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Calcium in PDB 5mqr: Sialidase BT_1020

Enzymatic activity of Sialidase BT_1020

All present enzymatic activity of Sialidase BT_1020:
3.2.1.187;

Protein crystallography data

The structure of Sialidase BT_1020, PDB code: 5mqr was solved by A.Basle, D.Ndeh, A.Rogowski, A.Cartmell, A.S.Luis, I.Venditto, A.Labourel, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.25 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 125.720, 316.998, 90.023, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.5

Other elements in 5mqr:

The structure of Sialidase BT_1020 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Sialidase BT_1020 (pdb code 5mqr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Sialidase BT_1020, PDB code: 5mqr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5mqr

Go back to Calcium Binding Sites List in 5mqr
Calcium binding site 1 out of 2 in the Sialidase BT_1020


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sialidase BT_1020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1201

b:30.4
occ:1.00
O A:HOH1350 3.1 23.0 1.0
O A:HOH1474 3.1 16.4 1.0
N A:GLY155 3.3 25.2 1.0
NE2 A:GLN377 3.4 25.8 1.0
N A:PHE156 3.4 24.6 1.0
NH2 A:ARG374 3.5 27.9 1.0
O A:PHE156 3.8 25.2 1.0
CB A:PHE156 3.9 24.1 1.0
CG2 A:VAL154 3.9 26.7 1.0
CA A:GLY155 4.0 25.4 1.0
CA A:PHE156 4.1 24.8 1.0
C A:GLY155 4.1 25.3 1.0
SE A:MSE80 4.2 28.1 1.0
CB A:MSE80 4.2 25.2 1.0
CD2 A:PHE156 4.2 23.3 1.0
CA A:VAL154 4.3 26.2 1.0
C A:VAL154 4.3 26.1 1.0
NE A:ARG374 4.3 27.1 1.0
CD A:GLN377 4.3 25.9 1.0
CZ A:ARG374 4.4 27.9 1.0
CG A:GLN377 4.4 25.6 1.0
O A:LEU81 4.4 25.0 1.0
C A:PHE156 4.5 25.2 1.0
ND2 A:ASN380 4.5 26.1 1.0
CG A:PHE156 4.6 23.8 1.0
CG A:MSE80 4.7 26.2 1.0
CB A:VAL154 4.7 26.6 1.0
N A:LEU81 4.8 24.6 1.0

Calcium binding site 2 out of 2 in 5mqr

Go back to Calcium Binding Sites List in 5mqr
Calcium binding site 2 out of 2 in the Sialidase BT_1020


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sialidase BT_1020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1209

b:28.7
occ:1.00
O A:ASP455 2.4 26.6 1.0
O A:ASP458 2.4 25.9 1.0
O A:HOH1583 2.4 21.7 1.0
OD1 A:ASP453 2.4 26.8 1.0
O A:HOH2008 2.5 24.6 1.0
OD2 A:ASP453 2.6 26.8 1.0
OE1 A:GLU598 2.7 36.3 1.0
CG A:ASP453 2.9 27.0 1.0
C A:ASP455 3.5 26.8 1.0
C A:ASP458 3.6 25.1 1.0
CD A:GLU598 3.7 39.2 1.0
O A:HOH1808 4.1 24.8 1.0
OE2 A:GLU598 4.1 42.0 1.0
N A:ASP455 4.3 27.6 1.0
N A:ASP458 4.3 26.3 1.0
CA A:TYR459 4.3 24.0 1.0
CA A:ASP455 4.3 27.2 1.0
CB A:ASP453 4.4 27.5 1.0
O A:THR572 4.4 26.4 1.0
N A:TYR459 4.4 24.1 1.0
O A:HOH1554 4.4 44.5 1.0
N A:PRO456 4.5 27.1 1.0
O A:HOH2090 4.5 38.5 1.0
CB A:TYR459 4.5 23.8 1.0
CA A:PRO456 4.5 27.1 1.0
CB A:ASP455 4.5 27.0 1.0
C A:PRO456 4.6 26.6 1.0
CA A:ASP458 4.6 25.6 1.0
O A:HOH1774 4.7 24.9 1.0
N A:PHE457 4.9 26.4 1.0
O A:PRO456 5.0 25.7 1.0
CG A:GLU598 5.0 38.0 1.0

Reference:

D.Ndeh, A.Rogowski, A.Cartmell, A.S.Luis, A.Basle, J.Gray, I.Venditto, J.Briggs, X.Zhang, A.Labourel, N.Terrapon, F.Buffetto, S.Nepogodiev, Y.Xiao, R.A.Field, Y.Zhu, M.A.O'neill, B.R.Urbanowicz, W.S.York, G.J.Davies, D.W.Abbott, M.C.Ralet, E.C.Martens, B.Henrissat, H.J.Gilbert. Complex Pectin Metabolism By Gut Bacteria Reveals Novel Catalytic Functions. Nature V. 544 65 2017.
ISSN: ISSN 0028-0836
PubMed: 28329766
DOI: 10.1038/NATURE21725
Page generated: Sat Dec 12 05:38:41 2020

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