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Magnesium in PDB 5x7r: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose

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

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

Protein crystallography data

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose, PDB code: 5x7r 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) 152.46 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 184.333, 271.260, 133.928, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.8

Other elements in 5x7r:

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

Nickel (Ni) 4 atoms
Calcium (Ca) 6 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose (pdb code 5x7r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose, PDB code: 5x7r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in 5x7r

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Magnesium binding site 1 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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

b:31.8
occ:1.00
 O A:HOH2286 2.0 35.0 1.0
OE2 A:GLU283 2.1 29.2 1.0
OE1 B:GLN571 2.1 28.0 1.0
O A:GLY285 2.1 35.2 1.0
O A:HOH2378 2.2 28.8 1.0
O A:HOH2056 2.3 35.1 1.0
CD B:GLN571 3.1 27.8 1.0
CD A:GLU283 3.2 26.9 1.0
C A:GLY285 3.4 32.6 1.0
NE2 B:GLN571 3.5 28.1 1.0
CG A:GLU283 3.7 25.9 1.0
OE1 A:GLU290 4.0 46.2 1.0
O B:HOH2772 4.2 46.0 1.0
OE1 A:GLU283 4.2 26.5 1.0
CA A:GLY285 4.2 30.4 1.0
OD1 B:ASN569 4.3 41.0 1.0
N A:ILE286 4.3 31.4 1.0
O A:TRP284 4.4 24.0 1.0
O B:GLN570 4.4 31.3 1.0
CA A:ILE286 4.5 30.6 1.0
CG B:GLN571 4.5 28.8 1.0
CA B:ASN569 4.6 31.6 1.0
NE2 A:HIS294 4.6 32.9 1.0
CB A:ILE286 4.6 30.6 1.0
C B:ASN569 4.7 31.0 1.0
O B:ASN569 4.9 34.3 1.0
C A:TRP284 4.9 26.5 1.0
N A:GLY285 4.9 27.1 1.0

Magnesium binding site 2 out of 20 in 5x7r

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Magnesium binding site 2 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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

b:28.3
occ:1.00
 OE1 A:GLN654 1.9 52.7 1.0
ND1 A:HIS678 2.2 29.5 1.0
O A:HOH2287 2.2 46.0 1.0
O A:HOH2712 2.5 24.8 1.0
O A:HOH2005 2.6 31.8 1.0
CE1 A:HIS678 3.0 30.8 1.0
CD A:GLN654 3.0 46.6 1.0
CG A:HIS678 3.3 28.4 1.0
NE2 A:GLN654 3.6 50.3 1.0
CB A:HIS678 3.8 28.2 1.0
O A:HOH2659 3.9 48.1 1.0
CG A:LYS998 4.1 43.9 1.0
OG A:SER652 4.1 24.0 1.0
NE2 A:HIS678 4.2 29.3 1.0
CG A:GLN654 4.2 38.8 1.0
CD2 A:HIS678 4.4 28.6 1.0
CA A:HIS678 4.5 26.9 1.0
CA A:LYS998 4.5 31.8 1.0
CB A:SER652 4.7 23.6 1.0
CB A:LYS998 4.7 37.0 1.0
CD A:LYS998 4.9 52.0 1.0
O A:LYS653 5.0 26.5 1.0

Magnesium binding site 3 out of 20 in 5x7r

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Magnesium binding site 3 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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

b:43.4
occ:1.00
 O A:HOH2168 1.9 35.5 1.0
O A:HOH2588 1.9 41.1 1.0
O A:HOH2298 2.0 42.4 1.0
O A:HOH2105 2.1 41.3 1.0
O A:HOH2793 2.2 35.9 1.0
O A:HOH2072 2.3 39.5 1.0
O A:VAL69 4.0 37.5 1.0
O A:HOH2526 4.0 44.8 1.0
O A:HOH2825 4.1 52.3 1.0
OD2 A:ASP49 4.3 41.6 1.0
O A:ASP100 4.3 47.8 1.0
O A:HOH2709 4.4 40.5 1.0
O A:TRP99 4.4 42.8 1.0
O4 A:SO41701 4.5 78.2 1.0
O1 A:SO41701 4.6 82.8 1.0
CB A:ASP49 4.7 43.5 1.0
O A:LEU70 4.7 34.7 1.0
CA A:ALA101 4.7 44.6 1.0
CA A:LEU70 4.8 36.5 1.0
O2 A:SO41701 4.8 81.2 1.0
CB A:TRP99 4.9 42.1 1.0
C A:ASP100 4.9 47.2 1.0
S A:SO41701 4.9 84.1 1.0
CG A:ASP49 5.0 41.9 1.0
C A:VAL69 5.0 39.2 1.0

Magnesium binding site 4 out of 20 in 5x7r

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Magnesium binding site 4 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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

b:57.3
occ:1.00
 O A:HOH2791 1.9 51.2 1.0
O A:HOH2716 2.1 68.7 1.0
O A:HOH2581 2.1 52.3 1.0
OD1 A:ASP153 2.2 50.7 1.0
O A:HOH2617 2.3 72.8 1.0
O A:HOH2023 2.6 48.2 1.0
CG A:ASP153 3.3 50.2 1.0
OD2 A:ASP153 3.8 53.4 1.0
O A:GLU152 3.8 40.1 1.0
O A:HOH2683 4.2 52.2 1.0
O A:LYS243 4.3 35.6 1.0
C A:GLU152 4.5 40.4 1.0
CD2 A:TYR231 4.6 31.9 1.0
CB A:ASP153 4.6 44.8 1.0
O A:HOH2604 4.7 45.9 1.0
CA A:ASP153 4.9 41.5 1.0
CE2 A:TYR231 4.9 31.3 1.0
O A:THR244 4.9 37.0 1.0

Magnesium binding site 5 out of 20 in 5x7r

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Magnesium binding site 5 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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

b:53.8
occ:1.00
 O A:HOH2828 2.0 54.2 1.0
O A:HOH2477 2.0 45.4 1.0
O A:HOH2740 2.1 39.8 1.0
O A:HOH2786 2.2 48.2 1.0
O A:HOH2579 2.3 59.4 1.0
O A:HOH2823 2.3 50.6 1.0
OD1 A:ASN164 4.1 28.1 1.0
ND2 A:ASN183 4.2 30.6 1.0
O A:HOH2278 4.4 36.1 1.0
O A:THR162 4.5 35.2 1.0
O A:HOH2558 4.8 37.4 1.0
CA A:THR162 5.0 34.9 1.0

Magnesium binding site 6 out of 20 in 5x7r

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Magnesium binding site 6 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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

b:67.5
occ:1.00
 O A:HOH2364 2.0 50.0 1.0
O A:HOH2795 2.0 70.8 1.0
O A:HOH2762 2.1 52.8 1.0
O A:HOH2821 2.1 61.5 1.0
O A:HOH2576 2.2 62.1 1.0
O A:HOH2212 2.2 51.6 1.0
OE2 A:GLU347 3.7 60.1 1.0
O A:HOH2282 4.0 39.8 1.0
OD1 A:ASP296 4.2 31.9 1.0
OD2 A:ASP296 4.3 32.9 1.0
CD A:GLU347 4.7 54.8 1.0
CG A:ASP296 4.7 31.3 1.0
OE1 A:GLU347 4.9 61.4 1.0

Magnesium binding site 7 out of 20 in 5x7r

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Magnesium binding site 7 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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

b:34.3
occ:1.00
 O A:HOH2447 2.0 31.0 1.0
O A:HOH2532 2.0 36.2 1.0
O A:HOH2766 2.0 35.0 1.0
O A:HOH2259 2.1 35.0 1.0
OD2 A:ASP316 2.1 31.7 1.0
O A:HOH2331 2.1 33.0 1.0
CG A:ASP316 3.1 33.4 1.0
OD1 A:ASP316 3.3 33.5 1.0
OG1 A:THR329 4.1 31.7 1.0
OE1 A:GLU319 4.1 40.1 1.0
NE A:ARG326 4.1 38.6 1.0
OD2 A:ASP330 4.4 40.4 1.0
CB A:ASP316 4.4 31.4 1.0
N A:THR329 4.4 30.5 1.0
O A:TRP327 4.4 31.9 1.0
CD A:ARG326 4.7 38.7 1.0
CA A:ASN328 4.8 29.7 1.0
CD A:GLU319 4.9 38.8 1.0
NH2 A:ARG326 4.9 38.4 1.0
OE2 A:GLU319 4.9 44.3 1.0
CZ A:ARG326 5.0 38.7 1.0

Magnesium binding site 8 out of 20 in 5x7r

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Magnesium binding site 8 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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 Complexed with Isomaltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:39.8
occ:1.00
 O A:HOH2024 1.8 33.8 1.0
OD2 A:ASP1183 2.0 42.6 1.0
O A:HOH2462 2.1 43.3 1.0
OD2 A:ASP376 2.2 38.6 1.0
O A:HOH2094 2.2 40.1 1.0
O A:HOH2666 2.3 48.5 1.0
CG A:ASP1183 3.0 41.7 1.0
CG A:ASP376 3.0 36.5 1.0
OD1 A:ASP376 3.3 35.9 1.0
OD1 A:ASP1183 3.3 40.8 1.0
NI A:NI1502 3.6 43.3 1.0
O A:HOH2369 3.8 52.3 1.0
O A:HOH2096 3.9 44.6 1.0
CB A:ASP1183 4.3 42.1 1.0
O A:ASP376 4.3 33.5 1.0
CB A:ASP376 4.3 34.2 1.0
C A:ASP376 4.4 33.2 1.0
N A:SER377 4.8 32.6 1.0
CA A:SER377 4.9 35.6 1.0
CA A:ASP376 5.0 32.4 1.0

Magnesium binding site 9 out of 20 in 5x7r

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Magnesium binding site 9 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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 Complexed with Isomaltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:33.3
occ:1.00
 O A:HOH2451 1.9 40.3 1.0
O A:HOH2592 1.9 42.1 1.0
O A:HOH2568 2.0 49.7 1.0
O A:HOH2780 2.0 55.8 1.0
O A:HOH2048 2.3 36.3 1.0
NE2 A:HIS1009 2.3 33.8 1.0
CD2 A:HIS1009 3.1 33.2 1.0
CE1 A:HIS1009 3.4 33.2 1.0
OD1 A:ASP1008 3.8 40.4 1.0
OD2 A:ASP1008 4.1 44.8 1.0
ND2 A:ASN1109 4.2 28.8 1.0
O A:HOH2654 4.3 41.3 1.0
CG A:HIS1009 4.4 31.7 1.0
CG A:ASP1008 4.4 39.8 1.0
OD2 A:ASP1019 4.4 36.1 1.0
ND1 A:HIS1009 4.4 32.3 1.0
OD1 A:ASN1109 5.0 31.5 1.0

Magnesium binding site 10 out of 20 in 5x7r

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Magnesium binding site 10 out of 20 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose


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 Complexed with Isomaltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:58.8
occ:1.00
 O A:HOH2412 2.0 49.3 1.0
O A:HOH2401 2.2 41.9 1.0
O A:HOH2796 2.3 58.5 1.0
O A:HOH2752 2.3 51.8 1.0
O A:HOH2813 2.3 56.7 1.0
O A:HOH2819 2.3 58.5 1.0
O A:VAL1193 3.9 33.1 1.0
OD1 A:ASN1144 4.0 32.6 1.0
O A:HOH2789 4.5 40.9 1.0
O1 A:MES1712 4.6 38.4 1.0
ND2 A:ASN1144 4.8 33.6 1.0
CG A:ASN1144 4.8 32.3 1.0
C2 A:MES1712 4.9 38.1 1.0
C A:VAL1193 4.9 32.0 1.0
C6 A:MES1712 5.0 38.5 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: Tue Aug 12 23:20:10 2025

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