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Calcium in PDB 7nit: X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum

Enzymatic activity of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum

All present enzymatic activity of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum:
3.2.1.23;

Protein crystallography data

The structure of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum, PDB code: 7nit was solved by O.V.Moroz, E.Blagova, A.A.Lebedev, F.Sanchez Rodriguez, D.J.Rigden, J.W.Tams, R.Wilting, J.K.Vester, E.Longhin, K.B.R.Krogh, R.A.Pache, G.J.Davies, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 199.58 / 2.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 116.947, 130.042, 200.58, 86.99, 84.83, 83.79
R / Rfree (%) 21.4 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum (pdb code 7nit). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum, PDB code: 7nit:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7nit

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Calcium binding site 1 out of 6 in the X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2304

b:116.8
occ:1.00
 O A:ALA1070 2.3 71.8 1.0
OD1 A:ASP1073 2.3 106.7 1.0
OE1 A:GLU1204 2.3 79.3 1.0
O A:THR1203 2.3 90.8 1.0
O A:SER1075 2.3 105.5 1.0
O A:HOH2401 2.4 86.4 1.0
CG A:ASP1073 3.1 81.6 1.0
OD2 A:ASP1073 3.4 82.3 1.0
C A:THR1203 3.4 76.4 1.0
C A:SER1075 3.5 95.6 1.0
C A:ALA1070 3.5 62.6 1.0
CD A:GLU1204 3.6 89.2 1.0
N A:SER1075 3.8 79.8 1.0
O A:SER1089 4.0 93.5 1.0
CB A:GLU1204 4.0 77.3 1.0
CA A:SER1075 4.1 96.3 1.0
CA A:ILE1071 4.2 69.9 1.0
N A:GLU1204 4.2 79.6 1.0
N A:ASP1073 4.2 63.5 1.0
CA A:GLU1204 4.2 80.8 1.0
CB A:ASP1073 4.3 62.7 1.0
N A:ILE1071 4.3 67.2 1.0
CG A:GLU1204 4.3 90.1 1.0
CA A:THR1203 4.3 73.2 1.0
CB A:SER1075 4.4 102.3 1.0
C A:ILE1071 4.4 74.1 1.0
N A:GLY1074 4.4 69.7 1.0
OE2 A:GLU1204 4.5 80.2 1.0
CB A:THR1203 4.5 64.9 1.0
CA A:ALA1070 4.5 60.5 1.0
CA A:ASP1073 4.5 60.2 1.0
N A:THR1076 4.6 89.2 1.0
C A:ASP1073 4.6 62.0 1.0
CB A:ALA1070 4.7 58.4 1.0
O A:ILE1071 4.8 83.6 1.0
N A:LYS1072 4.8 80.2 1.0
C A:GLY1074 4.9 76.8 1.0
OG1 A:THR1203 4.9 71.8 1.0
CA A:THR1076 4.9 86.8 1.0

Calcium binding site 2 out of 6 in 7nit

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Calcium binding site 2 out of 6 in the X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2304

b:141.0
occ:1.00
 O B:SER1075 2.3 107.3 1.0
OE1 B:GLU1204 2.3 129.6 1.0
O B:ALA1070 2.3 101.8 1.0
O B:HOH2401 2.3 185.4 1.0
O B:THR1203 2.3 129.0 1.0
OD1 B:ASP1073 2.4 145.3 1.0
CG B:ASP1073 3.1 130.7 1.0
C B:THR1203 3.4 111.8 1.0
OD2 B:ASP1073 3.4 140.1 1.0
C B:SER1075 3.5 104.3 1.0
C B:ALA1070 3.5 103.5 1.0
CD B:GLU1204 3.5 110.0 1.0
N B:SER1075 3.8 103.3 1.0
CB B:GLU1204 4.0 114.3 1.0
O B:SER1089 4.0 119.1 1.0
CA B:SER1075 4.1 103.8 1.0
CA B:ILE1071 4.2 110.0 1.0
N B:GLU1204 4.2 128.1 1.0
CA B:GLU1204 4.2 113.6 1.0
N B:ASP1073 4.2 99.4 1.0
N B:ILE1071 4.3 121.2 1.0
CB B:ASP1073 4.3 104.3 1.0
CG B:GLU1204 4.3 100.6 1.0
CA B:THR1203 4.4 99.0 1.0
C B:ILE1071 4.4 113.1 1.0
N B:GLY1074 4.4 113.6 1.0
CB B:SER1075 4.5 111.6 1.0
OE2 B:GLU1204 4.5 118.7 1.0
CB B:THR1203 4.5 92.2 1.0
CA B:ALA1070 4.5 100.2 1.0
N B:THR1076 4.5 94.2 1.0
CA B:ASP1073 4.6 103.4 1.0
C B:ASP1073 4.7 113.9 1.0
O B:ILE1071 4.8 131.0 1.0
CB B:ALA1070 4.8 93.4 1.0
N B:LYS1072 4.8 96.6 1.0
CA B:THR1076 4.8 105.8 1.0
OG1 B:THR1203 4.9 91.4 1.0
C B:GLY1074 4.9 100.6 1.0

Calcium binding site 3 out of 6 in 7nit

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Calcium binding site 3 out of 6 in the X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2304

b:138.8
occ:1.00
 O C:ALA1070 2.3 93.9 1.0
O C:SER1075 2.3 133.0 1.0
OD1 C:ASP1073 2.3 111.0 1.0
OE1 C:GLU1204 2.3 113.1 1.0
O C:THR1203 2.3 120.5 1.0
O C:HOH2401 2.3 127.7 1.0
CG C:ASP1073 3.0 92.1 1.0
OD2 C:ASP1073 3.3 117.2 1.0
C C:THR1203 3.4 87.0 1.0
C C:SER1075 3.4 115.1 1.0
C C:ALA1070 3.5 75.1 1.0
CD C:GLU1204 3.6 97.5 1.0
N C:SER1075 3.8 82.2 1.0
O C:SER1089 4.0 94.0 1.0
CB C:GLU1204 4.0 87.6 1.0
CA C:SER1075 4.1 99.0 1.0
CA C:ILE1071 4.2 77.4 1.0
N C:ASP1073 4.2 67.1 1.0
N C:GLU1204 4.2 78.6 1.0
CA C:GLU1204 4.2 70.5 1.0
CB C:ASP1073 4.2 77.4 1.0
N C:ILE1071 4.3 83.9 1.0
CG C:GLU1204 4.3 96.2 1.0
CA C:THR1203 4.4 76.6 1.0
N C:GLY1074 4.4 83.0 1.0
CB C:SER1075 4.4 100.1 1.0
C C:ILE1071 4.4 83.7 1.0
OE2 C:GLU1204 4.5 90.9 1.0
CA C:ALA1070 4.5 69.2 1.0
CB C:THR1203 4.5 76.4 1.0
N C:THR1076 4.5 106.5 1.0
CA C:ASP1073 4.5 76.0 1.0
C C:ASP1073 4.6 78.7 1.0
CB C:ALA1070 4.7 65.3 1.0
O C:ILE1071 4.8 91.8 1.0
N C:LYS1072 4.8 70.2 1.0
CA C:THR1076 4.8 87.2 1.0
OG1 C:THR1203 4.9 83.7 1.0
C C:GLY1074 4.9 85.9 1.0

Calcium binding site 4 out of 6 in 7nit

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Calcium binding site 4 out of 6 in the X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2304

b:146.7
occ:1.00
 O D:ALA1070 2.3 93.7 1.0
O D:SER1075 2.3 122.0 1.0
O D:THR1203 2.3 134.2 1.0
O D:HOH2401 2.3 98.6 1.0
OD1 D:ASP1073 2.4 128.4 1.0
OE1 D:GLU1204 2.4 112.8 1.0
CG D:ASP1073 3.1 113.8 1.0
OD2 D:ASP1073 3.4 119.2 1.0
C D:THR1203 3.4 111.5 1.0
C D:SER1075 3.4 110.8 1.0
C D:ALA1070 3.5 77.4 1.0
CD D:GLU1204 3.6 119.8 1.0
N D:SER1075 3.8 102.5 1.0
O D:SER1089 4.0 121.0 1.0
CB D:GLU1204 4.0 120.9 1.0
CA D:SER1075 4.1 107.0 1.0
CA D:ILE1071 4.2 102.7 1.0
N D:GLU1204 4.2 116.0 1.0
CA D:GLU1204 4.2 109.0 1.0
N D:ASP1073 4.3 92.3 1.0
CB D:ASP1073 4.3 96.1 1.0
N D:ILE1071 4.3 90.3 1.0
CA D:THR1203 4.3 99.9 1.0
CG D:GLU1204 4.3 137.0 1.0
CB D:SER1075 4.4 98.0 1.0
N D:GLY1074 4.4 79.8 1.0
C D:ILE1071 4.5 118.1 1.0
CB D:THR1203 4.5 94.5 1.0
CA D:ALA1070 4.5 76.4 1.0
OE2 D:GLU1204 4.5 121.1 1.0
N D:THR1076 4.5 107.0 1.0
CA D:ASP1073 4.6 94.4 1.0
C D:ASP1073 4.7 86.7 1.0
CB D:ALA1070 4.7 73.9 1.0
O D:ILE1071 4.8 115.4 1.0
N D:LYS1072 4.8 110.0 1.0
CA D:THR1076 4.9 96.0 1.0
OG1 D:THR1203 4.9 95.4 1.0
C D:GLY1074 4.9 93.1 1.0

Calcium binding site 5 out of 6 in 7nit

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Calcium binding site 5 out of 6 in the X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2304

b:279.1
occ:1.00
 O E:ALA1070 2.3 276.9 1.0
O E:SER1075 2.3 243.0 1.0
O E:HOH2401 2.3 239.7 1.0
OE1 E:GLU1204 2.3 255.4 1.0
OD1 E:ASP1073 2.3 235.4 1.0
O E:THR1203 2.3 285.4 1.0
CG E:ASP1073 3.1 240.7 1.0
OD2 E:ASP1073 3.4 268.8 1.0
C E:THR1203 3.4 257.9 1.0
C E:SER1075 3.4 204.1 1.0
C E:ALA1070 3.5 251.4 1.0
CD E:GLU1204 3.6 226.3 1.0
N E:SER1075 3.8 190.3 1.0
CB E:GLU1204 4.0 221.9 1.0
O E:SER1089 4.0 271.0 1.0
CA E:SER1075 4.1 188.5 1.0
CA E:ILE1071 4.2 279.1 1.0
CA E:GLU1204 4.2 226.0 1.0
N E:GLU1204 4.2 239.6 1.0
N E:ASP1073 4.2 266.0 1.0
CB E:ASP1073 4.3 236.7 1.0
N E:ILE1071 4.3 261.2 1.0
CG E:GLU1204 4.3 213.7 1.0
CA E:THR1203 4.4 251.2 1.0
C E:ILE1071 4.4 296.0 1.0
N E:GLY1074 4.4 217.2 1.0
CB E:SER1075 4.4 171.2 1.0
OE2 E:GLU1204 4.5 218.3 1.0
CB E:THR1203 4.5 238.7 1.0
CA E:ALA1070 4.5 234.9 1.0
N E:THR1076 4.5 202.4 1.0
CA E:ASP1073 4.6 255.2 1.0
C E:ASP1073 4.7 246.6 1.0
CB E:ALA1070 4.7 213.8 1.0
O E:ILE1071 4.8 332.2 1.0
N E:LYS1072 4.8 281.7 1.0
CA E:THR1076 4.8 209.5 1.0
OG1 E:THR1203 4.9 228.7 1.0
C E:GLY1074 4.9 202.5 1.0

Calcium binding site 6 out of 6 in 7nit

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Calcium binding site 6 out of 6 in the X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of A Multidomain Bbgiii From Bifidobacterium Bifidum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2304

b:216.1
occ:1.00
 O F:SER1075 2.3 190.8 1.0
O F:ALA1070 2.3 144.9 1.0
OD1 F:ASP1073 2.3 160.1 1.0
O F:HOH2401 2.3 158.7 1.0
OE1 F:GLU1204 2.3 189.3 1.0
O F:THR1203 2.3 204.2 1.0
CG F:ASP1073 3.0 163.9 1.0
OD2 F:ASP1073 3.3 170.4 1.0
C F:THR1203 3.4 153.7 1.0
C F:SER1075 3.5 168.3 1.0
C F:ALA1070 3.5 128.9 1.0
CD F:GLU1204 3.6 145.4 1.0
N F:SER1075 3.8 132.9 1.0
O F:SER1089 4.0 197.2 1.0
CB F:GLU1204 4.0 153.5 1.0
CA F:SER1075 4.1 148.7 1.0
CA F:ILE1071 4.2 152.6 1.0
N F:GLU1204 4.2 143.0 1.0
CA F:GLU1204 4.2 155.5 1.0
N F:ASP1073 4.2 169.6 1.0
CB F:ASP1073 4.2 152.1 1.0
N F:ILE1071 4.3 146.4 1.0
CG F:GLU1204 4.3 137.6 1.0
CA F:THR1203 4.3 143.1 1.0
N F:GLY1074 4.4 141.0 1.0
CB F:SER1075 4.4 158.1 1.0
C F:ILE1071 4.4 151.3 1.0
CB F:THR1203 4.5 139.9 1.0
OE2 F:GLU1204 4.5 128.8 1.0
CA F:ALA1070 4.5 127.6 1.0
N F:THR1076 4.5 160.6 1.0
CA F:ASP1073 4.6 156.7 1.0
C F:ASP1073 4.7 148.3 1.0
CB F:ALA1070 4.8 111.3 1.0
O F:ILE1071 4.8 143.3 1.0
N F:LYS1072 4.8 142.0 1.0
CA F:THR1076 4.8 142.0 1.0
OG1 F:THR1203 4.9 143.6 1.0
C F:GLY1074 4.9 129.1 1.0

Reference:

O.V.Moroz, E.Blagova, A.A.Lebedev, F.Sanchez Rodriguez, D.J.Rigden, J.W.Tams, R.Wilting, J.K.Vester, E.Longhin, G.H.Hansen, K.B.R.M.Krogh, R.A.Pache, G.J.Davies, K.S.Wilson. Multitasking in the Gut: the X-Ray Structure of the Multidomain Bbgiii From Bifidobacterium Bifidum Offers Possible Explanations For Its Alternative Functions. Acta Crystallogr D Struct V. 77 1564 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 34866612
DOI: 10.1107/S2059798321010949
Page generated: Wed Jul 9 23:41:15 2025

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