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Magnesium in PDB 5x7s: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative

Enzymatic activity of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative

All present enzymatic activity of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative:
3.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative, PDB code: 5x7s was solved by Z.Fujimoto, N.Kishine, N.Suzuki, M.Momma, H.Ichinose, A.Kimura, K.Funane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 151.54 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 182.815, 270.920, 133.341, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.9

Other elements in 5x7s:

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Terbium (Tb) 7 atoms
Calcium (Ca) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative (pdb code 5x7s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative, PDB code: 5x7s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5x7s

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Magnesium binding site 1 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:50.6
occ:1.00
 O A:HOH2167 1.9 48.1 1.0
O A:HOH2543 1.9 43.7 1.0
O A:HOH2277 2.1 44.9 1.0
O A:HOH2536 2.1 46.2 1.0
O A:HOH2048 2.1 53.6 1.0
O A:HOH2222 2.3 51.9 1.0
O A:VAL69 4.1 46.0 1.0
OD2 A:ASP49 4.2 53.1 1.0
O A:HOH2390 4.3 52.4 1.0
O A:ASP100 4.3 58.5 1.0
O A:TRP99 4.4 47.8 1.0
CB A:ASP49 4.7 52.9 1.0
OD2 A:ASP68 4.8 87.6 1.0
CA A:ALA101 4.8 56.8 1.0
CB A:TRP99 4.9 55.3 1.0
CA A:LEU70 4.9 44.3 1.0
C A:ASP100 4.9 58.4 1.0
CD2 A:LEU70 4.9 48.4 1.0
O A:LEU70 5.0 42.5 1.0
CG A:ASP49 5.0 55.1 1.0

Magnesium binding site 2 out of 7 in 5x7s

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Magnesium binding site 2 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:63.2
occ:1.00
 O A:HOH2544 1.7 64.4 1.0
O A:HOH2542 1.9 66.7 1.0
O A:HOH2095 2.2 54.8 1.0
O A:HOH2004 2.3 45.5 1.0
O A:HOH2158 2.3 78.1 1.0
O A:HOH2530 3.1 83.2 1.0
O A:GLU152 4.1 59.4 1.0
O A:LYS243 4.1 49.4 1.0
O A:HOH2328 4.4 47.6 1.0
OD1 A:ASP153 4.4 63.2 1.0
O A:THR244 4.6 55.0 1.0
CA A:THR244 4.7 51.7 1.0
O A:HOH2178 4.7 43.4 1.0
CD2 A:TYR231 4.9 41.0 1.0
C A:GLU152 4.9 57.8 1.0

Magnesium binding site 3 out of 7 in 5x7s

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Magnesium binding site 3 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:95.0
occ:1.00
 O A:HOH2552 1.8 57.7 1.0
O A:HOH2276 1.9 58.4 1.0
O A:HOH2452 2.1 56.0 1.0
O A:HOH2261 2.2 51.0 1.0
O A:HOH2482 2.2 69.6 1.0
O A:HOH2421 2.4 49.3 1.0
OE2 A:GLU347 3.8 81.9 1.0
OD1 A:ASP296 4.1 36.2 1.0
OD2 A:ASP296 4.3 50.2 1.0
CG A:ASP296 4.7 47.0 1.0
CD A:GLU347 4.7 78.2 1.0
OE1 A:GLU347 4.7 78.6 1.0
CB A:GLU292 4.9 49.0 1.0

Magnesium binding site 4 out of 7 in 5x7s

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Magnesium binding site 4 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:56.1
occ:1.00
 O A:HOH2383 1.8 46.0 1.0
O A:HOH2232 1.9 45.8 1.0
O A:HOH2504 2.0 51.8 1.0
O A:HOH2230 2.1 46.1 1.0
OD2 A:ASP316 2.2 44.9 1.0
O A:HOH2243 2.3 56.9 1.0
CG A:ASP316 3.2 46.7 1.0
OD1 A:ASP316 3.6 42.3 1.0
OE1 A:GLU319 4.0 50.8 1.0
NE A:ARG326 4.2 53.2 1.0
CB A:ASP316 4.4 46.6 1.0
OG1 A:THR329 4.5 45.0 1.0
OD2 A:ASP330 4.6 59.8 1.0
O A:TRP327 4.6 52.4 1.0
N A:THR329 4.7 44.5 1.0
NH2 A:ARG326 4.8 49.9 1.0
O A:HOH2303 4.9 53.6 1.0
CD A:GLU319 4.9 51.6 1.0
CD A:ARG326 4.9 53.8 1.0
CZ A:ARG326 4.9 54.3 1.0
OE2 A:GLU319 4.9 63.5 1.0

Magnesium binding site 5 out of 7 in 5x7s

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Magnesium binding site 5 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:57.4
occ:1.00
 O B:HOH2267 1.9 58.5 1.0
O B:HOH2575 2.0 58.0 1.0
O B:HOH2042 2.0 56.8 1.0
O B:HOH2562 2.1 41.1 1.0
O B:HOH2056 2.1 55.1 1.0
O B:HOH2045 2.2 37.4 1.0
O B:HOH2243 4.0 48.9 1.0
O B:VAL69 4.1 60.5 1.0
O B:ASP100 4.1 62.4 1.0
O B:TRP99 4.1 54.6 1.0
OD2 B:ASP49 4.3 55.0 1.0
CA B:ALA101 4.6 63.3 1.0
CB B:ASP49 4.6 63.2 1.0
O B:LEU70 4.7 46.4 1.0
CB B:TRP99 4.7 61.1 1.0
C B:ASP100 4.7 67.1 1.0
CA B:LEU70 4.7 52.7 1.0
N B:ALA101 4.8 65.7 1.0
CD2 B:LEU70 4.9 59.7 1.0
C B:TRP99 4.9 60.6 1.0
O B:HOH2501 4.9 54.1 1.0
CG B:ASP49 4.9 60.9 1.0
OD1 B:ASP68 4.9 85.8 1.0

Magnesium binding site 6 out of 7 in 5x7s

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Magnesium binding site 6 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1602

b:58.7
occ:1.00
 O B:HOH2567 1.7 50.8 1.0
O B:HOH2242 1.9 54.0 1.0
O B:HOH2187 2.1 56.4 1.0
O B:HOH2544 2.2 73.2 1.0
O B:HOH2551 2.3 73.2 1.0
O B:HOH2012 2.6 46.9 1.0
O B:GLU152 4.0 48.6 1.0
OD1 B:ASP153 4.0 66.9 1.0
O B:LYS243 4.5 45.7 1.0
C B:GLU152 4.7 61.2 1.0
CD2 B:TYR231 4.8 45.1 1.0
CA B:ASP153 5.0 61.6 1.0

Magnesium binding site 7 out of 7 in 5x7s

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Magnesium binding site 7 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1603

b:41.3
occ:1.00
 O B:HOH2479 1.9 46.5 1.0
O B:HOH2257 1.9 49.5 1.0
O B:HOH2134 2.1 47.9 1.0
O B:HOH2111 2.2 40.4 1.0
O B:HOH2164 2.2 47.4 1.0
OD2 B:ASP316 2.3 51.3 1.0
CG B:ASP316 3.1 50.0 1.0
OD1 B:ASP316 3.2 42.5 1.0
OG1 B:THR329 3.9 45.1 1.0
OE1 B:GLU319 4.1 50.1 1.0
NE B:ARG326 4.2 56.0 1.0
O B:TRP327 4.4 47.2 1.0
OD2 B:ASP330 4.4 51.8 1.0
CB B:ASP316 4.5 54.1 1.0
N B:THR329 4.5 46.8 1.0
NH2 B:ARG326 4.6 62.0 1.0
CA B:ASN328 4.8 44.5 1.0
CZ B:ARG326 4.9 58.6 1.0
OE2 B:GLU319 5.0 58.1 1.0
CD B:GLU319 5.0 47.6 1.0
O B:HOH2554 5.0 40.3 1.0

Reference:

Z.Fujimoto, N.Suzuki, N.Kishine, H.Ichinose, M.Momma, A.Kimura, K.Funane. Carbohydrate-Binding Architecture of the Multi-Modular Alpha-1,6-Glucosyltransferase From Paenibacillus Sp. 598K, Which Produces Alpha-1,6-Glucosyl-Alpha-Glucosaccharides From Starch Biochem. J. V. 474 2763 2017.
ISSN: ESSN 1470-8728
PubMed: 28698247
DOI: 10.1042/BCJ20170152
Page generated: Mon Dec 14 21:26:39 2020

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