Sodium in PDB 6y76: AP01 - A Redesigned Transferrin Receptor Apical Domain

Protein crystallography data

The structure of AP01 - A Redesigned Transferrin Receptor Apical Domain, PDB code: 6y76 was solved by G.Oberdorfer, S.A.Berger, S.Bjelic, D.Sjorstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.70 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 33.122, 119.558, 33.167, 90.00, 112.25, 90.00
R / Rfree (%) 23.4 / 27.5

Sodium Binding Sites:

The binding sites of Sodium atom in the AP01 - A Redesigned Transferrin Receptor Apical Domain (pdb code 6y76). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the AP01 - A Redesigned Transferrin Receptor Apical Domain, PDB code: 6y76:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6y76

Go back to Sodium Binding Sites List in 6y76
Sodium binding site 1 out of 3 in the AP01 - A Redesigned Transferrin Receptor Apical Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of AP01 - A Redesigned Transferrin Receptor Apical Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:28.0
occ:1.00
OG1 A:THR53 2.4 25.8 0.4
O A:HOH324 2.8 20.1 1.0
CG2 A:THR53 2.8 25.0 0.6
CE A:MET143 3.0 30.5 1.0
CE2 A:TYR52 3.3 29.9 1.0
CD2 A:TYR52 3.3 29.9 1.0
N A:TYR52 3.4 26.7 1.0
CZ A:TYR52 3.5 31.4 1.0
CG A:TYR52 3.5 24.9 1.0
N A:THR53 3.6 26.6 0.6
N A:THR53 3.6 26.7 0.4
CE1 A:TYR52 3.7 32.9 1.0
CB A:THR53 3.7 24.9 0.4
CD1 A:TYR52 3.7 30.8 1.0
CD2 A:LEU51 3.8 20.5 1.0
CB A:THR53 3.9 24.7 0.6
CA A:LEU51 4.0 22.8 1.0
OH A:TYR52 4.2 32.1 1.0
C A:LEU51 4.2 25.8 1.0
CA A:TYR52 4.2 24.7 1.0
CB A:MET143 4.2 17.0 1.0
CB A:LEU51 4.3 19.6 1.0
CA A:THR53 4.3 27.8 0.4
C A:TYR52 4.3 28.0 1.0
CA A:THR53 4.4 27.9 0.6
CB A:TYR52 4.4 21.8 1.0
CG A:LEU51 4.5 23.3 1.0
SD A:MET143 4.6 23.2 1.0
CG A:MET143 4.6 24.1 1.0
CG2 A:THR53 4.8 27.8 0.4
CG1 A:VAL38 5.0 16.9 1.0
CD1 A:LEU51 5.0 18.2 1.0

Sodium binding site 2 out of 3 in 6y76

Go back to Sodium Binding Sites List in 6y76
Sodium binding site 2 out of 3 in the AP01 - A Redesigned Transferrin Receptor Apical Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of AP01 - A Redesigned Transferrin Receptor Apical Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:32.8
occ:1.00
CD1 B:LEU14 3.7 25.0 1.0
CD2 B:LEU17 3.8 33.4 1.0
O B:HOH353 3.8 37.0 1.0
CB B:LEU17 4.3 25.2 1.0
CG B:LEU17 4.4 21.4 1.0
CD1 B:LEU17 4.4 21.3 1.0

Sodium binding site 3 out of 3 in 6y76

Go back to Sodium Binding Sites List in 6y76
Sodium binding site 3 out of 3 in the AP01 - A Redesigned Transferrin Receptor Apical Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of AP01 - A Redesigned Transferrin Receptor Apical Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:32.6
occ:1.00
O B:HOH316 3.4 29.7 1.0
O B:HOH353 4.1 37.0 1.0
O B:HOH376 4.2 39.4 1.0

Reference:

D.J.Sjostrom, S.A.Berger, G.Oberdorfer, S.Bjelic. Computational Backbone Design Enables Soluble Engineering of Transferrin Receptor Apical Domain. Proteins V. 88 1569 2020.
ISSN: ESSN 1097-0134
PubMed: 32592192
DOI: 10.1002/PROT.25974
Page generated: Tue Dec 15 16:14:56 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy