Atomistry » Magnesium » PDB 5wti-5x7u » 5x7s
Atomistry »
  Magnesium »
    PDB 5wti-5x7u »
      5x7s »

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

Go back to Magnesium Binding Sites List in 5x7s
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

Go back to Magnesium Binding Sites List in 5x7s
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

Go back to Magnesium Binding Sites List in 5x7s
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

Go back to Magnesium Binding Sites List in 5x7s
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

Go back to Magnesium Binding Sites List in 5x7s
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

Go back to Magnesium Binding Sites List in 5x7s
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

Go back to Magnesium Binding Sites List in 5x7s
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 Sep 30 09:03:20 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy