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Sodium in PDB 4o1r: Crystal Structure of Npudnab Intein

Protein crystallography data

The structure of Crystal Structure of Npudnab Intein, PDB code: 4o1r was solved by A.S.Aranko, J.S.Oeemig, D.Zhou, T.Kajander, A.Wlodawer, H.Iwai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.05 / 1.40
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 61.054, 61.054, 122.179, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.9

Other elements in 4o1r:

The structure of Crystal Structure of Npudnab Intein also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Npudnab Intein (pdb code 4o1r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Npudnab Intein, PDB code: 4o1r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4o1r

Go back to Sodium Binding Sites List in 4o1r
Sodium binding site 1 out of 3 in the Crystal Structure of Npudnab Intein


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 Npudnab Intein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:14.5
occ:1.00
O A:PRO89 2.3 13.0 1.0
O A:HOH332 2.4 22.7 1.0
O A:HOH343 2.4 26.3 1.0
OG1 A:THR88 2.4 13.7 1.0
CB A:THR88 3.3 13.0 1.0
C A:PRO89 3.5 13.0 1.0
C A:THR88 3.9 13.1 1.0
N A:GLU91 4.0 11.9 1.0
N A:PRO89 4.0 13.0 1.0
O A:THR88 4.2 12.0 1.0
CA A:THR88 4.2 12.9 1.0
CA A:PRO89 4.4 13.3 1.0
C A:LYS90 4.4 12.9 1.0
CB A:LYS90 4.4 14.1 1.0
N A:LYS90 4.4 13.2 1.0
CG2 A:THR88 4.4 13.4 1.0
CD A:PRO89 4.5 13.3 1.0
CB A:GLU91 4.6 11.9 1.0
CA A:LYS90 4.6 13.7 1.0
CA A:GLU91 4.6 12.1 1.0
O A:HOH571 4.6 58.6 1.0
O A:HOH346 4.9 25.2 1.0
CB A:PRO89 4.9 14.3 1.0

Sodium binding site 2 out of 3 in 4o1r

Go back to Sodium Binding Sites List in 4o1r
Sodium binding site 2 out of 3 in the Crystal Structure of Npudnab Intein


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 Npudnab Intein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:23.5
occ:1.00
O A:HOH412 2.4 41.8 1.0
O A:HOH358 2.4 29.3 1.0
O A:ASP12 2.4 24.2 1.0
O A:HOH318 2.4 19.9 1.0
O A:HOH411 2.5 35.5 1.0
C A:ASP12 3.6 23.8 1.0
O A:SER13 4.2 19.2 1.0
C A:SER13 4.2 19.0 1.0
O A:HOH453 4.3 39.6 1.0
CA A:SER13 4.4 19.6 1.0
N A:SER13 4.5 21.0 1.0
CA A:ASP12 4.6 24.9 1.0
O A:VAL11 4.6 23.3 1.0
N A:GLY14 4.7 17.9 1.0
O A:HOH444 4.8 40.5 1.0

Sodium binding site 3 out of 3 in 4o1r

Go back to Sodium Binding Sites List in 4o1r
Sodium binding site 3 out of 3 in the Crystal Structure of Npudnab Intein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Npudnab Intein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:32.5
occ:1.00
O A:HOH487 2.1 54.1 1.0
O A:HOH322 2.2 22.8 1.0
O A:ILE78 2.3 15.9 1.0
O A:HOH384 2.4 49.3 1.0
O A:HOH347 2.5 30.4 1.0
C A:ILE78 3.6 14.5 1.0
O A:HOH438 4.0 43.3 1.0
OD1 A:ASN79 4.2 21.1 1.0
CG1 A:ILE78 4.3 16.2 1.0
O A:HOH327 4.3 23.4 1.0
CA A:ASN79 4.4 15.9 1.0
N A:ASN79 4.5 14.9 1.0
O A:HOH402 4.5 46.5 1.0
CA A:ILE78 4.6 14.2 1.0
O A:HOH560 4.7 60.2 1.0
O A:HOH465 4.7 41.5 1.0
CD1 A:ILE78 4.7 17.9 1.0
CB A:ILE78 4.9 14.0 1.0
CG A:ASN79 5.0 18.0 1.0

Reference:

A.S.Aranko, J.S.Oeemig, D.Zhou, T.Kajander, A.Wlodawer, H.Iwai. Structure-Based Engineering and Comparison of Novel Split Inteins For Protein Ligation. Mol Biosyst V. 10 1023 2014.
ISSN: ISSN 1742-206X
PubMed: 24574026
DOI: 10.1039/C4MB00021H
Page generated: Tue Dec 15 06:56:22 2020

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