Atomistry » Calcium » PDB 6mrl-6n7k » 6mvh
Atomistry »
  Calcium »
    PDB 6mrl-6n7k »
      6mvh »

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: Tue Jul 16 11:28:56 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy