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Calcium in PDB 5jy7: Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase

Enzymatic activity of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase

All present enzymatic activity of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase:
2.7.1.175; 3.2.1.1; 5.4.99.16;

Protein crystallography data

The structure of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase, PDB code: 5jy7 was solved by K.Futterer, A.A.Kermani, G.S.Besra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.90 / 3.60
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 315.680, 315.680, 124.950, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 28.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase (pdb code 5jy7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase, PDB code: 5jy7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5jy7

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Calcium binding site 1 out of 8 in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:20.0
occ:1.00
 OD1 A:ASN132 2.2 71.9 1.0
OD2 A:ASP200 2.4 75.6 1.0
O A:TYR234 2.6 74.1 1.0
O A:LEU235 2.6 78.5 1.0
OE2 A:GLU237 2.8 78.7 1.0
CG A:ASP200 3.2 75.5 1.0
OE1 A:GLU237 3.2 82.6 1.0
CG A:ASN132 3.4 69.9 1.0
CD A:GLU237 3.4 81.3 1.0
C A:LEU235 3.4 77.2 1.0
CB A:ASP200 3.5 77.8 1.0
C A:TYR234 3.6 72.5 1.0
CA A:LEU235 3.6 74.2 1.0
O A:LEU201 3.8 80.5 1.0
ND2 A:ASN132 3.9 69.5 1.0
N A:LEU235 4.0 72.4 1.0
O A:ASN132 4.1 72.5 1.0
OD1 A:ASP200 4.1 73.6 1.0
CA A:ASP200 4.5 76.9 1.0
CB A:ASN132 4.6 67.9 1.0
N A:PHE236 4.6 78.4 1.0
N A:LEU201 4.7 77.7 1.0
CD1 A:TRP191 4.7 81.8 1.0
NE1 A:TRP191 4.8 80.8 1.0
C A:ASN132 4.8 70.2 1.0
C A:ASP200 4.8 78.7 1.0
CA A:TYR234 4.8 70.6 1.0
CA A:ASN132 4.8 69.0 1.0
CG A:GLU237 4.9 83.3 1.0
CB A:TYR234 4.9 69.3 1.0
C A:LEU201 5.0 81.4 1.0

Calcium binding site 2 out of 8 in 5jy7

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Calcium binding site 2 out of 8 in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:20.0
occ:1.00
 O B:LEU235 2.4 50.9 1.0
OD1 B:ASN132 2.4 46.1 1.0
OD2 B:ASP200 2.6 47.7 1.0
O B:TYR234 2.7 47.7 1.0
OE2 B:GLU237 2.8 50.2 1.0
OE1 B:GLU237 3.1 52.7 1.0
C B:LEU235 3.3 50.3 1.0
CD B:GLU237 3.3 51.9 1.0
CG B:ASP200 3.3 47.4 1.0
CG B:ASN132 3.6 44.8 1.0
CB B:ASP200 3.6 48.9 1.0
CA B:LEU235 3.6 48.5 1.0
O B:LEU201 3.7 51.7 1.0
C B:TYR234 3.7 47.0 1.0
N B:LEU235 4.1 47.3 1.0
O B:ASN132 4.1 46.5 1.0
ND2 B:ASN132 4.2 44.2 1.0
OD1 B:ASP200 4.3 46.1 1.0
N B:PHE236 4.5 51.4 1.0
CA B:ASP200 4.6 48.4 1.0
N B:LEU201 4.7 49.4 1.0
CD1 B:TRP191 4.7 51.2 1.0
CB B:ASN132 4.8 43.8 1.0
C B:LEU201 4.8 52.1 1.0
CG B:GLU237 4.8 53.2 1.0
C B:ASP200 4.8 49.7 1.0
NE1 B:TRP191 4.8 50.8 1.0
C B:ASN132 4.9 45.1 1.0
CB B:LEU235 5.0 48.9 1.0
CA B:ASN132 5.0 44.6 1.0
CA B:TYR234 5.0 45.7 1.0

Calcium binding site 3 out of 8 in 5jy7

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Calcium binding site 3 out of 8 in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:20.0
occ:1.00
 O C:LEU235 2.4 52.0 1.0
OD2 C:ASP200 2.6 48.6 1.0
OE2 C:GLU237 2.6 51.8 1.0
OD1 C:ASN132 2.6 47.6 1.0
O C:TYR234 2.7 50.2 1.0
OE1 C:GLU237 2.9 53.0 1.0
CD C:GLU237 3.1 53.0 1.0
C C:LEU235 3.3 52.1 1.0
CG C:ASP200 3.3 47.8 1.0
CB C:ASP200 3.6 48.3 1.0
O C:LEU201 3.6 50.3 1.0
CA C:LEU235 3.7 50.7 1.0
C C:TYR234 3.8 50.1 1.0
CG C:ASN132 3.8 46.4 1.0
N C:LEU235 4.2 50.3 1.0
O C:ASN132 4.3 46.3 1.0
ND2 C:ASN132 4.4 45.9 1.0
OD1 C:ASP200 4.4 46.6 1.0
N C:PHE236 4.5 53.6 1.0
CD1 C:TRP191 4.6 51.3 1.0
CA C:ASP200 4.6 47.2 1.0
CG C:GLU237 4.6 54.6 1.0
NE1 C:TRP191 4.7 51.6 1.0
N C:LEU201 4.7 47.7 1.0
C C:LEU201 4.8 50.1 1.0
C C:ASP200 4.9 47.9 1.0
CA C:PHE236 5.0 55.2 1.0
CB C:ASN132 5.0 45.6 1.0

Calcium binding site 4 out of 8 in 5jy7

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Calcium binding site 4 out of 8 in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:20.0
occ:1.00
 OD2 D:ASP200 2.3 88.2 1.0
OD1 D:ASN132 2.4 86.3 1.0
O D:LEU235 2.8 95.1 1.0
O D:TYR234 2.8 91.0 1.0
OE2 D:GLU237 2.8 94.3 1.0
CG D:ASP200 3.0 86.7 1.0
OE1 D:GLU237 3.2 97.3 1.0
CB D:ASP200 3.2 88.2 1.0
CD D:GLU237 3.4 96.9 1.0
CG D:ASN132 3.4 83.8 1.0
C D:LEU235 3.7 95.0 1.0
O D:LEU201 3.7 92.7 1.0
C D:TYR234 3.9 90.4 1.0
CA D:LEU235 3.9 92.1 1.0
ND2 D:ASN132 4.0 82.6 1.0
O D:ASN132 4.0 84.3 1.0
OD1 D:ASP200 4.0 84.2 1.0
CA D:ASP200 4.2 86.2 1.0
N D:LEU235 4.3 90.9 1.0
N D:LEU201 4.5 87.6 1.0
CD1 D:TRP191 4.5 93.5 1.0
C D:ASP200 4.6 87.9 1.0
NE1 D:TRP191 4.7 93.8 1.0
CB D:ASN132 4.7 82.1 1.0
C D:LEU201 4.7 92.4 1.0
C D:ASN132 4.8 82.3 1.0
N D:PHE236 4.8 97.6 1.0
CA D:ASN132 4.9 82.6 1.0
CG D:GLU237 4.9 99.6 1.0

Calcium binding site 5 out of 8 in 5jy7

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Calcium binding site 5 out of 8 in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca601

b:20.0
occ:1.00
 O E:LEU235 2.4 0.7 1.0
O E:LEU201 2.7 0.5 1.0
OD1 E:ASN132 2.7 0.3 1.0
C E:LEU235 3.3 0.1 1.0
CA E:LEU235 3.5 0.6 1.0
O E:ASN132 3.5 0.3 1.0
O E:TYR234 3.6 0.1 1.0
OD2 E:ASP200 3.6 0.2 1.0
OE1 E:GLU237 3.8 0.3 1.0
CG E:ASN132 3.8 0.2 1.0
C E:LEU201 3.8 0.0 1.0
CD1 E:TYR203 3.9 0.2 1.0
CB E:ASP200 3.9 0.5 1.0
OE2 E:GLU237 4.0 0.7 1.0
N E:LEU201 4.0 0.5 1.0
CG E:ASP200 4.0 0.9 1.0
C E:TYR234 4.3 0.7 1.0
N E:LEU235 4.3 0.8 1.0
CD E:GLU237 4.3 0.6 1.0
CE1 E:TYR203 4.4 0.6 1.0
C E:ASN132 4.4 0.2 1.0
CA E:LEU201 4.4 0.6 1.0
CA E:ASN132 4.5 0.0 1.0
C E:ASP200 4.5 0.0 1.0
CB E:LEU235 4.5 0.7 1.0
N E:PHE236 4.5 0.2 1.0
CA E:ASP200 4.6 1.0 1.0
CB E:ASN132 4.7 0.6 1.0
ND2 E:ASN132 4.7 0.0 1.0
CB E:LEU201 4.8 0.8 1.0
CD2 E:LEU235 4.8 0.8 1.0
CG E:TYR203 4.9 0.8 1.0
N E:TYR203 4.9 0.7 1.0
N E:ASN202 4.9 0.6 1.0
OD1 E:ASP200 5.0 1.0 1.0

Calcium binding site 6 out of 8 in 5jy7

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Calcium binding site 6 out of 8 in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca601

b:20.0
occ:1.00
 CE1 F:PHE236 2.6 0.1 1.0
CD1 F:PHE236 2.8 0.4 1.0
CD1 F:LEU235 3.1 0.8 1.0
CB F:LEU235 3.3 0.2 1.0
CD2 F:TYR203 3.4 0.4 1.0
CB F:PHE252 3.4 0.7 1.0
CZ F:PHE236 3.6 0.5 1.0
CG F:TYR203 3.6 0.0 1.0
CG F:LEU235 3.7 0.8 1.0
CB F:TYR203 3.7 0.5 1.0
CG F:PHE252 3.8 1.0 1.0
CA F:THR249 3.9 0.1 1.0
CG F:PHE236 3.9 0.0 1.0
CD2 F:PHE252 3.9 0.3 1.0
CE2 F:TYR203 4.1 0.1 1.0
O F:GLU248 4.1 0.3 1.0
O F:THR249 4.3 0.1 1.0
N F:PHE236 4.4 0.1 1.0
CD1 F:TYR203 4.5 0.1 1.0
CD1 F:PHE252 4.6 0.6 1.0
CD2 F:LEU235 4.6 0.2 1.0
CA F:LEU235 4.6 0.9 1.0
CE2 F:PHE236 4.6 0.2 1.0
N F:THR249 4.6 0.1 1.0
C F:THR249 4.6 0.7 1.0
OG1 F:THR249 4.6 0.9 1.0
C F:GLU248 4.7 0.9 1.0
C F:LEU235 4.7 0.8 1.0
CD2 F:PHE236 4.7 0.5 1.0
CB F:THR249 4.7 0.1 1.0
CB F:PHE236 4.8 0.4 1.0
CA F:PHE252 4.9 0.8 1.0
CG2 F:THR249 4.9 0.1 1.0
CE2 F:PHE252 4.9 0.2 1.0
CZ F:TYR203 4.9 0.3 1.0

Calcium binding site 7 out of 8 in 5jy7

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Calcium binding site 7 out of 8 in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca601

b:20.0
occ:1.00
 O G:LEU235 2.6 0.8 1.0
OE1 G:GLU237 2.7 0.5 1.0
OD2 G:ASP200 2.7 0.3 1.0
OE2 G:GLU237 2.9 0.0 1.0
OD1 G:ASN132 3.1 0.5 1.0
CD G:GLU237 3.2 0.3 1.0
O G:LEU201 3.2 0.6 1.0
CB G:ASP200 3.3 0.5 1.0
CG G:ASP200 3.3 0.4 1.0
O G:TYR234 3.3 0.9 1.0
C G:LEU235 3.7 0.7 1.0
CA G:LEU235 4.1 0.8 1.0
CG G:ASN132 4.2 0.6 1.0
CA G:ASP200 4.3 0.7 1.0
C G:LEU201 4.3 0.1 1.0
O G:ASN132 4.3 0.3 1.0
N G:LEU201 4.4 0.4 1.0
C G:TYR234 4.4 0.0 1.0
CD1 G:TRP191 4.4 0.4 1.0
C G:ASP200 4.4 1.0 1.0
OD1 G:ASP200 4.5 0.6 1.0
NE1 G:TRP191 4.7 0.5 1.0
CG G:GLU237 4.7 0.2 1.0
ND2 G:ASN132 4.7 0.1 1.0
CG2 G:VAL157 4.7 0.1 1.0
N G:LEU235 4.8 0.3 1.0
N G:PHE236 4.8 0.4 1.0
CA G:LEU201 5.0 0.8 1.0

Calcium binding site 8 out of 8 in 5jy7

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Calcium binding site 8 out of 8 in the Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Complex of Mycobacterium Smegmatis Trehalose Synthase with Maltokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca601

b:20.0
occ:1.00
 O H:LEU201 2.5 0.0 1.0
OD1 H:ASN132 2.7 0.1 1.0
O H:ASN132 2.9 0.2 1.0
O H:LEU235 3.0 0.0 1.0
CD1 H:TYR203 3.4 0.5 1.0
C H:LEU201 3.5 0.5 1.0
N H:LEU201 3.5 0.3 1.0
CA H:LEU235 3.7 0.3 1.0
CG H:ASN132 3.7 0.5 1.0
C H:LEU235 3.8 0.3 1.0
CE1 H:TYR203 3.8 0.9 1.0
C H:ASN132 3.8 0.5 1.0
CA H:ASN132 3.9 0.1 1.0
CA H:LEU201 3.9 0.2 1.0
OD2 H:ASP200 4.0 0.3 1.0
CB H:ASP200 4.1 0.8 1.0
CB H:LEU201 4.1 0.4 1.0
O H:TYR234 4.1 0.5 1.0
C H:ASP200 4.2 0.8 1.0
CG H:ASP200 4.2 0.5 1.0
CB H:ASN132 4.4 0.4 1.0
CA H:ASP200 4.4 0.9 1.0
CD2 H:LEU235 4.5 1.0 1.0
CG H:TYR203 4.6 0.6 1.0
CB H:LEU235 4.6 0.3 1.0
OE1 H:GLU237 4.6 0.9 1.0
N H:LEU235 4.6 0.1 1.0
ND2 H:ASN132 4.7 0.1 1.0
N H:ASN202 4.7 0.0 1.0
C H:TYR234 4.8 0.1 1.0
OE2 H:GLU237 4.8 0.5 1.0
N H:TYR203 4.8 0.8 1.0
CB H:TYR203 5.0 0.0 1.0

Reference:

A.A.Kermani, R.Roy, C.Gopalasingam, K.I.Kocurek, T.R.Patel, L.J.Alderwick, G.S.Besra, K.Futterer. Crystal Structure of the Tres-PEP2 Complex, Initiating Alpha-Glucan Synthesis in the Glge Pathway of Mycobacteria. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 30877199
DOI: 10.1074/JBC.RA118.004297
Page generated: Mon Jul 15 06:38:48 2024

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