Calcium in PDB 6tr4: Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose

Protein crystallography data

The structure of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose, PDB code: 6tr4 was solved by C.D.Owen, H.Wu, E.Crost, A.Colvile, N.Juge, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.64 / 1.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.780, 74.060, 76.509, 82.47, 80.43, 70.41
R / Rfree (%) 14.1 / 16.1

Other elements in 6tr4:

The structure of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose (pdb code 6tr4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose, PDB code: 6tr4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6tr4

Go back to Calcium Binding Sites List in 6tr4
Calcium binding site 1 out of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:7.4
occ:1.00
 O A:ASN397 2.2 8.7 1.0
O A:ASN402 2.3 8.8 1.0
OE2 A:GLU499 2.3 9.9 1.0
O A:SER498 2.4 7.8 1.0
OD1 A:ASP400 2.4 9.6 1.0
O A:THR405 2.5 8.4 1.0
OG1 A:THR405 2.5 9.5 1.0
CD A:GLU499 3.4 9.2 1.0
C A:THR405 3.4 9.0 1.0
C A:ASN402 3.4 9.1 1.0
C A:ASN397 3.5 9.2 1.0
CG A:ASP400 3.5 9.6 1.0
C A:SER498 3.6 7.8 1.0
CB A:THR405 3.7 9.7 1.0
OD2 A:ASP400 3.9 9.8 1.0
CA A:THR405 3.9 9.7 1.0
N A:ASN402 4.0 9.4 1.0
N A:THR405 4.0 9.9 1.0
CA A:ASN402 4.1 9.3 1.0
CG A:GLU499 4.1 8.6 1.0
CA A:SER498 4.2 7.7 1.0
OE1 A:GLU499 4.2 10.0 1.0
CA A:ASN397 4.3 9.6 1.0
CB A:ASN402 4.3 9.7 1.0
N A:MET398 4.4 8.8 1.0
N A:TYR406 4.4 8.8 1.0
N A:ASP403 4.5 9.0 1.0
CB A:SER498 4.5 7.7 1.0
CA A:MET398 4.5 8.8 1.0
CB A:ASN397 4.6 9.9 1.0
N A:GLU499 4.7 7.8 1.0
N A:ASP400 4.7 9.7 1.0
CA A:ASP403 4.7 9.2 1.0
CB A:ASP400 4.8 10.0 1.0
N A:ASP401 4.8 9.8 1.0
C A:ASP403 4.8 9.4 1.0
C A:MET398 4.8 8.8 1.0
CA A:TYR406 4.8 8.8 1.0
CG2 A:THR405 4.9 10.0 1.0
CA A:GLU499 4.9 8.1 1.0

Calcium binding site 2 out of 6 in 6tr4

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Calcium binding site 2 out of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:8.3
occ:1.00
 O A:LYS174 2.2 9.8 1.0
O A:GLY158 2.3 7.6 1.0
O A:HOH1097 2.3 10.9 1.0
O A:SER156 2.3 7.2 1.0
OD1 A:ASP172 2.4 9.0 1.0
O A:HOH821 2.5 8.2 1.0
OD2 A:ASP172 2.5 10.4 1.0
CG A:ASP172 2.8 9.7 1.0
C A:SER156 3.3 7.5 1.0
C A:LYS174 3.5 10.7 1.0
C A:GLY158 3.5 7.4 1.0
CA A:SER156 3.9 7.8 1.0
O A:HOH947 3.9 14.5 1.0
N A:TYR176 4.2 8.2 1.0
N A:GLY158 4.2 7.0 1.0
C A:TYR157 4.3 7.1 1.0
CB A:ASP172 4.3 10.1 1.0
N A:ASP175 4.3 10.3 1.0
CA A:TYR159 4.4 8.0 1.0
CA A:ASP175 4.4 10.2 1.0
OE1 A:GLN215 4.4 7.9 1.0
N A:TYR157 4.4 7.1 1.0
N A:TYR159 4.4 7.5 1.0
CB A:SER156 4.4 8.1 1.0
N A:LYS174 4.4 10.7 1.0
N A:LYS160 4.4 9.4 1.0
CA A:LYS174 4.5 11.4 1.0
CA A:GLY158 4.5 7.1 1.0
O A:TYR157 4.6 7.6 1.0
CA A:TYR157 4.7 7.0 1.0
C A:ASP175 4.7 9.1 1.0
O A:HOH823 4.8 17.1 1.0
O A:PRO155 4.8 8.7 1.0
CB A:LYS174 4.9 13.0 1.0
O A:HOH1111 4.9 14.6 1.0
C A:TYR159 4.9 8.7 1.0
CB A:TYR176 5.0 7.2 1.0

Calcium binding site 3 out of 6 in 6tr4

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Calcium binding site 3 out of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca608

b:12.8
occ:1.00
 O A:GLY197 2.2 8.3 1.0
O A:LEU188 2.2 7.6 1.0
OE2 A:GLU230 2.3 8.1 1.0
O A:HOH1222 2.3 13.8 1.0
O A:HOH1062 2.4 20.0 1.0
O A:HOH1025 2.4 9.3 1.0
O A:HOH928 2.7 16.2 1.0
CD A:GLU230 3.3 7.8 1.0
C A:LEU188 3.4 7.2 1.0
C A:GLY197 3.5 7.8 1.0
OE1 A:GLU230 3.6 8.0 1.0
CA A:LEU188 4.0 6.8 1.0
CA A:GLY197 4.2 8.4 1.0
O A:ASN229 4.2 8.4 1.0
N A:HIS198 4.5 7.5 1.0
N A:GLY189 4.5 7.9 1.0
O A:HOH1050 4.5 23.6 1.0
O A:ASN190 4.6 8.9 1.0
CA A:HIS198 4.6 7.6 1.0
CG A:GLU230 4.6 7.3 1.0
O A:TYR193 4.6 7.4 1.0
CB A:LEU188 4.7 6.7 1.0
CB A:ASN229 4.8 8.2 1.0
CA A:GLY189 4.8 8.4 1.0
O A:ILE187 4.9 7.4 1.0
N A:ASN190 4.9 9.0 1.0
O A:HOH1173 4.9 35.4 1.0
C A:GLY189 4.9 8.9 1.0
C A:ASN229 5.0 7.9 1.0
C A:ASN190 5.0 9.2 1.0
OD1 A:ASN229 5.0 9.4 1.0

Calcium binding site 4 out of 6 in 6tr4

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Calcium binding site 4 out of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:8.5
occ:1.00
 O B:LYS174 2.2 9.8 1.0
O B:GLY158 2.3 7.5 1.0
O B:SER156 2.3 7.4 1.0
O B:HOH1201 2.4 10.2 1.0
OD1 B:ASP172 2.4 9.3 1.0
O B:HOH911 2.5 9.5 1.0
OD2 B:ASP172 2.5 10.5 1.0
CG B:ASP172 2.8 9.6 1.0
C B:SER156 3.3 7.3 1.0
C B:LYS174 3.5 10.7 1.0
C B:GLY158 3.5 7.4 1.0
CA B:SER156 3.9 7.8 1.0
O B:HOH986 4.0 14.1 1.0
N B:TYR176 4.2 8.4 1.0
N B:GLY158 4.2 6.9 1.0
C B:TYR157 4.3 7.0 1.0
CB B:ASP172 4.3 9.9 1.0
N B:ASP175 4.3 10.6 1.0
CA B:TYR159 4.4 8.1 1.0
CA B:ASP175 4.4 10.5 1.0
OE1 B:GLN215 4.4 8.0 1.0
N B:TYR159 4.4 7.6 1.0
N B:TYR157 4.4 7.2 1.0
N B:LYS174 4.4 10.8 1.0
CB B:SER156 4.4 7.9 1.0
CA B:LYS174 4.4 11.5 1.0
N B:LYS160 4.4 9.2 1.0
CA B:GLY158 4.5 7.1 1.0
O B:TYR157 4.6 7.1 1.0
C B:ASP175 4.7 9.5 1.0
CA B:TYR157 4.7 6.9 1.0
O B:HOH879 4.8 16.0 1.0
O B:PRO155 4.8 9.0 1.0
CB B:LYS174 4.8 12.9 1.0
O B:HOH1224 4.9 13.7 1.0
C B:TYR159 4.9 8.6 1.0
CB B:TYR176 5.0 7.4 1.0

Calcium binding site 5 out of 6 in 6tr4

Go back to Calcium Binding Sites List in 6tr4
Calcium binding site 5 out of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:7.2
occ:1.00
 O B:ASN397 2.3 8.4 1.0
OE2 B:GLU499 2.3 11.1 1.0
O B:ASN402 2.3 8.7 1.0
O B:SER498 2.4 7.6 1.0
OD1 B:ASP400 2.4 9.5 1.0
OG1 B:THR405 2.5 8.7 1.0
O B:THR405 2.5 7.8 1.0
CD B:GLU499 3.3 10.7 1.0
C B:THR405 3.4 8.5 1.0
C B:ASN402 3.5 9.3 1.0
CG B:ASP400 3.5 10.2 1.0
C B:ASN397 3.5 8.5 1.0
C B:SER498 3.6 7.7 1.0
CB B:THR405 3.7 8.9 1.0
OD2 B:ASP400 3.8 11.1 1.0
CA B:THR405 3.9 9.1 1.0
N B:ASN402 3.9 10.3 1.0
N B:THR405 4.0 9.3 1.0
CA B:ASN402 4.1 9.7 1.0
CG B:GLU499 4.1 9.7 1.0
OE1 B:GLU499 4.2 11.8 1.0
CA B:SER498 4.2 7.5 1.0
CA B:ASN397 4.3 9.0 1.0
CB B:ASN402 4.3 10.0 1.0
N B:MET398 4.4 8.6 1.0
CB B:SER498 4.5 7.7 1.0
N B:TYR406 4.5 8.2 1.0
N B:ASP403 4.5 9.1 1.0
CA B:MET398 4.5 8.4 1.0
CB B:ASN397 4.6 9.3 1.0
N B:ASP400 4.6 10.5 1.0
N B:GLU499 4.7 7.9 1.0
CA B:ASP403 4.7 9.3 1.0
CB B:ASP400 4.8 10.5 1.0
N B:ASP401 4.8 11.7 1.0
CG2 B:THR405 4.8 9.1 1.0
C B:MET398 4.8 8.8 1.0
CA B:TYR406 4.9 8.2 1.0
C B:ASP403 4.9 9.4 1.0
CA B:GLU499 4.9 8.5 1.0

Calcium binding site 6 out of 6 in 6tr4

Go back to Calcium Binding Sites List in 6tr4
Calcium binding site 6 out of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:14.7
occ:1.00
 O B:HOH1292 2.2 18.6 1.0
O B:LEU188 2.2 7.2 1.0
O B:GLY197 2.2 8.5 1.0
O B:HOH1171 2.2 28.3 1.0
OE2 B:GLU230 2.3 8.2 1.0
O B:HOH1137 2.4 9.9 1.0
O B:HOH1000 2.8 21.9 1.0
CD B:GLU230 3.3 8.0 1.0
C B:LEU188 3.4 7.2 1.0
C B:GLY197 3.4 8.2 1.0
OE1 B:GLU230 3.6 8.1 1.0
CA B:LEU188 4.0 6.8 1.0
CA B:GLY197 4.2 8.5 1.0
O B:ASN229 4.2 8.4 1.0
O B:HOH1199 4.3 25.0 1.0
N B:HIS198 4.4 7.8 1.0
N B:GLY189 4.5 7.6 1.0
O B:ASN190 4.5 9.4 1.0
O B:TYR193 4.6 7.3 1.0
CG B:GLU230 4.6 7.7 1.0
CA B:HIS198 4.6 7.7 1.0
CB B:LEU188 4.6 6.9 1.0
O B:HOH1443 4.7 23.1 1.0
CA B:GLY189 4.8 8.4 1.0
CB B:ASN229 4.8 8.1 1.0
O B:ILE187 4.8 7.2 1.0
N B:ASN190 4.8 9.1 1.0
C B:GLY189 4.8 9.0 1.0
C B:ASN190 4.9 9.4 1.0
C B:ASN229 5.0 8.0 1.0
OD1 B:ASN229 5.0 9.3 1.0

Reference:

H.Wu, O.Rebello, E.H.Crost, C.D.Owen, S.Walpole, C.Bennati-Granier, D.Ndeh, S.Monaco, T.Hicks, A.Colvile, P.A.Urbanowicz, M.A.Walsh, J.Angulo, D.I.R.Spencer, N.Juge. Fucosidases From the Human Gut Symbiont Ruminococcus Gnavus. Cell.Mol.Life Sci. 2020.
ISSN: ESSN 1420-9071
PubMed: 32333083
DOI: 10.1007/S00018-020-03514-X
Page generated: Sat Dec 12 07:44:52 2020

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