Calcium in PDB 6mvh: Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis

Enzymatic activity of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis

All present enzymatic activity of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis:
3.2.1.23;

Protein crystallography data

The structure of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis, PDB code: 6mvh was solved by S.J.Pellock, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.27 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.417, 137.407, 108.833, 90.00, 91.88, 90.00
R / Rfree (%) 20.9 / 26.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis (pdb code 6mvh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis, PDB code: 6mvh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6mvh

Go back to Calcium Binding Sites List in 6mvh
Calcium binding site 1 out of 4 in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:26.7
occ:1.00
 OD1 A:ASP43 2.3 22.4 1.0
O A:GLY44 2.3 24.8 1.0
OD2 A:ASP47 2.4 24.3 1.0
O A:ASP40 2.4 25.9 1.0
OD1 A:ASP521 2.5 25.4 1.0
OD2 A:ASP521 2.6 24.8 1.0
CG A:ASP521 2.9 27.1 1.0
CG A:ASP43 3.3 27.5 1.0
C A:ASP40 3.4 22.4 1.0
C A:GLY44 3.4 29.4 1.0
CG A:ASP47 3.5 24.9 1.0
N A:GLY44 3.7 24.3 1.0
OD2 A:ASP43 3.8 28.9 1.0
OD1 A:ASP47 4.0 33.2 1.0
CA A:ASP40 4.1 27.6 1.0
CA A:GLY44 4.1 26.8 1.0
C A:ASP43 4.2 23.5 1.0
N A:ASP47 4.2 24.7 1.0
N A:TYR48 4.2 23.0 1.0
N A:ASP43 4.4 24.4 1.0
CB A:ASP521 4.4 25.7 1.0
N A:GLY41 4.4 20.1 1.0
C A:ASP47 4.5 26.3 1.0
N A:GLY45 4.5 29.4 1.0
CB A:ASP40 4.5 25.5 1.0
CB A:ASP43 4.5 21.0 1.0
CA A:ASP43 4.6 28.8 1.0
CA A:GLY41 4.6 25.2 1.0
N A:ASN46 4.7 27.6 1.0
CA A:ASP47 4.7 26.8 1.0
CB A:ASP47 4.7 21.2 1.0
CA A:TYR48 4.7 27.1 1.0
CA A:GLY45 4.8 24.4 1.0
O A:ASP43 4.8 27.8 1.0
O A:ASP521 4.9 28.4 1.0
CB A:TYR48 4.9 24.4 1.0
N A:GLN42 4.9 23.4 1.0
O A:ASP47 5.0 25.0 1.0
C A:GLY45 5.0 28.4 1.0

Calcium binding site 2 out of 4 in 6mvh

Go back to Calcium Binding Sites List in 6mvh
Calcium binding site 2 out of 4 in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:23.8
occ:1.00
 O B:GLY44 2.3 24.3 1.0
OD2 B:ASP47 2.4 29.4 1.0
OD1 B:ASP43 2.4 23.8 1.0
OD1 B:ASP521 2.4 22.8 1.0
O B:ASP40 2.5 23.9 1.0
OD2 B:ASP521 2.5 24.1 1.0
O A:HOH935 2.6 30.0 1.0
CG B:ASP521 2.8 24.6 1.0
CG B:ASP47 3.4 31.9 1.0
C B:GLY44 3.4 23.1 1.0
C B:ASP40 3.5 22.8 1.0
CG B:ASP43 3.5 28.9 1.0
N B:GLY44 3.7 29.4 1.0
OD1 B:ASP47 3.9 30.4 1.0
OD2 B:ASP43 4.0 28.1 1.0
N B:TYR48 4.1 22.3 1.0
CA B:GLY44 4.1 25.3 1.0
N B:ASP47 4.1 27.4 1.0
CA B:ASP40 4.1 25.1 1.0
C B:ASP43 4.2 25.3 1.0
NZ A:LYS9 4.2 38.7 1.0
CB B:ASP521 4.3 23.5 1.0
O A:HOH948 4.3 34.5 1.0
N B:GLY41 4.4 23.2 1.0
N B:ASP43 4.4 24.0 1.0
C B:ASP47 4.5 26.0 1.0
N B:GLY45 4.5 28.3 1.0
CA B:GLY41 4.5 20.6 1.0
CB B:ASP47 4.6 22.2 1.0
CB B:ASP40 4.6 26.2 1.0
CA B:ASP43 4.6 24.5 1.0
CA B:ASP47 4.6 23.3 1.0
CA B:TYR48 4.6 23.8 1.0
CB B:ASP43 4.7 21.6 1.0
N B:ASN46 4.7 26.1 1.0
O B:ASP43 4.8 17.8 1.0
CB B:TYR48 4.8 21.2 1.0
CA B:GLY45 4.8 27.6 1.0
N B:GLN42 4.9 23.0 1.0
O B:ASP521 4.9 26.7 1.0
C B:GLY45 4.9 34.5 1.0
C B:GLY41 5.0 20.7 1.0

Calcium binding site 3 out of 4 in 6mvh

Go back to Calcium Binding Sites List in 6mvh
Calcium binding site 3 out of 4 in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca801

b:26.8
occ:1.00
 OD2 C:ASP47 2.3 31.3 1.0
OD1 C:ASP43 2.3 23.8 1.0
O C:GLY44 2.4 23.7 1.0
O C:ASP40 2.4 22.6 1.0
OD2 C:ASP521 2.4 25.4 1.0
OD1 C:ASP521 2.5 26.6 1.0
CG C:ASP521 2.8 26.3 1.0
CG C:ASP43 3.4 19.4 1.0
CG C:ASP47 3.4 29.2 1.0
C C:GLY44 3.5 29.4 1.0
N C:GLY44 3.5 27.6 1.0
C C:ASP40 3.5 25.2 1.0
OD1 C:ASP47 3.9 33.0 1.0
OD2 C:ASP43 3.9 29.7 1.0
C C:ASP43 4.0 25.7 1.0
CA C:GLY44 4.1 26.8 1.0
N C:ASP47 4.2 27.9 1.0
N C:ASP43 4.2 25.5 1.0
CA C:ASP40 4.2 24.8 1.0
CB C:ASP521 4.3 22.4 1.0
N C:TYR48 4.3 25.2 1.0
CA C:ASP43 4.4 23.4 1.0
CB C:ASP43 4.5 20.7 1.0
N C:GLY41 4.5 22.5 1.0
C C:ASP47 4.6 27.4 1.0
N C:GLY45 4.6 35.0 1.0
CB C:ASP47 4.6 27.6 1.0
O C:ASP43 4.6 24.4 1.0
N C:ASN46 4.7 25.5 1.0
CA C:ASP47 4.7 26.4 1.0
CA C:GLY41 4.7 22.8 1.0
CB C:ASP40 4.7 26.5 1.0
O C:ASP521 4.8 23.2 1.0
CA C:TYR48 4.8 24.6 1.0
N C:GLN42 4.9 21.0 1.0
CB C:TYR48 4.9 24.6 1.0
C C:GLY45 5.0 27.8 1.0
CA C:GLY45 5.0 28.0 1.0
C C:GLY41 5.0 26.5 1.0

Calcium binding site 4 out of 4 in 6mvh

Go back to Calcium Binding Sites List in 6mvh
Calcium binding site 4 out of 4 in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Roseburia Hominis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:33.3
occ:1.00
 OD1 D:ASP43 2.3 29.4 1.0
O D:ASP40 2.4 26.3 1.0
OD2 D:ASP47 2.4 30.7 1.0
O D:GLY44 2.5 36.8 1.0
OD1 D:ASP521 2.5 29.9 1.0
OD2 D:ASP521 2.7 31.5 1.0
CG D:ASP521 2.9 29.7 1.0
C D:ASP40 3.3 25.2 1.0
CG D:ASP43 3.4 30.8 1.0
CG D:ASP47 3.5 30.0 1.0
C D:GLY44 3.6 35.0 1.0
N D:GLY44 3.7 29.4 1.0
OD2 D:ASP43 3.8 30.5 1.0
CA D:ASP40 3.9 27.4 1.0
OD1 D:ASP47 4.0 38.2 1.0
CA D:GLY44 4.2 31.7 1.0
N D:ASP47 4.3 28.9 1.0
C D:ASP43 4.3 29.1 1.0
N D:TYR48 4.3 26.1 1.0
N D:GLY41 4.3 21.7 1.0
CB D:ASP40 4.4 27.1 1.0
N D:ASP43 4.4 29.8 1.0
CB D:ASP521 4.4 32.3 1.0
CA D:GLY41 4.5 25.5 1.0
CB D:ASP43 4.6 24.5 1.0
C D:ASP47 4.6 28.1 1.0
CA D:ASP43 4.6 30.7 1.0
N D:GLY45 4.7 39.7 1.0
N D:ASN46 4.7 31.7 1.0
CB D:ASP47 4.7 29.7 1.0
CA D:TYR48 4.7 28.8 1.0
CA D:ASP47 4.8 34.6 1.0
CB D:TYR48 4.8 26.6 1.0
N D:GLN42 4.9 28.0 1.0
O D:ASP43 5.0 28.6 1.0
O D:ASP521 5.0 32.3 1.0
C D:GLY41 5.0 28.6 1.0

Reference:

S.J.Pellock, W.G.Walton, S.M.Ervin, D.Torres-Rivera, B.C.Creekmore, G.Bergan, Z.D.Dunn, B.Li, A.Tripathy, M.R.Redinbo. Discovery and Characterization of Fmn-Binding Beta-Glucuronidases in the Human Gut Microbiome. J. Mol. Biol. V. 431 970 2019.
ISSN: ESSN 1089-8638
PubMed: 30658055
DOI: 10.1016/J.JMB.2019.01.013
Page generated: Sat Dec 12 07:13:51 2020

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