occ:0.20
O A:HOH320 2.8 76.4 1.0
RB A:RB203 3.4 41.4 0.4
OG1 A:THR63 3.8 29.4 1.0
OG1 B:THR63 3.9 30.4 1.0
CB A:THR63 4.8 34.6 1.0
CB B:THR63 4.8 31.7 1.0

Barium binding site 3 out of 4 in 8ayp

Go back to Barium Binding Sites List in 8ayp
Barium binding site 3 out of 4 in the Nak C-Di Mutant with Rb+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Nak C-Di Mutant with Rb+ and BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba211

b:97.5
occ:0.24
RB C:RB210 4.1 47.7 0.3
OG1 D:THR63 4.2 47.3 1.0
OG1 C:THR63 4.3 45.8 1.0
CE2 C:PHE91 4.7 61.8 1.0
CZ D:PHE91 4.8 54.9 1.0
CZ C:PHE91 4.9 58.2 1.0
CE1 D:PHE91 5.0 57.4 1.0

Barium binding site 4 out of 4 in 8ayp

Go back to Barium Binding Sites List in 8ayp
Barium binding site 4 out of 4 in the Nak C-Di Mutant with Rb+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Nak C-Di Mutant with Rb+ and BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba210

b:102.5
occ:0.26
O C:HOH302 2.7 89.2 1.0
O D:GLY65 3.9 76.3 1.0
C D:GLY65 4.0 76.1 1.0
O C:VAL64 4.1 50.2 1.0
O D:VAL64 4.1 56.5 1.0
CA D:GLY65 4.3 64.2 1.0
CA C:GLY65 4.4 65.0 1.0
RB D:RB209 4.4 37.6 0.6
C C:GLY65 4.4 69.1 1.0
O D:CYS66 4.5 105.5 1.0
N C:CYS66 4.6 81.4 1.0
N D:CYS66 4.6 86.8 1.0
O C:CYS66 4.9 106.8 1.0
C D:CYS66 4.9 106.3 1.0
O C:GLY65 4.9 70.5 1.0
CA D:CYS66 5.0 98.1 1.0

Reference:

F.K.Schackert, J.Biedermann, S.Abdolvand, S.Minniberger, C.Song, A.J.R.Plested, P.Carloni, H.Sun. Mechanism of Calcium Permeation in A Glutamate Receptor Ion Channel. J.Chem.Inf.Model. 2023.
ISSN: ESSN 1549-960X
PubMed: 36758214
DOI: 10.1021/ACS.JCIM.2C01494
Page generated: Wed Jul 10 16:11:04 2024

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