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Magnesium 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:

Chlorine (Cl) 4 atoms
Calcium (Ca) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose, PDB code: 6tr4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6tr4

Go back to Magnesium Binding Sites List in 6tr4
Magnesium binding site 1 out of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg603

b:8.8
occ:1.00
 O A:SER107 2.0 9.4 1.0
O A:HOH749 2.0 12.1 1.0
O A:HOH748 2.1 11.5 1.0
O A:THR110 2.1 8.9 1.0
O A:HOH781 2.1 11.8 1.0
OD2 A:ASP113 2.1 8.9 1.0
CG A:ASP113 3.1 8.7 1.0
C A:SER107 3.2 9.6 1.0
C A:THR110 3.3 9.3 1.0
OD1 A:ASP113 3.5 9.0 1.0
N A:SER107 3.8 9.3 1.0
CA A:GLU111 4.0 10.8 0.5
CA A:SER107 4.0 9.4 1.0
N A:GLU111 4.1 9.9 0.5
N A:GLU111 4.1 9.8 0.5
CA A:GLU111 4.1 10.6 0.5
O A:HOH1331 4.1 26.9 1.0
OE2 A:GLU111 4.2 15.7 0.5
N A:GLU108 4.2 10.0 0.5
N A:GLU108 4.2 9.9 0.5
N A:THR110 4.3 9.1 1.0
CB A:ASP113 4.4 8.0 1.0
OD1 A:ASP106 4.4 15.9 1.0
CA A:GLU108 4.4 10.6 0.5
CA A:GLU108 4.4 10.5 0.5
O A:HOH702 4.4 25.7 1.0
O A:HOH1069 4.4 21.4 1.0
CA A:THR110 4.4 9.1 1.0
CB A:SER107 4.4 9.1 1.0
CD A:GLU111 4.6 14.2 0.5
C A:GLU108 4.7 10.4 0.5
C A:GLU111 4.7 9.9 0.5
C A:GLU111 4.7 10.0 0.5
OE2 A:GLU108 4.7 15.7 0.5
C A:GLU108 4.8 10.5 0.5
C A:ASP106 4.8 9.8 1.0
CG2 A:THR110 4.8 8.8 1.0
OE1 A:GLU111 4.9 15.9 0.5

Magnesium binding site 2 out of 5 in 6tr4

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Magnesium binding site 2 out of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg604

b:8.8
occ:1.00
 O B:HOH1380 2.0 10.3 1.0
O A:HOH1319 2.0 10.0 1.0
O A:HOH920 2.1 7.6 1.0
O B:HOH1315 2.1 11.2 1.0
O A:HOH892 2.1 7.7 1.0
O A:HOH795 2.1 8.2 1.0
O A:HOH962 4.1 14.6 1.0
O B:HOH1200 4.1 15.2 1.0
O B:HOH1234 4.1 14.8 1.0
O A:HOH1084 4.2 12.7 1.0
O A:LYS37 4.2 7.2 1.0
OD1 A:ASP403 4.2 9.5 1.0
O A:HOH1364 4.2 13.9 1.0
OD2 A:ASP403 4.2 10.1 1.0
O A:HOH719 4.3 19.0 1.0
O A:HOH1000 4.3 26.0 1.0
NZ B:LYS391 4.3 12.7 1.0
OE1 A:GLU434 4.4 8.2 1.0
O A:HOH861 4.5 13.2 1.0
CE A:LYS37 4.6 7.7 1.0
OE2 A:GLU39 4.6 8.8 1.0
CG A:ASP403 4.7 9.3 1.0

Magnesium binding site 3 out of 5 in 6tr4

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Magnesium binding site 3 out of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg605

b:16.4
occ:1.00
 O A:PHE75 2.1 12.1 1.0
OD1 A:ASP74 2.1 19.2 1.0
OE1 A:GLU131 2.1 11.9 1.0
O A:HOH766 2.1 15.7 1.0
O A:HOH1141 2.1 19.3 1.0
O A:HOH1113 2.2 22.8 1.0
CG A:ASP74 3.1 18.2 1.0
CD A:GLU131 3.3 10.7 1.0
C A:PHE75 3.3 11.5 1.0
OD2 A:ASP74 3.6 21.5 1.0
N A:PHE75 3.9 12.2 1.0
CA A:PHE75 4.0 11.3 1.0
CG A:GLU131 4.1 10.1 1.0
OE2 A:GLU131 4.1 11.7 1.0
O A:HOH1112 4.2 25.0 1.0
C A:ASP74 4.2 13.8 1.0
OE1 A:GLU78 4.3 15.5 0.5
OE1 A:GLU78 4.3 13.7 0.5
N A:ASP76 4.3 11.3 1.0
CB A:GLU131 4.3 9.2 1.0
CB A:PHE75 4.3 10.5 1.0
CB A:ASP74 4.4 16.7 1.0
N A:ALA77 4.5 10.8 1.0
O A:HOH828 4.5 12.5 1.0
CA A:ASP76 4.6 11.9 1.0
OH A:TYR119 4.6 10.8 1.0
O A:ASP74 4.7 14.4 1.0
CA A:ASP74 4.7 15.2 1.0
CB A:ASN121 4.8 21.9 1.0
O A:HOH1351 4.8 21.8 1.0
ND2 A:ASN121 4.9 22.4 1.0
OE2 A:GLU78 5.0 14.9 0.5

Magnesium binding site 4 out of 5 in 6tr4

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Magnesium binding site 4 out of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg702

b:8.5
occ:1.00
 O B:SER107 2.0 8.6 1.0
O B:HOH832 2.1 13.1 1.0
O B:HOH820 2.1 12.2 1.0
O B:HOH980 2.1 10.7 1.0
OD2 B:ASP113 2.1 8.6 1.0
O B:THR110 2.1 8.8 1.0
CG B:ASP113 3.1 8.5 1.0
C B:SER107 3.2 8.9 1.0
C B:THR110 3.3 9.0 1.0
OD1 B:ASP113 3.5 8.9 1.0
N B:SER107 3.8 8.7 1.0
CA B:SER107 4.0 8.6 1.0
CA B:GLU111 4.0 11.1 1.0
N B:GLU111 4.1 9.8 1.0
O B:HOH813 4.1 31.7 1.0
OE2 B:GLU111 4.1 27.0 1.0
O B:HOH1462 4.2 36.5 1.0
N B:GLU108 4.2 9.2 0.5
N B:GLU108 4.2 9.4 0.5
OD1 B:ASP106 4.3 15.9 1.0
N B:THR110 4.3 8.9 1.0
CB B:ASP113 4.3 8.0 1.0
CB B:SER107 4.4 8.5 1.0
O B:HOH804 4.4 22.5 1.0
CA B:GLU108 4.4 9.9 0.5
CA B:THR110 4.5 8.7 1.0
O B:HOH1180 4.5 22.0 1.0
CA B:GLU108 4.5 10.2 0.5
CD B:GLU111 4.6 21.3 1.0
C B:GLU111 4.7 10.1 1.0
C B:GLU108 4.7 9.6 0.5
C B:ASP106 4.8 9.1 1.0
CG2 B:THR110 4.9 8.3 1.0
OE1 B:GLU111 4.9 28.0 1.0
C B:GLU108 4.9 9.9 0.5

Magnesium binding site 5 out of 5 in 6tr4

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Magnesium binding site 5 out of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg703

b:12.3
occ:1.00
 OD1 B:ASP74 2.0 14.8 1.0
O B:PHE75 2.0 11.1 1.0
OE1 B:GLU131 2.1 11.1 1.0
O B:HOH1168 2.1 16.9 1.0
O B:HOH1184 2.1 16.4 1.0
O B:HOH1099 2.2 13.7 1.0
CG B:ASP74 3.0 15.3 1.0
CD B:GLU131 3.2 9.9 1.0
C B:PHE75 3.3 10.5 1.0
OD2 B:ASP74 3.5 16.8 1.0
N B:PHE75 3.8 11.0 1.0
CA B:PHE75 4.0 10.4 1.0
OE2 B:GLU131 4.1 10.7 1.0
CG B:GLU131 4.1 9.2 1.0
C B:ASP74 4.1 12.2 1.0
O B:HOH1228 4.1 22.6 1.0
CB B:ASP74 4.2 14.2 1.0
O B:HOH1410 4.3 33.5 1.0
N B:ASP76 4.3 10.7 1.0
OE1 B:GLU78 4.3 17.9 1.0
CB B:PHE75 4.3 9.9 1.0
CB B:GLU131 4.4 8.5 1.0
O B:HOH824 4.5 12.0 1.0
N B:ALA77 4.5 10.6 1.0
OH B:TYR119 4.5 10.0 1.0
CA B:ASP76 4.5 11.4 1.0
O B:ASP74 4.6 12.4 1.0
CA B:ASP74 4.6 13.3 1.0
CB B:ASN121 4.7 17.7 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: Tue Oct 1 19:05:46 2024

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