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Calcium in PDB 5msx: Glycoside Hydrolase BT_3662

Protein crystallography data

The structure of Glycoside Hydrolase BT_3662, PDB code: 5msx 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) 49.44 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.827, 129.181, 158.080, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Glycoside Hydrolase BT_3662 (pdb code 5msx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Glycoside Hydrolase BT_3662, PDB code: 5msx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5msx

Go back to Calcium Binding Sites List in 5msx
Calcium binding site 1 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Glycoside Hydrolase BT_3662 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:14.4
occ:1.00
O A:HOH633 2.4 16.8 1.0
O A:HOH655 2.4 13.6 1.0
O A:HOH625 2.4 13.5 1.0
O A:HOH618 2.5 14.6 1.0
O A:HOH608 2.5 13.5 1.0
O A:HOH670 2.5 9.7 1.0
NE2 A:HIS261 2.6 16.8 1.0
CE1 A:HIS261 3.6 15.8 1.0
CD2 A:HIS261 3.6 16.5 1.0
OG A:SER39 4.0 17.6 1.0
O A:ALA156 4.1 17.2 1.0
O A:GLY262 4.2 16.5 1.0
O A:PRO95 4.3 17.2 1.0
O A:PRO203 4.3 16.6 1.0
O A:HOH637 4.5 28.5 1.0
O A:ASP37 4.5 15.8 1.0
OE1 A:GLU157 4.6 24.3 1.0
O A:ALA94 4.7 15.2 1.0
ND1 A:HIS261 4.7 16.6 1.0
CG A:HIS261 4.8 16.1 1.0
CB A:ALA94 4.9 16.7 1.0
O A:ASP155 4.9 17.3 1.0
CA A:GLY202 5.0 17.5 1.0

Calcium binding site 2 out of 6 in 5msx

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Calcium binding site 2 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Glycoside Hydrolase BT_3662 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:25.6
occ:1.00
O A:PHE358 2.3 23.3 1.0
O A:SER366 2.4 17.5 1.0
OG A:SER366 2.4 16.7 1.0
O A:TRP455 2.5 18.6 1.0
O A:ALA363 2.5 21.1 1.0
OD1 A:ASP361 2.6 20.3 1.0
OE2 A:GLU456 2.6 38.3 1.0
C A:SER366 3.2 17.2 1.0
C A:PHE358 3.5 22.6 1.0
C A:ALA363 3.6 19.9 1.0
CB A:SER366 3.6 16.4 1.0
CG A:ASP361 3.6 21.8 1.0
C A:TRP455 3.6 18.9 1.0
CD A:GLU456 3.8 34.0 1.0
CA A:SER366 3.8 17.4 1.0
OD2 A:ASP361 3.9 22.5 1.0
N A:SER366 4.0 16.3 1.0
N A:ALA363 4.0 22.1 1.0
N A:ARG367 4.2 17.4 1.0
CA A:PHE358 4.2 21.9 1.0
CA A:ALA363 4.2 21.0 1.0
CG A:GLU456 4.3 30.9 1.0
CA A:TRP455 4.4 17.6 1.0
CB A:PHE358 4.5 21.6 1.0
CB A:ALA363 4.5 21.7 1.0
N A:ALA359 4.5 22.7 1.0
CA A:ARG367 4.6 18.0 1.0
N A:ASN364 4.7 18.3 1.0
N A:ASP361 4.7 22.0 1.0
N A:GLU456 4.7 20.5 1.0
CA A:ALA359 4.7 23.3 1.0
C A:ALA359 4.7 24.1 1.0
OE1 A:GLU456 4.8 38.2 1.0
CA A:GLU456 4.9 21.7 1.0
CA A:ASN364 4.9 18.1 1.0
CB A:ASP361 5.0 21.3 1.0
N A:VAL360 5.0 23.6 1.0

Calcium binding site 3 out of 6 in 5msx

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Calcium binding site 3 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Glycoside Hydrolase BT_3662 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:16.6
occ:1.00
O B:HOH654 2.4 17.6 1.0
O B:HOH619 2.4 18.7 1.0
O B:HOH648 2.4 15.4 1.0
O B:HOH664 2.5 16.5 1.0
O B:HOH608 2.5 13.2 1.0
NE2 B:HIS261 2.6 16.0 1.0
O B:HOH623 2.6 13.9 1.0
CE1 B:HIS261 3.5 16.6 1.0
CD2 B:HIS261 3.6 16.1 1.0
O B:ALA156 4.0 17.2 1.0
O B:GLY262 4.1 18.9 1.0
OG B:SER39 4.2 19.4 1.0
O B:PRO203 4.3 15.7 1.0
O B:PRO95 4.4 14.7 1.0
OE2 B:GLU157 4.5 25.8 1.0
O B:ASP37 4.6 19.0 1.0
ND1 B:HIS261 4.7 16.5 1.0
CG B:HIS261 4.7 16.4 1.0
O B:ALA94 4.8 16.4 1.0
O B:ASP155 4.9 16.6 1.0
CB B:ALA94 5.0 15.0 1.0
CA B:GLY202 5.0 16.2 1.0

Calcium binding site 4 out of 6 in 5msx

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Calcium binding site 4 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Glycoside Hydrolase BT_3662 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:33.2
occ:1.00
O B:ALA363 2.3 21.3 1.0
O B:PHE358 2.4 29.9 1.0
O B:TRP455 2.4 29.2 1.0
OG B:SER366 2.5 22.4 1.0
O B:SER366 2.5 23.8 1.0
OD1 B:ASP361 2.5 31.0 1.0
OE2 B:GLU456 2.6 45.6 1.0
C B:SER366 3.3 22.3 1.0
C B:ALA363 3.5 22.6 1.0
CG B:ASP361 3.5 31.2 1.0
C B:PHE358 3.6 31.0 1.0
C B:TRP455 3.6 29.2 1.0
CB B:SER366 3.7 22.0 1.0
CD B:GLU456 3.7 41.9 1.0
CA B:SER366 3.8 21.8 1.0
OD2 B:ASP361 3.8 29.9 1.0
N B:ALA363 3.9 24.8 1.0
N B:SER366 4.0 20.7 1.0
CA B:ALA363 4.1 24.1 1.0
CG B:GLU456 4.2 39.4 1.0
N B:ARG367 4.3 22.6 1.0
CA B:PHE358 4.3 30.9 1.0
CB B:ALA363 4.4 23.7 1.0
CA B:TRP455 4.4 26.7 1.0
N B:ASN364 4.5 21.3 1.0
N B:ASP361 4.6 30.9 1.0
N B:ALA359 4.6 32.0 1.0
CB B:PHE358 4.6 30.1 1.0
N B:GLU456 4.6 29.9 1.0
CA B:ARG367 4.7 24.0 1.0
OE1 B:GLU456 4.7 44.5 1.0
C B:ALA359 4.8 31.8 1.0
CA B:ALA359 4.8 32.4 1.0
CA B:ASN364 4.8 21.1 1.0
CA B:GLU456 4.8 31.6 1.0
CB B:ASP361 4.9 30.8 1.0
N B:GLY362 4.9 27.9 1.0

Calcium binding site 5 out of 6 in 5msx

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Calcium binding site 5 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Glycoside Hydrolase BT_3662 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:14.0
occ:1.00
O C:HOH691 2.3 11.7 1.0
O C:HOH670 2.3 15.7 1.0
O C:HOH673 2.3 15.9 1.0
O C:HOH638 2.4 11.4 1.0
O C:HOH649 2.5 13.1 1.0
O C:HOH647 2.6 13.6 1.0
NE2 C:HIS261 2.7 15.9 1.0
CD2 C:HIS261 3.6 15.7 1.0
CE1 C:HIS261 3.7 15.7 1.0
O C:ALA156 4.1 16.6 1.0
OG C:SER39 4.2 16.7 1.0
O C:GLY262 4.2 15.4 1.0
O C:PRO203 4.3 12.4 1.0
O C:PRO95 4.4 16.6 1.0
OE1 C:GLU157 4.6 17.0 1.0
O C:ASP37 4.6 17.5 1.0
O C:ALA94 4.7 17.7 1.0
ND1 C:HIS261 4.8 15.6 1.0
CG C:HIS261 4.8 15.6 1.0
O C:ASP155 4.9 16.1 1.0
CA C:GLY202 4.9 15.8 1.0
C C:ASP155 5.0 17.2 1.0

Calcium binding site 6 out of 6 in 5msx

Go back to Calcium Binding Sites List in 5msx
Calcium binding site 6 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Glycoside Hydrolase BT_3662 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:34.8
occ:1.00
O C:PHE358 2.3 21.1 1.0
O C:TRP455 2.4 21.7 1.0
O C:SER366 2.4 19.5 1.0
OD1 C:ASP361 2.4 25.8 1.0
O C:ALA363 2.4 22.1 1.0
OE2 C:GLU456 2.6 41.6 1.0
OG C:SER366 2.6 21.1 1.0
C C:SER366 3.2 20.9 1.0
CG C:ASP361 3.5 26.6 1.0
C C:PHE358 3.5 24.9 1.0
C C:ALA363 3.6 21.2 1.0
C C:TRP455 3.6 23.6 1.0
CB C:SER366 3.7 20.8 1.0
CD C:GLU456 3.7 41.3 1.0
OD2 C:ASP361 3.8 28.8 1.0
CA C:SER366 3.8 19.9 1.0
N C:SER366 4.0 18.6 1.0
N C:ALA363 4.1 23.7 1.0
N C:ARG367 4.2 20.5 1.0
CG C:GLU456 4.2 36.4 1.0
CA C:PHE358 4.3 26.3 1.0
CA C:ALA363 4.3 22.1 1.0
CA C:TRP455 4.4 22.6 1.0
N C:ALA359 4.5 24.9 1.0
CB C:ALA363 4.5 22.7 1.0
CB C:PHE358 4.5 24.2 1.0
CA C:ARG367 4.6 21.4 1.0
N C:GLU456 4.6 26.3 1.0
N C:ASN364 4.6 19.9 1.0
C C:ALA359 4.7 24.0 1.0
N C:ASP361 4.7 25.6 1.0
CA C:ALA359 4.7 24.1 1.0
OE1 C:GLU456 4.7 45.2 1.0
CA C:GLU456 4.8 28.4 1.0
CB C:ASP361 4.8 24.2 1.0
CA C:ASN364 4.9 18.9 1.0
N C:GLY362 4.9 24.7 1.0
O C:ALA359 4.9 24.4 1.0
N C:VAL360 5.0 24.9 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: Mon Jul 15 08:36:30 2024

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