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Calcium in PDB 8xvr: Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W

Protein crystallography data

The structure of Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W, PDB code: 8xvr 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) 41.59 / 2.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.57, 132.08, 121.78, 90, 110.29, 90
R / Rfree (%) 18 / 21.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W (pdb code 8xvr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W, PDB code: 8xvr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8xvr

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Calcium binding site 1 out of 8 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W


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 Mutant R544W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:17.1
occ:1.00
 OD1 A:ASN488 2.3 17.5 1.0
OE1 A:GLN449 2.3 19.2 1.0
O A:HOH930 2.3 15.0 1.0
OD1 A:ASP418 2.3 20.8 1.0
O A:TRP486 2.3 16.9 1.0
OD1 A:ASP520 2.4 14.8 1.0
OD2 A:ASP520 2.7 14.6 1.0
CG A:ASP520 2.9 14.6 1.0
CG A:ASP418 3.4 20.7 1.0
CG A:ASN488 3.5 18.8 1.0
CD A:GLN449 3.5 20.1 1.0
C A:TRP486 3.5 18.1 1.0
OD2 A:ASP418 3.8 19.0 1.0
N A:ASN488 4.0 18.3 1.0
NE2 A:GLN449 4.2 19.3 1.0
ND2 A:ASN488 4.2 18.3 1.0
CB A:ASP520 4.4 15.2 1.0
N A:ALA487 4.4 17.8 1.0
CA A:TRP486 4.4 19.9 1.0
O A:ASN419 4.4 18.3 1.0
CB A:GLN449 4.5 20.7 1.0
CA A:ALA487 4.5 17.8 1.0
N A:ASN419 4.5 20.6 1.0
C A:ALA487 4.5 18.2 1.0
CB A:ASN488 4.5 18.2 1.0
CG A:GLN449 4.6 20.4 1.0
OG A:SER442 4.6 16.5 1.0
CB A:TRP486 4.6 21.3 1.0
CA A:ASN488 4.7 17.8 1.0
CB A:SER442 4.7 16.2 1.0
CB A:ASP418 4.7 20.6 1.0
O A:HOH924 4.8 14.9 1.0
CA A:ASP418 4.9 19.8 1.0
NE2 A:GLN405 5.0 18.9 1.0

Calcium binding site 2 out of 8 in 8xvr

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Calcium binding site 2 out of 8 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W


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 Mutant R544W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:17.2
occ:1.00
 OD1 A:ASN317 2.3 20.0 1.0
O A:HOH1057 2.3 15.4 1.0
O A:ILE661 2.3 17.9 1.0
OD1 A:ASP659 2.3 15.7 1.0
OG A:SER666 2.3 22.0 1.0
O A:HOH1037 2.4 14.7 1.0
OD2 A:ASP659 2.5 15.1 1.0
CG A:ASP659 2.8 16.7 1.0
CG A:ASN317 3.4 21.3 1.0
C A:ILE661 3.4 18.8 1.0
CB A:SER666 3.4 22.6 1.0
ND2 A:ASN317 4.0 21.7 1.0
CB A:ILE661 4.0 19.2 1.0
CA A:ILE661 4.1 19.0 1.0
O A:GLY315 4.2 18.5 1.0
N A:ILE661 4.2 19.0 1.0
CB A:ASP659 4.3 16.6 1.0
OD1 A:ASP663 4.5 20.4 1.0
CA A:SER666 4.5 22.8 1.0
N A:TRP662 4.5 20.0 1.0
CB A:ASN317 4.5 19.9 1.0
CG2 A:ILE661 4.6 19.9 1.0
O A:HOH1013 4.6 15.3 1.0
O A:HOH926 4.6 15.6 1.0
OD2 A:ASP663 4.7 21.3 1.0
O A:ASP316 4.7 16.5 1.0
CA A:TRP662 4.7 20.6 1.0
C A:GLY315 4.8 17.9 1.0
CA A:ASN317 4.8 20.3 1.0
CG A:ASP663 4.8 22.8 1.0
N A:ASP663 4.9 22.3 1.0
CA A:ASP659 5.0 17.0 1.0

Calcium binding site 3 out of 8 in 8xvr

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Calcium binding site 3 out of 8 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W


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 Mutant R544W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:16.1
occ:1.00
 O B:TRP486 2.3 16.1 1.0
OD1 B:ASP418 2.3 17.5 1.0
OD1 B:ASN488 2.3 15.1 1.0
OE1 B:GLN449 2.3 18.1 1.0
O B:HOH961 2.3 15.5 1.0
OD1 B:ASP520 2.4 15.6 1.0
OD2 B:ASP520 2.6 16.6 1.0
CG B:ASP520 2.9 15.2 1.0
CG B:ASP418 3.4 18.4 1.0
CG B:ASN488 3.5 16.7 1.0
C B:TRP486 3.5 16.9 1.0
CD B:GLN449 3.5 18.4 1.0
OD2 B:ASP418 3.8 18.0 1.0
N B:ASN488 4.0 16.2 1.0
ND2 B:ASN488 4.2 16.7 1.0
NE2 B:GLN449 4.3 19.9 1.0
CB B:ASP520 4.4 14.4 1.0
CA B:TRP486 4.4 16.6 1.0
N B:ALA487 4.4 16.5 1.0
N B:ASN419 4.4 19.2 1.0
O B:ASN419 4.4 18.6 1.0
CA B:ALA487 4.4 15.7 1.0
C B:ALA487 4.5 15.9 1.0
CB B:GLN449 4.5 16.8 1.0
CB B:ASN488 4.5 16.1 1.0
CB B:TRP486 4.6 16.4 1.0
OG B:SER442 4.6 13.8 1.0
CG B:GLN449 4.6 17.4 1.0
CA B:ASN488 4.7 15.6 1.0
CB B:ASP418 4.7 18.8 1.0
CB B:SER442 4.7 13.8 1.0
CA B:ASP418 4.9 18.7 1.0
C B:ASN488 5.0 14.7 1.0

Calcium binding site 4 out of 8 in 8xvr

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Calcium binding site 4 out of 8 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W


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 Mutant R544W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:14.9
occ:1.00
 OD1 B:ASN317 2.3 14.2 1.0
OG B:SER666 2.3 15.3 1.0
O B:ILE661 2.3 14.8 1.0
O B:HOH1061 2.3 13.6 1.0
OD1 B:ASP659 2.3 12.3 1.0
O B:HOH1040 2.3 10.9 1.0
OD2 B:ASP659 2.6 12.3 1.0
CG B:ASP659 2.8 12.4 1.0
CG B:ASN317 3.4 15.1 1.0
CB B:SER666 3.4 16.9 1.0
C B:ILE661 3.4 15.3 1.0
ND2 B:ASN317 4.0 15.2 1.0
CB B:ILE661 4.0 15.4 1.0
CA B:ILE661 4.1 15.3 1.0
O B:GLY315 4.2 11.9 1.0
N B:ILE661 4.3 14.9 1.0
CB B:ASP659 4.3 12.8 1.0
OD1 B:ASP663 4.4 22.5 1.0
CA B:SER666 4.5 17.4 1.0
N B:TRP662 4.5 15.4 1.0
CB B:ASN317 4.5 16.2 1.0
CG2 B:ILE661 4.6 15.7 1.0
O B:HOH957 4.6 10.5 1.0
OD2 B:ASP663 4.7 21.1 1.0
O B:HOH1013 4.7 7.5 1.0
CG B:ASP663 4.7 21.9 1.0
CA B:TRP662 4.7 16.6 1.0
O B:ASP316 4.7 14.4 1.0
C B:GLY315 4.8 14.1 1.0
CA B:ASN317 4.8 16.1 1.0
N B:ASP663 4.9 21.3 1.0
CA B:ASP659 5.0 12.5 1.0

Calcium binding site 5 out of 8 in 8xvr

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Calcium binding site 5 out of 8 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W


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 Mutant R544W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca801

b:16.9
occ:1.00
 O C:TRP486 2.3 15.5 1.0
OD1 C:ASN488 2.3 14.2 1.0
OD1 C:ASP418 2.3 17.0 1.0
OE1 C:GLN449 2.3 18.4 1.0
O C:HOH1001 2.3 17.6 1.0
OD1 C:ASP520 2.3 15.4 1.0
OD2 C:ASP520 2.6 15.8 1.0
CG C:ASP520 2.8 15.7 1.0
CG C:ASP418 3.4 18.2 1.0
CG C:ASN488 3.5 14.3 1.0
C C:TRP486 3.5 15.5 1.0
CD C:GLN449 3.5 17.9 1.0
OD2 C:ASP418 3.9 17.3 1.0
N C:ASN488 3.9 14.6 1.0
ND2 C:ASN488 4.2 14.1 1.0
NE2 C:GLN449 4.3 18.2 1.0
CB C:ASP520 4.3 14.7 1.0
N C:ALA487 4.4 14.9 1.0
CA C:TRP486 4.4 15.6 1.0
N C:ASN419 4.4 18.2 1.0
CA C:ALA487 4.4 14.3 1.0
C C:ALA487 4.4 14.1 1.0
O C:ASN419 4.5 16.4 1.0
CB C:GLN449 4.5 16.2 1.0
CB C:ASN488 4.5 14.8 1.0
CB C:TRP486 4.6 15.5 1.0
OG C:SER442 4.6 14.6 1.0
CG C:GLN449 4.6 16.9 1.0
CA C:ASN488 4.7 14.3 1.0
CB C:ASP418 4.7 18.3 1.0
CB C:SER442 4.7 15.2 1.0
CA C:ASP418 4.9 18.0 1.0
O C:HOH979 4.9 22.2 1.0
C C:ASN488 5.0 14.5 1.0

Calcium binding site 6 out of 8 in 8xvr

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Calcium binding site 6 out of 8 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W


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 Mutant R544W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca802

b:14.3
occ:1.00
 OD1 C:ASN317 2.3 14.0 1.0
OG C:SER666 2.3 16.3 1.0
O C:ILE661 2.3 14.8 1.0
O C:HOH1066 2.3 16.1 1.0
OD1 C:ASP659 2.3 13.2 1.0
O C:HOH1022 2.3 11.2 1.0
OD2 C:ASP659 2.6 14.4 1.0
CG C:ASP659 2.8 13.8 1.0
CG C:ASN317 3.4 14.9 1.0
C C:ILE661 3.4 14.8 1.0
CB C:SER666 3.4 16.9 1.0
ND2 C:ASN317 4.0 15.5 1.0
CB C:ILE661 4.0 14.8 1.0
CA C:ILE661 4.1 14.3 1.0
O C:GLY315 4.2 13.5 1.0
N C:ILE661 4.2 14.7 1.0
CB C:ASP659 4.3 14.2 1.0
OD1 C:ASP663 4.4 21.9 1.0
CA C:SER666 4.5 17.6 1.0
N C:TRP662 4.5 15.9 1.0
CB C:ASN317 4.5 16.1 1.0
CG2 C:ILE661 4.6 14.9 1.0
O C:HOH1019 4.6 9.9 1.0
O C:HOH963 4.7 14.4 1.0
OD2 C:ASP663 4.7 19.6 1.0
CA C:TRP662 4.7 17.1 1.0
CG C:ASP663 4.7 21.7 1.0
O C:ASP316 4.7 16.4 1.0
C C:GLY315 4.7 15.0 1.0
CA C:ASN317 4.8 15.9 1.0
N C:ASP663 4.9 22.3 1.0
CA C:ASP659 5.0 14.0 1.0

Calcium binding site 7 out of 8 in 8xvr

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Calcium binding site 7 out of 8 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:19.6
occ:1.00
 OD1 D:ASP418 2.3 20.6 1.0
OD1 D:ASN488 2.3 18.2 1.0
O D:HOH935 2.3 18.0 1.0
OE1 D:GLN449 2.3 24.6 1.0
O D:TRP486 2.3 19.4 1.0
OD1 D:ASP520 2.4 15.7 1.0
OD2 D:ASP520 2.7 17.4 1.0
CG D:ASP520 2.9 16.3 1.0
CG D:ASP418 3.4 21.1 1.0
CG D:ASN488 3.5 19.1 1.0
CD D:GLN449 3.5 22.1 1.0
C D:TRP486 3.5 19.9 1.0
OD2 D:ASP418 3.8 20.9 1.0
N D:ASN488 4.0 19.0 1.0
NE2 D:GLN449 4.2 21.8 1.0
ND2 D:ASN488 4.2 19.4 1.0
CB D:ASP520 4.4 16.3 1.0
CA D:TRP486 4.4 20.7 1.0
N D:ALA487 4.4 19.6 1.0
O D:ASN419 4.4 20.9 1.0
N D:ASN419 4.5 19.9 1.0
CA D:ALA487 4.5 19.8 1.0
CB D:GLN449 4.5 21.8 1.0
C D:ALA487 4.5 20.2 1.0
CB D:ASN488 4.5 17.9 1.0
CG D:GLN449 4.6 22.1 1.0
OG D:SER442 4.6 19.7 1.0
CB D:TRP486 4.6 22.8 1.0
CB D:ASP418 4.7 20.3 1.0
CA D:ASN488 4.7 17.8 1.0
CB D:SER442 4.7 18.7 1.0
O D:HOH926 4.9 23.7 1.0
CA D:ASP418 4.9 20.2 1.0
NE2 D:GLN405 5.0 23.2 1.0

Calcium binding site 8 out of 8 in 8xvr

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Calcium binding site 8 out of 8 in the Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Inulosucrase From Lactobacillus Reuteri 121 Mutant R544W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca802

b:17.7
occ:1.00
 OD1 D:ASN317 2.3 20.4 1.0
O D:ILE661 2.3 18.2 1.0
O D:HOH1056 2.3 18.1 1.0
OD1 D:ASP659 2.3 16.8 1.0
OG D:SER666 2.3 21.1 1.0
O D:HOH1055 2.3 17.3 1.0
OD2 D:ASP659 2.6 16.9 1.0
CG D:ASP659 2.8 17.1 1.0
CG D:ASN317 3.4 22.5 1.0
C D:ILE661 3.4 18.7 1.0
CB D:SER666 3.5 22.5 1.0
CB D:ILE661 4.0 19.5 1.0
ND2 D:ASN317 4.0 22.8 1.0
CA D:ILE661 4.1 19.1 1.0
O D:GLY315 4.2 16.6 1.0
N D:ILE661 4.2 18.8 1.0
CB D:ASP659 4.3 17.1 1.0
OD1 D:ASP663 4.5 20.4 1.0
N D:TRP662 4.5 19.9 1.0
O D:HOH963 4.5 20.6 1.0
CA D:SER666 4.5 22.4 1.0
CG2 D:ILE661 4.5 19.5 1.0
CB D:ASN317 4.5 21.9 1.0
O D:HOH922 4.6 18.4 1.0
OD2 D:ASP663 4.6 21.0 1.0
O D:ASP316 4.7 19.1 1.0
CA D:TRP662 4.7 20.3 1.0
C D:GLY315 4.7 18.6 1.0
CG D:ASP663 4.8 23.0 1.0
CA D:ASN317 4.8 21.6 1.0
N D:ASP663 4.9 21.9 1.0
CA D:ASP659 5.0 17.0 1.0
CA D:GLY315 5.0 18.7 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 16:11:44 2025

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