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Magnesium in PDB 5x7o: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase

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

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

Protein crystallography data

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, PDB code: 5x7o was solved by Z.Fujimoto, N.Suzuki, N.Kishine, 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) 152.48 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 184.159, 271.934, 133.998, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.9

Other elements in 5x7o:

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

Nickel (Ni) 2 atoms
Calcium (Ca) 6 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase (pdb code 5x7o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, PDB code: 5x7o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 5x7o

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Magnesium binding site 1 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:33.2
occ:1.00
 O B:HOH2537 2.0 37.0 1.0
O A:GLY285 2.1 36.8 1.0
O B:HOH2358 2.1 32.3 1.0
OE2 A:GLU290 2.1 35.5 0.7
OE1 B:GLN571 2.1 32.4 1.0
OE2 A:GLU283 2.3 32.0 1.0
CD A:GLU290 3.1 40.0 0.7
CD B:GLN571 3.2 32.7 1.0
C A:GLY285 3.3 33.9 1.0
CD A:GLU283 3.4 33.0 1.0
OE1 A:GLU290 3.5 43.9 0.7
NE2 B:GLN571 3.6 31.4 1.0
CG A:GLU283 3.9 31.9 1.0
O B:HOH2585 4.2 52.6 1.0
CA A:GLY285 4.2 34.2 1.0
N A:ILE286 4.3 34.0 1.0
O B:GLN570 4.3 31.8 1.0
OE1 A:GLU283 4.4 32.6 1.0
CG A:GLU290 4.4 38.2 0.7
CA A:ILE286 4.4 33.6 1.0
O A:TRP284 4.5 28.4 1.0
OD1 B:ASN569 4.5 34.9 1.0
CG B:GLN571 4.5 31.5 1.0
OE1 A:GLU290 4.6 31.5 0.3
CB A:ILE286 4.6 33.1 1.0
NE2 A:HIS294 4.6 37.0 1.0
CA B:ASN569 4.7 34.0 1.0
C B:ASN569 4.9 35.3 1.0
N A:GLY285 4.9 31.1 1.0
C A:TRP284 4.9 30.4 1.0

Magnesium binding site 2 out of 15 in 5x7o

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Magnesium binding site 2 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:39.0
occ:1.00
 O A:HOH2383 1.9 40.8 1.0
O A:HOH2359 2.0 38.5 1.0
O A:HOH2914 2.0 41.8 1.0
O A:HOH2277 2.1 40.3 1.0
O A:HOH2948 2.1 40.5 1.0
O A:HOH2065 2.1 37.9 1.0
O A:HOH2241 3.9 54.4 1.0
O A:HOH2365 4.0 41.7 1.0
O A:VAL69 4.2 37.3 1.0
O A:TRP99 4.2 42.2 1.0
O A:ASP100 4.2 44.1 1.0
O A:HOH2657 4.3 37.4 1.0
OD2 A:ASP49 4.4 46.8 1.0
CB A:TRP99 4.6 41.3 1.0
O A:LEU70 4.7 32.4 1.0
CA A:ALA101 4.7 44.9 1.0
C A:ASP100 4.8 46.6 1.0
CB A:ASP49 4.8 46.3 1.0
CA A:LEU70 4.8 34.2 1.0
OD2 A:ASP68 4.9 60.0 1.0
C A:TRP99 4.9 44.6 1.0
N A:ALA101 4.9 45.0 1.0
CD2 A:LEU70 5.0 37.1 1.0

Magnesium binding site 3 out of 15 in 5x7o

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Magnesium binding site 3 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:60.5
occ:1.00
 O A:HOH2892 1.9 54.7 1.0
O A:HOH2063 2.0 50.0 1.0
O A:HOH2889 2.0 60.2 1.0
O A:HOH2913 2.2 91.3 1.0
O A:HOH2556 2.2 60.0 1.0
O A:HOH2034 2.7 40.3 1.0
O A:GLU152 3.9 39.4 1.0
OD1 A:ASP153 4.2 45.6 1.0
O A:HOH2425 4.2 42.4 1.0
O A:LYS243 4.4 36.4 1.0
O A:HOH2170 4.5 40.1 1.0
C A:GLU152 4.6 41.5 1.0
CD2 A:TYR231 4.9 31.4 1.0
CB A:GLU152 5.0 44.8 1.0

Magnesium binding site 4 out of 15 in 5x7o

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Magnesium binding site 4 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:84.6
occ:1.00
 O A:HOH2971 2.0 75.4 1.0
O A:HOH2290 2.0 54.1 1.0
O A:HOH2833 2.4 44.3 1.0
O A:HOH2560 2.4 66.3 1.0
O A:HOH2936 2.5 80.0 1.0
O A:HOH2979 2.8 65.1 1.0
O A:HOH2770 3.9 46.7 1.0
OD1 A:ASN164 4.2 26.9 1.0
ND2 A:ASN183 4.3 31.9 1.0
O A:THR162 4.4 33.4 1.0
O A:HOH2265 4.6 38.3 1.0
O A:HOH2635 4.8 33.5 1.0
CA A:THR162 4.9 34.0 1.0
C A:THR162 5.0 34.1 1.0

Magnesium binding site 5 out of 15 in 5x7o

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Magnesium binding site 5 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:65.3
occ:1.00
 O A:HOH2270 1.9 55.9 1.0
O A:HOH2890 1.9 65.1 1.0
O A:HOH2852 2.1 52.9 1.0
O A:HOH2887 2.2 52.0 1.0
O A:HOH2204 2.2 56.3 1.0
O A:HOH2974 2.3 60.0 1.0
O A:HOH2025 3.9 39.2 1.0
OE2 A:GLU347 4.1 60.6 1.0
OD2 A:ASP296 4.1 40.3 1.0
OD1 A:ASP296 4.1 37.2 1.0
CG A:ASP296 4.6 37.0 1.0
O A:HOH2935 4.8 53.2 1.0
CB A:GLU292 4.8 36.6 1.0
OE1 A:GLU292 4.9 40.5 1.0
CD A:GLU292 5.0 42.1 1.0
CG A:GLU292 5.0 38.0 1.0
CD A:GLU347 5.0 54.9 1.0

Magnesium binding site 6 out of 15 in 5x7o

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Magnesium binding site 6 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:48.4
occ:1.00
 O A:HOH2596 1.9 38.6 1.0
O A:HOH2842 1.9 43.9 1.0
O A:HOH2416 2.1 40.8 1.0
O A:HOH2459 2.2 43.0 1.0
O A:HOH2310 2.2 41.0 1.0
OD2 A:ASP316 2.2 37.0 1.0
CG A:ASP316 3.2 37.5 1.0
OD1 A:ASP316 3.5 38.2 1.0
OG1 A:THR329 4.1 37.0 1.0
OE1 A:GLU319 4.1 43.8 1.0
NE A:ARG326 4.2 42.2 1.0
O A:TRP327 4.5 33.6 1.0
CB A:ASP316 4.5 35.9 1.0
N A:THR329 4.6 35.8 1.0
O A:HOH2040 4.7 54.9 1.0
OD2 A:ASP330 4.7 48.7 1.0
CD A:ARG326 4.8 40.5 1.0
OE2 A:GLU319 4.9 45.3 1.0
CD A:GLU319 4.9 41.2 1.0
NH2 A:ARG326 4.9 41.1 1.0
CA A:ASN328 5.0 32.6 1.0

Magnesium binding site 7 out of 15 in 5x7o

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Magnesium binding site 7 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:74.5
occ:1.00
 O A:HOH2296 1.9 63.7 1.0
O A:HOH2692 2.1 62.0 1.0
O A:HOH2740 2.2 57.6 1.0
O A:HOH2968 2.2 66.8 1.0
O A:HOH2119 2.3 53.9 1.0
O A:HOH2835 2.8 63.4 1.0
NH2 A:ARG1173 3.9 35.4 1.0
O A:HOH2679 4.0 45.3 1.0
OD2 A:ASP1134 4.0 33.6 1.0
O A:HOH2624 4.0 50.9 1.0
NE A:ARG1173 4.3 33.1 1.0
O A:HOH2376 4.3 36.2 1.0
CZ A:ARG1173 4.4 32.9 1.0
OE2 A:GLU1274 4.4 36.3 1.0
OE1 A:GLU1274 4.4 43.0 1.0
OD2 A:ASP684 4.7 39.6 1.0
CG A:ASP1134 4.8 30.0 1.0
CD A:GLU1274 4.8 37.7 1.0
CB A:ASP1134 4.9 28.5 1.0

Magnesium binding site 8 out of 15 in 5x7o

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Magnesium binding site 8 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:64.9
occ:1.00
 O A:HOH2976 2.0 53.9 1.0
O A:HOH2901 2.2 53.2 1.0
O A:HOH2233 2.2 37.8 1.0
O A:HOH2977 2.2 72.6 1.0
O A:HOH2672 2.3 65.8 1.0
O A:HOH2978 2.4 54.9 1.0
OD2 A:ASP889 4.1 44.9 1.0
OD1 A:ASP889 4.2 45.5 1.0
O A:HOH2921 4.2 52.7 1.0
O A:HOH2920 4.4 42.2 1.0
O A:HOH2912 4.5 36.0 1.0
CG A:LYS887 4.5 38.9 1.0
CG A:ASP889 4.5 42.2 1.0
CD A:LYS887 4.5 40.8 1.0

Magnesium binding site 9 out of 15 in 5x7o

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Magnesium binding site 9 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1607

b:27.7
occ:1.00
 OE2 B:GLU290 2.0 31.7 0.7
O B:HOH2456 2.1 37.8 1.0
O B:GLY285 2.1 33.0 1.0
O A:HOH2511 2.2 26.6 1.0
OE1 A:GLN571 2.3 33.8 1.0
OE2 B:GLU283 2.3 29.9 1.0
CD B:GLU290 3.1 36.2 0.7
CD A:GLN571 3.3 32.5 1.0
CD B:GLU283 3.3 30.4 1.0
C B:GLY285 3.3 33.6 1.0
OE1 B:GLU290 3.5 37.9 0.7
NE2 A:GLN571 3.6 30.4 1.0
CG B:GLU283 3.8 30.9 1.0
O B:HOH2297 4.0 57.7 1.0
CA B:GLY285 4.2 32.6 1.0
N B:ILE286 4.3 32.3 1.0
OE1 B:GLU283 4.3 32.6 1.0
CA B:ILE286 4.4 33.5 1.0
O A:GLN570 4.4 31.1 1.0
O A:HOH2732 4.4 49.9 1.0
CG B:GLU290 4.4 34.9 0.7
OD1 A:ASN569 4.5 34.2 1.0
O B:TRP284 4.5 32.4 1.0
NE2 B:HIS294 4.5 32.0 1.0
CB B:ILE286 4.5 34.2 1.0
CG A:GLN571 4.6 30.9 1.0
OE1 B:GLU290 4.8 33.1 0.3
CA A:ASN569 4.8 32.8 1.0
N B:GLY285 5.0 31.1 1.0
C A:ASN569 5.0 32.8 1.0
C B:TRP284 5.0 31.9 1.0

Magnesium binding site 10 out of 15 in 5x7o

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Magnesium binding site 10 out of 15 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:61.3
occ:1.00
 O B:HOH2975 2.0 82.2 1.0
O B:HOH2972 2.1 47.8 1.0
O B:HOH2083 2.1 75.9 1.0
O B:HOH2239 2.2 37.1 1.0
O B:HOH2974 2.3 57.5 1.0
O B:HOH2913 2.3 49.5 1.0
O B:HOH2932 4.0 48.5 1.0
OD2 B:ASP889 4.1 51.0 1.0
OD1 B:ASP889 4.3 49.1 1.0
O B:HOH2923 4.4 37.6 1.0
CD B:LYS887 4.5 40.6 1.0
CG B:ASP889 4.6 47.5 1.0
CG B:LYS887 4.6 41.2 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 Sep 30 09:02:19 2024

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