Sodium in PDB 8df2: The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase

The structure of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase, PDB code: 8df2 was solved by B.J.Medley, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.93 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.581, 146.094, 147.289, 90, 90, 90
R / Rfree (%)	22.2 / 27

The structure of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Zinc	(Zn)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase (pdb code 8df2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase, PDB code: 8df2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:50.9 occ:1.00 O A:PRO314 4.1 34.0 1.0 CG A:PRO314 4.8 31.3 1.0

Sodium binding site 2 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:45.1 occ:1.00 NE A:ARG260 3.5 45.5 1.0 CD A:ARG260 4.2 42.6 1.0 OG1 A:THR209 4.3 43.4 1.0 CB A:LYS212 4.3 40.9 1.0 CG A:ARG260 4.4 41.8 1.0 CD A:LYS212 4.4 37.6 1.0 NH2 A:ARG260 4.4 37.1 1.0 CZ A:ARG260 4.5 38.5 1.0 CG A:LYS212 4.7 41.4 1.0

Sodium binding site 3 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:50.5 occ:1.00 CB A:PRO165 3.8 40.0 1.0 NH2 A:ARG70 3.8 30.9 1.0 NH1 A:ARG70 3.8 36.0 1.0 CZ A:ARG70 4.3 35.2 1.0 CG A:PRO165 4.5 39.7 1.0 CA A:PRO165 4.8 39.7 1.0

Sodium binding site 4 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:40.7 occ:1.00 O B:VAL27 3.5 33.6 1.0 N B:TRP29 4.1 29.2 1.0 C B:SER28 4.3 30.1 1.0 CA B:SER28 4.3 30.9 1.0 O B:TRP29 4.3 32.1 1.0 OG1 B:THR30 4.5 33.9 1.0 C B:VAL27 4.5 33.0 1.0 C B:TRP29 4.6 30.7 1.0 CA B:TRP29 4.7 29.8 1.0 N B:SER28 4.8 29.2 1.0 O B:SER28 5.0 28.8 1.0

Sodium binding site 5 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:47.8 occ:1.00 CD2 B:TYR171 4.0 39.4 1.0 CG B:TYR171 4.3 44.7 1.0 CG2 B:ILE216 4.3 37.1 1.0 CD1 B:TYR217 4.4 44.6 1.0 CE1 B:TYR217 4.4 45.0 1.0 O B:ILE216 4.5 38.4 1.0 CE2 B:TYR171 4.5 43.1 1.0 CB B:TYR171 4.5 39.8 1.0 CD1 B:TYR171 5.0 45.8 1.0

Sodium binding site 6 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:53.8 occ:1.00 NE B:ARG260 3.3 50.7 1.0 OG1 B:THR209 3.6 54.0 1.0 CD B:LYS212 3.7 44.4 1.0 NH2 B:ARG260 3.8 43.8 1.0 CZ B:ARG260 4.0 46.4 1.0 CB B:LYS212 4.2 48.2 1.0 CD B:ARG260 4.2 47.3 1.0 CG B:LYS212 4.4 39.9 1.0 CG2 B:THR209 4.6 53.1 1.0 CB B:THR209 4.7 54.7 1.0 CA B:LYS212 4.9 44.9 1.0 N B:LYS212 4.9 44.5 1.0

Sodium binding site 7 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:48.1 occ:1.00 CB B:PRO165 3.9 43.3 1.0 NH2 B:ARG70 3.9 35.7 1.0 NH1 B:ARG70 4.0 38.7 1.0 CZ B:ARG70 4.4 39.5 1.0 CG B:PRO165 4.5 41.6 1.0 CA B:PRO165 4.7 44.0 1.0

Sodium binding site 8 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:52.2 occ:1.00 NE C:ARG260 3.3 50.6 1.0 CD C:ARG260 4.0 54.7 1.0 CB C:LYS212 4.1 48.7 1.0 CD C:LYS212 4.2 42.7 1.0 CZ C:ARG260 4.3 52.0 1.0 NH2 C:ARG260 4.3 49.3 1.0 CG C:ARG260 4.4 53.9 1.0 CG C:LYS212 4.5 43.9 1.0 CA C:LYS212 4.8 48.2 1.0 N C:LYS212 4.8 52.7 1.0

Sodium binding site 9 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:48.2 occ:1.00 N C:ARG210 3.3 62.8 1.0 CB C:ASN213 3.7 46.1 1.0 CA C:THR209 3.7 66.4 1.0 CG C:ASN213 3.7 42.5 1.0 SD C:MET200 3.8 75.7 1.0 ND2 C:ASN213 3.9 42.1 1.0 C C:THR209 3.9 65.3 1.0 CB C:ARG210 4.1 56.9 1.0 OD1 C:ASN213 4.2 35.2 1.0 CA C:ARG210 4.3 55.5 1.0 O C:ARG210 4.9 52.5 1.0 N C:THR209 4.9 62.8 1.0 CE C:MET200 4.9 53.6 1.0 CG C:MET200 5.0 67.1 1.0 O C:THR209 5.0 64.5 1.0

Sodium binding site 10 out of 12 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:20.6 occ:1.00 N C:PHE295 3.2 26.2 1.0 O B:HOH611 3.2 30.0 1.0 N B:PHE295 3.2 26.8 1.0 CA C:SER294 3.5 27.7 1.0 CD2 B:PHE295 3.6 22.5 1.0 CB C:SER294 3.6 23.4 1.0 CA B:SER294 3.6 29.0 1.0 CD2 C:PHE295 3.7 26.3 1.0 CB B:SER294 3.8 26.1 1.0 C C:SER294 3.8 23.8 1.0 C B:SER294 3.9 29.3 1.0 CB C:PHE295 4.2 24.8 1.0 CB B:PHE295 4.2 24.4 1.0 CA C:PHE295 4.2 27.4 1.0 CA B:PHE295 4.2 27.2 1.0 OG C:SER294 4.3 26.8 1.0 CG B:PHE295 4.3 24.3 1.0 CG C:PHE295 4.3 26.5 1.0 OG B:SER294 4.4 29.5 1.0 CE2 B:PHE295 4.5 25.3 1.0 CE2 C:PHE295 4.6 29.6 1.0 O C:ALA293 4.6 26.7 1.0 O B:PHE295 4.6 28.4 1.0 O C:PHE295 4.7 23.6 1.0 O B:ALA293 4.7 27.9 1.0 N C:SER294 4.8 22.9 1.0 C B:PHE295 4.9 29.7 1.0 N B:SER294 4.9 27.2 1.0 C C:PHE295 4.9 27.4 1.0

B.J.Medley, L.Leclaire, N.Thompson, K.E.Mahoney, B.Pluvinage, M.A.H.Parson, J.E.Burke, S.Malaker, W.Wakarchuk, A.B.Boraston. A Previously Uncharacterized O-Glycopeptidase From Akkermansia Muciniphila Requires the Tn-Antigen For Cleavage of the Peptide Bond. J.Biol.Chem. V. 298 02439 2022.
ISSN: ESSN 1083-351X
PubMed: 36049519
DOI: 10.1016/J.JBC.2022.102439