Sodium in PDB 9cld: Crystal Structure of Maltose Binding Protein (Apo)

The structure of Crystal Structure of Maltose Binding Protein (Apo), PDB code: 9cld was solved by E.Habel, R.L.Frkic, C.J.Jackson, T.Huber, G.Otting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.99 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.819, 64.524, 57.64, 90, 101.17, 90
R / Rfree (%)	15.5 / 17.4

The structure of Crystal Structure of Maltose Binding Protein (Apo) also contains other interesting chemical elements:

Cadmium

(Cd)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Maltose Binding Protein (Apo) (pdb code 9cld). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Maltose Binding Protein (Apo), PDB code: 9cld:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Maltose Binding Protein (Apo)


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 Maltose Binding Protein (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:34.5 occ:1.00 OE2 A:GLU310 3.0 58.9 1.0 HG3 A:GLU310 3.8 32.3 1.0 CD A:GLU310 3.9 41.4 1.0 O A:HOH709 4.1 47.4 1.0 O A:HOH690 4.3 39.3 1.0 CG A:GLU310 4.3 32.3 1.0 HB3 A:GLU310 4.4 23.7 1.0 HE1 A:TYR307 4.5 21.1 1.0 OE1 A:GLU310 4.9 48.6 1.0 CB A:GLU310 4.9 23.7 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Maltose Binding Protein (Apo)


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 Maltose Binding Protein (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na414 b:25.9 occ:1.00 O A:HOH783 2.1 67.1 1.0 O A:VAL35 2.1 21.4 1.0 O A:HOH538 2.1 42.2 1.0 O A:HOH634 2.4 36.2 1.0 H A:VAL35 3.2 23.2 1.0 C A:VAL35 3.3 18.9 1.0 HB A:VAL35 3.4 21.7 1.0 O A:HOH562 3.4 30.0 1.0 O A:HOH726 3.8 32.6 1.0 N A:VAL35 3.8 23.2 1.0 CA A:VAL35 3.9 21.0 1.0 HA A:THR36 4.0 17.9 1.0 O A:HOH514 4.0 69.0 1.0 CB A:VAL35 4.1 21.7 1.0 HG3 A:LYS34 4.1 40.2 1.0 OE1 A:GLU28 4.2 43.0 1.0 HA A:LYS25 4.3 19.4 1.0 N A:THR36 4.4 17.4 1.0 HG12 A:VAL35 4.5 22.3 1.0 HA3 A:GLY24 4.6 16.1 1.0 CA A:THR36 4.7 17.9 1.0 HA A:LYS34 4.7 29.0 1.0 N A:LYS25 4.8 17.6 1.0 C A:GLY24 4.8 17.2 1.0 HB2 A:GLU28 4.8 25.0 1.0 O A:ALA21 4.8 15.7 1.0 HB2 A:LYS25 4.8 23.3 1.0 HA A:VAL35 4.9 21.0 1.0 O A:GLY24 4.9 17.6 1.0 CG1 A:VAL35 4.9 22.3 1.0 H A:LYS25 5.0 17.6 1.0 H A:VAL37 5.0 15.0 1.0 CA A:LYS25 5.0 19.4 1.0 C A:LYS34 5.0 23.6 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Maltose Binding Protein (Apo)


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 Maltose Binding Protein (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na418 b:42.4 occ:1.00 OE2 A:GLU309 2.2 31.4 1.0 O A:HOH750 2.3 50.0 1.0 O A:HOH744 2.4 48.3 1.0 OE1 A:GLU309 2.5 31.7 1.0 CD A:GLU309 2.7 29.4 1.0 O A:HOH771 4.1 62.0 1.0 CG A:GLU309 4.2 22.7 1.0 HB3 A:LYS305 4.3 15.1 1.0 HA A:SER306 4.3 14.7 1.0 O A:HOH550 4.4 42.3 1.0 HG2 A:GLU309 4.6 22.7 1.0 HG3 A:GLU309 4.6 22.7 1.0 O A:HOH794 4.6 46.7 1.0 HB2 A:LYS305 4.8 15.1 1.0 HB2 A:GLU309 4.9 20.0 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Maltose Binding Protein (Apo)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Maltose Binding Protein (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na420 b:20.3 occ:1.00 O A:HOH677 2.0 67.8 1.0 OD2 A:ASP184 2.2 31.0 1.0 O A:HOH745 2.5 54.5 1.0 O A:HOH635 2.6 48.2 1.0 HG2 A:GLN365 2.9 20.3 1.0 CG A:ASP184 3.2 26.0 1.0 OD1 A:ASP184 3.5 28.0 1.0 HG2 A:LYS362 3.8 38.7 1.0 HB3 A:GLN365 3.9 19.6 1.0 CG A:GLN365 3.9 20.3 1.0 HA A:LYS362 4.1 25.9 1.0 O A:HOH650 4.1 77.0 1.0 HG3 A:GLN365 4.2 20.3 1.0 CB A:GLN365 4.4 19.6 1.0 CB A:ASP184 4.5 22.7 1.0 HE3 A:LYS362 4.6 49.1 1.0 HB2 A:ASP184 4.6 22.7 1.0 HB3 A:LYS362 4.6 29.4 1.0 CG A:LYS362 4.7 38.7 1.0 HB2 A:GLN365 4.7 19.6 1.0 HB3 A:ASP184 4.8 22.7 1.0 CD A:GLN365 4.8 18.3 1.0 HE21 A:GLN365 4.9 17.6 1.0 HG1 A:THR366 4.9 29.0 1.0 CA A:LYS362 4.9 25.9 1.0 O A:LYS362 5.0 25.9 1.0 CB A:LYS362 5.0 29.4 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Maltose Binding Protein (Apo)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Maltose Binding Protein (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na421 b:29.8 occ:1.00 O A:HOH789 2.0 49.3 1.0 O A:HOH742 2.3 70.8 1.0 O A:HOH698 2.3 55.3 1.0 OE2 A:GLU131 2.6 32.1 1.0 OE1 A:GLU131 2.7 33.5 1.0 CD A:GLU131 2.9 32.6 1.0 H A:LYS127 3.1 22.3 1.0 HB2 A:LYS127 3.5 23.9 1.0 HG3 A:LYS127 3.9 30.2 1.0 HA A:PRO126 3.9 22.8 1.0 N A:LYS127 3.9 22.3 1.0 CG A:GLU131 4.2 32.8 1.0 CB A:LYS127 4.3 23.9 1.0 HG2 A:GLU131 4.3 32.8 1.0 HG3 A:GLU131 4.4 32.8 1.0 H A:THR128 4.5 20.6 1.0 CG A:LYS127 4.5 30.2 1.0 HG23 A:THR128 4.6 22.9 1.0 CA A:LYS127 4.7 21.7 1.0 CA A:PRO126 4.8 22.8 1.0 O A:HOH540 4.8 61.3 1.0 C A:PRO126 4.9 23.3 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Maltose Binding Protein (Apo)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Maltose Binding Protein (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na422 b:26.3 occ:1.00 O A:HOH811 2.7 50.3 1.0 O A:HOH670 3.4 46.6 1.0 O A:HOH546 5.0 49.1 1.0

H.Qianzhu, E.Abdelkader, A.Welegedara, E.Habel, N.Paul, R.Frkic, C.Jackson, T.Huber, G.Otting. Rendering Proteins Fluorescent Inconspicuously: Genetically Encoded 4-Cyanotryptophan Conserves Their Structure and Enables the Detection of Ligand Binding Sites. Angew.Chem.Int.Ed.Engl. 21000 2024.
ISSN: ESSN 1521-3773
PubMed: 39632265
DOI: 10.1002/ANIE.202421000