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

Protein crystallography data

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

Other elements in 8df2:

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

Sodium (Na) 12 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase, PDB code: 8df2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8df2

Go back to Calcium Binding Sites List in 8df2
Calcium binding site 1 out of 4 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca502

b:31.4
occ:1.00
 O A:SER344 2.3 30.8 1.0
O A:PRO340 2.3 30.6 1.0
OD1 A:ASP339 2.3 31.0 1.0
O A:GLY342 2.4 35.0 1.0
OD1 A:ASP347 2.5 32.9 1.0
O A:HOH674 2.8 29.7 1.0
CG A:ASP347 3.3 32.2 1.0
OD2 A:ASP347 3.3 35.6 1.0
CG A:ASP339 3.4 34.6 1.0
C A:SER344 3.5 33.0 1.0
C A:PRO340 3.5 31.7 1.0
C A:GLY342 3.6 39.6 1.0
OD2 A:ASP339 3.9 35.7 1.0
O A:HOH627 4.0 28.9 1.0
N A:SER344 4.0 33.0 1.0
C A:GLY343 4.1 34.7 1.0
N A:PRO340 4.1 29.1 1.0
N A:GLY342 4.1 34.5 1.0
O A:HOH636 4.2 31.5 1.0
C A:PRO341 4.2 32.5 1.0
C A:ASP339 4.3 32.8 1.0
CA A:SER344 4.3 34.7 1.0
CA A:PRO340 4.4 29.4 1.0
O A:GLY343 4.4 35.2 1.0
CD A:PRO340 4.4 30.7 1.0
N A:ASP345 4.4 30.5 1.0
N A:GLY343 4.4 37.5 1.0
CA A:GLY342 4.4 33.8 1.0
N A:PRO341 4.5 35.8 1.0
CA A:PRO341 4.5 33.0 1.0
CA A:ASP345 4.5 31.2 1.0
O A:PRO341 4.5 33.0 1.0
CB A:ASP339 4.5 30.7 1.0
CA A:GLY343 4.5 33.4 1.0
O A:HOH676 4.7 34.1 1.0
CA A:ASP339 4.7 31.0 1.0
O A:ASP339 4.7 33.6 1.0
CB A:ASP347 4.7 28.7 1.0
CB A:PRO340 4.8 34.4 1.0
N A:ASP347 4.9 30.9 1.0

Calcium binding site 2 out of 4 in 8df2

Go back to Calcium Binding Sites List in 8df2
Calcium binding site 2 out of 4 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca502

b:32.9
occ:1.00
 O B:PRO340 2.3 28.6 1.0
OD1 B:ASP347 2.3 31.2 1.0
OD1 B:ASP339 2.3 27.6 1.0
O B:SER344 2.3 32.6 1.0
O B:GLY342 2.5 28.0 1.0
O B:HOH672 2.7 27.5 1.0
CG B:ASP347 3.1 30.5 1.0
OD2 B:ASP347 3.2 27.7 1.0
CG B:ASP339 3.4 27.3 1.0
C B:PRO340 3.5 29.1 1.0
C B:SER344 3.5 31.4 1.0
C B:GLY342 3.6 30.3 1.0
OD2 B:ASP339 3.9 27.8 1.0
N B:PRO340 4.0 28.6 1.0
N B:SER344 4.1 28.0 1.0
C B:GLY343 4.1 29.9 1.0
CD B:PRO340 4.2 29.5 1.0
N B:GLY342 4.2 31.6 1.0
C B:PRO341 4.2 30.3 1.0
C B:ASP339 4.3 27.0 1.0
CA B:PRO340 4.3 29.3 1.0
O B:HOH603 4.3 28.7 1.0
CA B:SER344 4.4 30.8 1.0
O B:GLY343 4.4 33.5 1.0
N B:PRO341 4.5 24.9 1.0
N B:ASP345 4.5 30.1 1.0
CA B:ASP345 4.5 31.5 1.0
N B:GLY343 4.5 34.5 1.0
CB B:ASP339 4.5 26.9 1.0
CA B:GLY343 4.6 30.9 1.0
CA B:GLY342 4.6 29.3 1.0
CA B:PRO341 4.6 26.6 1.0
CB B:ASP347 4.6 27.3 1.0
O B:PRO341 4.6 26.6 1.0
CA B:ASP339 4.6 25.8 1.0
CB B:PRO340 4.7 27.2 1.0
O B:ASP339 4.7 29.1 1.0
O B:HOH677 4.8 34.7 1.0
N B:ASP347 4.8 27.7 1.0
CG B:PRO340 5.0 29.1 1.0

Calcium binding site 3 out of 4 in 8df2

Go back to Calcium Binding Sites List in 8df2
Calcium binding site 3 out of 4 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
C:Ca502

b:34.8
occ:1.00
 O C:PRO340 2.3 31.3 1.0
O C:SER344 2.3 34.0 1.0
O C:GLY342 2.3 34.3 1.0
OD1 C:ASP347 2.5 34.4 1.0
OD1 C:ASP339 2.5 34.6 1.0
O C:HOH663 2.7 32.2 1.0
CG C:ASP347 3.3 33.5 1.0
OD2 C:ASP347 3.3 36.0 1.0
C C:GLY342 3.5 36.2 1.0
C C:SER344 3.5 33.7 1.0
C C:PRO340 3.5 32.0 1.0
CG C:ASP339 3.6 34.0 1.0
N C:SER344 4.0 36.5 1.0
C C:GLY343 4.1 37.8 1.0
N C:GLY342 4.1 32.6 1.0
OD2 C:ASP339 4.1 34.8 1.0
N C:PRO340 4.1 29.8 1.0
C C:PRO341 4.1 32.3 1.0
O C:HOH605 4.1 32.0 1.0
CA C:SER344 4.3 36.9 1.0
CA C:PRO340 4.3 30.8 1.0
O C:GLY343 4.4 35.6 1.0
N C:GLY343 4.4 37.2 1.0
O C:PRO341 4.4 33.6 1.0
C C:ASP339 4.4 31.2 1.0
CA C:GLY342 4.4 31.1 1.0
CD C:PRO340 4.4 31.7 1.0
CA C:GLY343 4.5 33.4 1.0
N C:PRO341 4.5 30.3 1.0
N C:ASP345 4.5 31.9 1.0
CA C:PRO341 4.5 30.9 1.0
CA C:ASP345 4.6 31.9 1.0
CB C:ASP339 4.7 31.6 1.0
CB C:ASP347 4.7 27.2 1.0
CB C:PRO340 4.7 29.1 1.0
CA C:ASP339 4.8 31.8 1.0
O C:ASP339 4.9 28.7 1.0
N C:ASP347 5.0 29.9 1.0

Calcium binding site 4 out of 4 in 8df2

Go back to Calcium Binding Sites List in 8df2
Calcium binding site 4 out of 4 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
D:Ca502

b:36.2
occ:1.00
 O D:PRO340 2.2 33.1 1.0
OD1 D:ASP339 2.4 33.9 1.0
O D:SER344 2.4 35.3 1.0
O D:GLY342 2.5 37.1 1.0
OD1 D:ASP347 2.5 37.7 1.0
O D:HOH666 2.5 37.5 1.0
CG D:ASP347 3.3 37.3 1.0
CG D:ASP339 3.4 34.9 1.0
OD2 D:ASP347 3.4 38.9 1.0
C D:PRO340 3.4 34.4 1.0
C D:SER344 3.6 34.0 1.0
C D:GLY342 3.6 36.4 1.0
OD2 D:ASP339 4.0 32.7 1.0
N D:PRO340 4.0 34.0 1.0
N D:GLY342 4.1 38.7 1.0
N D:SER344 4.1 39.0 1.0
C D:PRO341 4.1 34.1 1.0
C D:GLY343 4.2 36.1 1.0
O D:HOH604 4.2 32.9 1.0
C D:ASP339 4.3 32.3 1.0
CD D:PRO340 4.3 34.5 1.0
CA D:PRO340 4.3 32.8 1.0
O D:HOH609 4.4 34.2 1.0
O D:PRO341 4.4 33.4 1.0
N D:PRO341 4.4 36.1 1.0
CA D:SER344 4.4 36.1 1.0
CA D:PRO341 4.4 35.0 1.0
CA D:GLY342 4.5 37.0 1.0
O D:GLY343 4.5 35.0 1.0
N D:ASP345 4.5 30.1 1.0
N D:GLY343 4.5 34.1 1.0
CB D:ASP339 4.6 31.0 1.0
CA D:ASP345 4.6 33.7 1.0
CA D:GLY343 4.6 35.8 1.0
CA D:ASP339 4.6 30.1 1.0
O D:HOH650 4.7 40.3 1.0
O D:ASP339 4.7 32.8 1.0
CB D:PRO340 4.8 34.3 1.0
CB D:ASP347 4.8 33.2 1.0
N D:ASP347 5.0 35.9 1.0

Reference:

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
Page generated: Fri Jul 19 07:56:03 2024

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