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Calcium in PDB 7dt1: The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase

Enzymatic activity of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase

All present enzymatic activity of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase:
2.4.1.5;

Protein crystallography data

The structure of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase, PDB code: 7dt1 was solved by W.K.Yang, Y.H.Yong, L.Wu, S.Chen, J.H.Zhou, J.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.73 / 2.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.83, 106.08, 106.02, 90, 104.83, 90
R / Rfree (%) 19.4 / 25.6

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase (pdb code 7dt1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase, PDB code: 7dt1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 7dt1

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Calcium binding site 1 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1101

b:21.2
occ:1.00
 OE2 A:GLU397 2.1 14.6 1.0
OD1 A:ASP403 2.4 19.5 1.0
O A:GLU397 2.4 20.6 1.0
OD1 A:ASN905 2.4 16.6 1.0
O A:HOH1307 2.4 16.0 1.0
O A:ASN447 2.6 18.9 1.0
OD2 A:ASP403 2.6 17.0 1.0
CG A:ASP403 2.9 18.1 1.0
CD A:GLU397 3.2 19.1 1.0
CG A:ASN905 3.5 17.6 1.0
C A:GLU397 3.5 19.6 1.0
CG A:GLU397 3.7 17.0 1.0
C A:ASN447 3.7 16.2 1.0
O A:HOH1527 4.2 16.4 1.0
CA A:GLU397 4.2 18.2 1.0
ND2 A:ASN905 4.2 15.7 1.0
O A:ASN905 4.2 18.6 1.0
OE1 A:GLU397 4.3 21.4 1.0
CB A:ASP403 4.4 15.1 1.0
CA A:ILE448 4.4 15.4 1.0
CG2 A:ILE448 4.5 12.9 1.0
N A:ILE448 4.5 13.1 1.0
CB A:ASN447 4.6 14.9 1.0
CB A:GLU397 4.6 17.7 1.0
O A:ILE404 4.6 20.4 1.0
N A:LEU398 4.6 17.8 1.0
CB A:ASN905 4.6 16.9 1.0
CA A:ASN447 4.7 15.7 1.0
O A:HOH1393 4.7 19.0 1.0
CA A:ASN905 4.7 15.4 1.0
CA A:LEU398 4.8 18.5 1.0
ND2 A:ASN996 4.8 19.1 1.0
C A:ASN905 4.9 17.3 1.0

Calcium binding site 2 out of 11 in 7dt1

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Calcium binding site 2 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1102

b:38.1
occ:1.00
 O A:HOH1223 2.3 30.0 1.0
OD1 A:ASP443 2.6 26.5 1.0
O A:HOH1685 2.6 27.1 1.0
O A:HOH1270 2.7 32.7 1.0
OE2 A:GLU481 3.0 24.6 1.0
OE1 A:GLU481 3.0 27.9 1.0
O A:HOH1637 3.0 29.4 1.0
CD A:GLU481 3.3 23.5 1.0
O A:HOH1643 3.6 30.8 1.0
CG A:ASP443 3.6 22.0 1.0
OD2 A:ASP443 3.9 23.5 1.0
OD2 A:ASP553 3.9 23.1 1.0
O A:HOH1573 4.2 20.6 1.0
O A:HOH1490 4.4 21.7 1.0
NH1 A:ARG441 4.5 18.8 1.0
N A:ALA444 4.5 19.6 1.0
NH2 A:ARG441 4.7 18.4 1.0
CB A:ALA444 4.7 11.8 1.0
CG A:ASP553 4.8 25.6 1.0
CG A:GLU481 4.8 16.2 1.0
OD1 A:ASP553 4.9 23.1 1.0
CA A:ALA444 4.9 18.8 1.0
CB A:ASP443 4.9 20.3 1.0
O A:HOH1741 4.9 37.3 1.0

Calcium binding site 3 out of 11 in 7dt1

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Calcium binding site 3 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:62.9
occ:1.00
 O A:HOH1421 3.7 28.8 1.0
ND2 A:ASN1002 3.9 35.2 1.0
OD2 A:ASP352 4.0 24.0 1.0
O A:LEU1000 4.2 25.8 1.0
OD1 A:ASN1002 4.6 32.9 1.0
CG A:ASN1002 4.6 32.2 1.0
O A:HOH1402 4.7 22.6 1.0
OG A:SER334 4.8 18.6 1.0
O A:HOH1705 4.8 55.0 1.0
CG A:ASP352 4.9 24.6 1.0
CB A:LEU1000 5.0 21.4 1.0
OD1 A:ASP576 5.0 38.6 1.0
CB A:ASP352 5.0 22.2 1.0
CB A:SER575 5.0 23.4 1.0

Calcium binding site 4 out of 11 in 7dt1

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Calcium binding site 4 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:47.9
occ:1.00
 O A:SER462 2.5 23.9 1.0
O A:HOH1463 2.9 30.0 1.0
C A:SER462 3.6 27.8 1.0
CA A:SER462 4.2 23.4 1.0
O A:ASN461 4.4 24.9 1.0
O A:ILE463 4.7 22.6 1.0
CE1 A:TYR966 4.7 22.9 1.0
N A:ILE463 4.7 25.6 1.0
C A:ILE463 4.8 25.7 1.0
CA A:ILE463 5.0 23.2 1.0

Calcium binding site 5 out of 11 in 7dt1

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Calcium binding site 5 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1105

b:64.0
occ:1.00
 O A:ASN853 3.0 35.3 1.0
O A:HOH1465 3.6 47.3 1.0
O A:HOH1219 3.7 32.7 1.0
O A:HOH1531 4.1 41.9 1.0
C A:ASN853 4.1 35.5 1.0
OD1 A:ASN858 4.4 35.5 1.0
CG A:ASN858 4.5 36.2 1.0
CA A:ASN853 4.6 37.4 1.0
ND2 A:ASN858 4.7 34.1 1.0
CB A:ASN853 4.7 31.1 1.0
O1 A:EDO1130 5.0 39.7 1.0

Calcium binding site 6 out of 11 in 7dt1

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Calcium binding site 6 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1101

b:18.1
occ:1.00
 OE1 B:GLU397 2.3 15.6 1.0
OD1 B:ASN905 2.3 17.0 1.0
OD1 B:ASP403 2.4 19.2 1.0
O B:GLU397 2.4 16.9 1.0
O B:HOH1277 2.5 13.9 1.0
OD2 B:ASP403 2.5 18.4 1.0
O B:ASN447 2.6 15.5 1.0
CG B:ASP403 2.8 18.9 1.0
CD B:GLU397 3.2 17.1 1.0
CG B:GLU397 3.5 13.1 1.0
CG B:ASN905 3.5 16.6 1.0
C B:GLU397 3.5 16.7 1.0
C B:ASN447 3.7 16.1 1.0
CA B:GLU397 4.0 17.1 1.0
ND2 B:ASN905 4.1 14.2 1.0
O B:ASN905 4.2 17.4 1.0
CB B:ASP403 4.3 19.1 1.0
CB B:GLU397 4.3 14.1 1.0
OE2 B:GLU397 4.3 22.1 1.0
O B:HOH1406 4.3 22.7 1.0
CA B:ILE448 4.4 17.0 1.0
CG2 B:ILE448 4.4 12.4 1.0
O B:ILE404 4.5 17.5 1.0
N B:ILE448 4.5 12.5 1.0
N B:LEU398 4.6 19.2 1.0
CB B:ASN905 4.6 15.6 1.0
ND2 B:ASN996 4.7 16.3 1.0
CB B:ASN447 4.7 18.4 1.0
CA B:ASN905 4.7 14.8 1.0
CA B:ASN447 4.8 15.0 1.0
O B:HOH1400 4.8 15.5 1.0
CA B:LEU398 4.9 19.1 1.0
C B:ASN905 4.9 14.5 1.0

Calcium binding site 7 out of 11 in 7dt1

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Calcium binding site 7 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1102

b:36.0
occ:1.00
 O B:HOH1375 2.2 29.9 1.0
O B:HOH1401 2.4 14.9 1.0
OD1 B:ASP443 2.5 19.8 1.0
OE2 B:GLU481 2.5 26.4 1.0
O B:HOH1456 2.5 24.2 1.0
OE1 B:GLU481 2.7 26.9 1.0
O B:HOH1656 2.7 23.3 1.0
CD B:GLU481 2.9 25.5 1.0
OD2 B:ASP553 3.7 27.5 1.0
CG B:ASP443 3.7 19.8 1.0
O B:HOH1695 3.9 34.5 1.0
NH2 B:ARG441 4.2 17.0 1.0
OD2 B:ASP443 4.3 19.0 1.0
O B:HOH1538 4.4 24.7 1.0
NH1 B:ARG441 4.4 17.6 1.0
CG B:GLU481 4.5 22.1 1.0
O B:HOH1300 4.5 22.8 1.0
N B:ALA444 4.5 18.7 1.0
O B:HOH1606 4.6 21.7 1.0
CG B:ASP553 4.6 28.0 1.0
CZ B:ARG441 4.8 20.3 1.0
OD1 B:ASP553 4.8 26.6 1.0
CB B:ASP443 4.8 18.9 1.0
CZ B:TYR861 4.9 18.9 1.0
OH B:TYR861 4.9 14.8 1.0
NE2 B:HIS552 5.0 23.4 1.0

Calcium binding site 8 out of 11 in 7dt1

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Calcium binding site 8 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1103

b:44.4
occ:1.00
 OD2 B:ASP630 2.4 32.1 1.0
O B:LYS639 2.5 30.2 1.0
O B:HOH1319 2.5 40.9 1.0
O B:HOH1669 2.6 33.4 1.0
ND2 B:ASN638 3.5 41.8 1.0
CG B:ASP630 3.6 24.2 1.0
C B:LYS639 3.7 24.8 1.0
CG B:ASN638 3.9 33.4 1.0
OD1 B:ASP630 4.3 22.3 1.0
CB B:ASN638 4.4 26.6 1.0
N B:LYS639 4.4 22.5 1.0
CA B:SER640 4.4 24.6 1.0
OD1 B:ASN638 4.5 51.8 1.0
C B:ASN638 4.5 27.5 1.0
N B:SER640 4.5 21.4 1.0
O B:HOH1432 4.6 21.3 1.0
CB B:ASP630 4.6 20.9 1.0
CA B:LYS639 4.7 22.9 1.0
O B:HOH1749 4.8 35.0 1.0
O B:HOH1773 4.8 43.3 1.0
CA B:ASN638 4.8 27.2 1.0
O B:ASN638 4.8 25.5 1.0
CA B:CA1106 4.8 58.4 1.0
C B:SER640 4.9 21.6 1.0

Calcium binding site 9 out of 11 in 7dt1

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Calcium binding site 9 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1104

b:61.5
occ:1.00
 O B:HOH1780 3.0 50.0 1.0
OD2 B:ASP350 3.6 26.6 1.0
O B:HOH1352 3.7 28.7 1.0
OD1 B:ASP350 3.8 23.8 1.0
CG B:ASP350 4.0 24.4 1.0
O B:HOH1235 4.1 33.8 1.0
O B:HOH1668 4.4 21.8 1.0
O B:HOH1748 4.6 33.8 1.0
O B:HOH1348 4.6 30.6 1.0
CD2 B:LEU399 4.9 20.4 1.0

Calcium binding site 10 out of 11 in 7dt1

Go back to Calcium Binding Sites List in 7dt1
Calcium binding site 10 out of 11 in the The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of The Structure of Lactobacillus Fermentum 4,6-Alpha-Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1105

b:60.1
occ:1.00
 O B:HOH1532 2.5 30.2 1.0
O A:HOH1518 2.6 39.7 1.0
O B:ASN337 2.9 24.1 1.0
O A:HOH1702 3.0 43.1 1.0
OD2 B:ASP931 3.3 22.7 1.0
O A:HOH1232 3.6 30.6 1.0
N B:TYR339 4.0 23.2 1.0
C B:SER338 4.1 24.5 1.0
O1 A:EDO1116 4.1 58.6 1.0
C B:ASN337 4.1 19.3 1.0
CG B:ASP931 4.2 19.8 1.0
CB A:ASP518 4.3 36.2 1.0
CA B:TYR339 4.3 22.4 1.0
CA B:SER338 4.4 21.5 1.0
O B:SER338 4.5 27.7 1.0
OD1 B:ASP931 4.6 22.4 1.0
CB B:TYR339 4.6 23.6 1.0
O A:ASP518 4.7 29.4 1.0
N B:SER338 4.8 18.1 1.0
C1 A:EDO1116 4.8 55.3 1.0
CG A:ASP518 4.9 43.1 1.0

Reference:

W.Yang, L.Sheng, S.Chen, L.Wang, L.Su, J.Wu. Characterization of A New 4,6-Alpha-Glucanotransferase From Limosilactobacillus Fermentum Ncc 3057 with Ability of Synthesizing Low Molecular Mass Isomalto-/Maltopolysaccharide Food Biosci V. 46 01514 2022.
ISSN: ISSN 2212-4292
DOI: 10.1016/J.FBIO.2021.101514
Page generated: Fri Jul 19 00:09:54 2024

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