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Calcium in PDB 8xvp: Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121

Enzymatic activity of Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121

All present enzymatic activity of Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121:
2.4.1.9;

Protein crystallography data

The structure of Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121, PDB code: 8xvp was solved by D.Ni, X.Hou, M.Cheng, W.Xu, Y.Rao, W.Mu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.42 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.91, 98.69, 139.49, 90, 90, 90
R / Rfree (%) 20 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 (pdb code 8xvp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121, PDB code: 8xvp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8xvp

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Calcium binding site 1 out of 6 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121


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 Inulosucrase From Lactobacillus Reuteri 121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:24.3
occ:1.00
 O A:TRP486 2.3 24.9 1.0
OD1 A:ASN488 2.3 24.6 1.0
OD1 A:ASP418 2.3 26.4 1.0
OE1 A:GLN449 2.3 25.3 1.0
O A:HOH951 2.3 28.3 1.0
OD1 A:ASP520 2.5 22.4 1.0
OD2 A:ASP520 2.6 23.8 1.0
CG A:ASP520 2.9 21.9 1.0
CG A:ASN488 3.4 22.6 1.0
CG A:ASP418 3.4 28.1 1.0
C A:TRP486 3.5 23.6 1.0
CD A:GLN449 3.5 27.5 1.0
OD2 A:ASP418 3.9 29.0 1.0
N A:ASN488 3.9 20.6 1.0
ND2 A:ASN488 4.2 25.1 1.0
NE2 A:GLN449 4.3 26.7 1.0
CB A:ASP520 4.3 22.1 1.0
CA A:TRP486 4.4 25.4 1.0
O A:ASN419 4.4 26.0 1.0
C A:ALA487 4.4 21.3 1.0
OG A:SER442 4.4 24.4 1.0
N A:ASN419 4.4 26.3 1.0
N A:ALA487 4.4 23.2 1.0
CA A:ALA487 4.4 22.3 1.0
CB A:GLN449 4.4 26.8 1.0
CB A:ASN488 4.5 22.3 1.0
O A:HOH904 4.5 27.4 1.0
CG A:GLN449 4.6 26.3 1.0
CB A:TRP486 4.6 27.7 1.0
CA A:ASN488 4.6 22.4 1.0
CB A:SER442 4.7 23.4 1.0
CB A:ASP418 4.7 27.1 1.0
CA A:ASP418 4.8 27.7 1.0
NE2 A:GLN405 4.8 24.3 1.0
C A:ASN488 5.0 23.0 1.0

Calcium binding site 2 out of 6 in 8xvp

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Calcium binding site 2 out of 6 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121


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 Inulosucrase From Lactobacillus Reuteri 121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:29.8
occ:1.00
 O A:ILE661 2.3 30.5 1.0
OD1 A:ASN317 2.3 34.2 1.0
OG A:SER666 2.3 38.3 1.0
O A:HOH928 2.3 32.5 1.0
OD1 A:ASP659 2.3 32.2 1.0
O A:HOH960 2.3 29.7 1.0
OD2 A:ASP659 2.4 34.8 1.0
CG A:ASP659 2.7 33.1 1.0
C A:ILE661 3.4 31.4 1.0
CB A:SER666 3.4 38.0 1.0
CG A:ASN317 3.5 38.6 1.0
CB A:ILE661 3.9 33.9 1.0
CA A:ILE661 4.0 31.4 1.0
N A:ILE661 4.1 33.2 1.0
ND2 A:ASN317 4.1 35.8 1.0
O A:GLY315 4.2 31.6 1.0
CB A:ASP659 4.2 33.0 1.0
OD1 A:ASP663 4.4 29.4 1.0
OD2 A:ASP663 4.5 33.3 1.0
N A:TRP662 4.5 29.7 1.0
CA A:SER666 4.5 39.1 1.0
CG2 A:ILE661 4.5 32.5 1.0
O A:HOH962 4.6 28.8 1.0
O A:HOH1011 4.6 31.6 1.0
CG A:ASP663 4.6 31.9 1.0
CA A:TRP662 4.6 31.3 1.0
CB A:ASN317 4.6 37.1 1.0
N A:ASP663 4.8 32.2 1.0
C A:GLY315 4.8 30.9 1.0
O A:ASP316 4.8 35.7 1.0
CA A:ASN317 4.9 37.0 1.0
OG A:SER665 4.9 41.5 1.0
C A:TRP662 5.0 29.9 1.0
CA A:ASP659 5.0 29.9 1.0

Calcium binding site 3 out of 6 in 8xvp

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Calcium binding site 3 out of 6 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121


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 Inulosucrase From Lactobacillus Reuteri 121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:30.8
occ:1.00
 N A:TYR331 3.2 36.1 1.0
O A:HOH1077 3.4 34.4 1.0
CA A:GLY330 3.8 33.9 1.0
C A:GLY330 4.0 37.5 1.0
CB A:TYR331 4.1 32.0 1.0
CA A:TYR331 4.1 33.5 1.0
CD2 A:TYR331 4.1 33.7 1.0
O A:TYR331 4.2 32.8 1.0
C A:TYR331 4.4 33.4 1.0
CG A:TYR331 4.6 32.6 1.0

Calcium binding site 4 out of 6 in 8xvp

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Calcium binding site 4 out of 6 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121


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 Inulosucrase From Lactobacillus Reuteri 121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:29.2
occ:1.00
 OD1 B:ASN317 2.3 34.0 1.0
O B:HOH1036 2.3 26.1 1.0
O B:HOH947 2.3 28.5 1.0
OG B:SER666 2.3 34.3 1.0
OD2 B:ASP659 2.4 30.8 1.0
O B:ILE661 2.4 31.1 1.0
OD1 B:ASP659 2.4 25.8 1.0
CG B:ASP659 2.7 28.7 1.0
CG B:ASN317 3.4 35.6 1.0
CB B:SER666 3.5 36.9 1.0
C B:ILE661 3.5 29.6 1.0
CB B:ILE661 4.0 33.8 1.0
O B:GLY315 4.1 31.7 1.0
ND2 B:ASN317 4.1 36.4 1.0
CA B:ILE661 4.1 31.2 1.0
N B:ILE661 4.2 30.9 1.0
CB B:ASP659 4.2 29.0 1.0
OD1 B:ASP663 4.5 32.0 1.0
CG2 B:ILE661 4.5 32.0 1.0
O B:HOH934 4.5 26.4 1.0
CA B:SER666 4.5 39.0 1.0
OD2 B:ASP663 4.5 33.8 1.0
N B:TRP662 4.6 28.8 1.0
CB B:ASN317 4.6 35.1 1.0
O B:HOH1028 4.7 30.9 1.0
O B:ASP316 4.7 29.0 1.0
CG B:ASP663 4.7 33.2 1.0
C B:GLY315 4.7 31.8 1.0
CA B:TRP662 4.8 35.2 1.0
CA B:ASN317 4.8 32.1 1.0
N B:ASP663 4.9 33.3 1.0
CA B:ASP659 5.0 27.3 1.0

Calcium binding site 5 out of 6 in 8xvp

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Calcium binding site 5 out of 6 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:37.6
occ:1.00
 OD1 B:ASN488 2.3 39.0 1.0
OD1 B:ASP418 2.3 40.5 1.0
O B:HOH963 2.3 35.5 1.0
OE1 B:GLN449 2.3 46.3 1.0
O B:TRP486 2.3 41.7 1.0
OD1 B:ASP520 2.4 33.0 1.0
OD2 B:ASP520 2.6 32.8 1.0
CG B:ASP520 2.8 31.6 1.0
CG B:ASN488 3.4 37.8 1.0
CG B:ASP418 3.4 36.0 1.0
CD B:GLN449 3.5 43.2 1.0
C B:TRP486 3.6 38.2 1.0
OD2 B:ASP418 3.8 37.4 1.0
N B:ASN488 4.0 37.7 1.0
ND2 B:ASN488 4.0 41.1 1.0
O B:ASN419 4.3 46.2 1.0
NE2 B:GLN449 4.3 42.7 1.0
CB B:ASP520 4.3 29.2 1.0
OG B:SER442 4.3 35.3 1.0
CA B:TRP486 4.5 41.0 1.0
N B:ASN419 4.5 36.3 1.0
CB B:ASN488 4.5 37.6 1.0
CB B:GLN449 4.5 43.6 1.0
C B:ALA487 4.5 40.2 1.0
N B:ALA487 4.5 38.4 1.0
CA B:ALA487 4.5 36.4 1.0
CB B:SER442 4.6 37.3 1.0
CG B:GLN449 4.6 42.4 1.0
O B:HOH905 4.6 36.2 1.0
CA B:ASN488 4.7 35.4 1.0
CB B:TRP486 4.7 43.3 1.0
CB B:ASP418 4.7 36.3 1.0
OE1 B:GLN405 4.7 39.4 1.0
NE2 B:GLN405 4.7 41.9 1.0
CA B:ASP418 4.9 34.2 1.0

Calcium binding site 6 out of 6 in 8xvp

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Calcium binding site 6 out of 6 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:35.7
occ:1.00
 N B:ILE395 3.3 30.6 1.0
CG1 B:ILE395 3.7 33.9 1.0
CA B:HIS394 3.9 30.6 1.0
CB B:HIS394 3.9 30.8 1.0
CB B:ILE395 3.9 32.3 1.0
C B:HIS394 4.1 31.3 1.0
CA B:ILE395 4.2 30.8 1.0
O B:ILE395 4.6 30.0 1.0
CD1 B:ILE395 4.7 35.8 1.0
C B:ILE395 4.9 29.5 1.0

Reference:

D.Ni, X.Hou, M.Cheng, W.Xu, Y.Rao, W.Mu. Structure-Guided Tunnel Engineering to Reveal the Molecular Basis of Sugar Chain Extension of Inulosucrase To Be Published.
Page generated: Sat Feb 8 16:11:43 2025

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