Atomistry » Nickel » PDB 5tvr-5xgz » 5x7r
Atomistry »
  Nickel »
    PDB 5tvr-5xgz »
      5x7r »

Nickel 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:

Magnesium (Mg) 20 atoms
Calcium (Ca) 6 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Isomaltohexaose, PDB code: 5x7r:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 5x7r

Go back to Nickel Binding Sites List in 5x7r
Nickel binding site 1 out of 4 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 Nickel with other atoms in the Ni 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:Ni1501

b:30.7
occ:1.00
 O A:HOH2187 2.1 27.8 1.0
O A:HOH2421 2.2 27.4 1.0
OD2 A:ASP196 2.2 28.2 1.0
NE2 A:HIS190 2.2 30.1 1.0
NE2 A:HIS187 2.2 26.0 1.0
O A:HOH2154 2.3 29.7 1.0
CG A:ASP196 3.1 26.9 1.0
CE1 A:HIS190 3.1 31.9 1.0
CD2 A:HIS187 3.2 27.6 1.0
CE1 A:HIS187 3.2 27.3 1.0
CD2 A:HIS190 3.2 30.4 1.0
OD1 A:ASP196 3.4 25.7 1.0
O A:HOH2257 4.0 28.2 1.0
OE2 A:GLU175 4.2 36.0 1.0
ND1 A:HIS190 4.3 30.5 1.0
ND1 A:HIS187 4.3 27.5 1.0
CG A:HIS187 4.3 28.6 1.0
CG A:HIS190 4.3 30.7 1.0
O A:HOH2264 4.4 24.7 1.0
O A:SER170 4.4 24.7 1.0
OE1 A:GLU175 4.5 33.4 1.0
CB A:ASP196 4.5 26.2 1.0
NH2 A:ARG169 4.5 28.1 1.0
O A:HOH2808 4.7 37.1 1.0
CD A:GLU175 4.8 36.0 1.0
CB A:ARG169 4.9 25.3 1.0
NE A:ARG169 4.9 26.5 1.0

Nickel binding site 2 out of 4 in 5x7r

Go back to Nickel Binding Sites List in 5x7r
Nickel binding site 2 out of 4 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 Nickel with other atoms in the Ni 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:Ni1502

b:43.3
occ:1.00
 OD1 A:ASP1183 1.9 40.8 1.0
O A:HOH2719 1.9 27.9 1.0
O A:HOH2024 2.2 33.8 1.0
NE2 A:HIS1181 2.3 40.5 1.0
CG A:ASP1183 3.0 41.7 1.0
CD2 A:HIS1181 3.2 39.3 1.0
CE1 A:HIS1181 3.2 40.0 1.0
O A:HOH2096 3.5 44.6 1.0
OD2 A:ASP1183 3.6 42.6 1.0
MG A:MG1608 3.6 39.8 1.0
C6 A:GLC1472 3.8 56.4 1.0
O A:HOH2666 3.8 48.5 1.0
O5 A:GLC1472 4.0 59.1 1.0
OD2 A:ASP376 4.1 38.6 1.0
CB A:ASP1183 4.3 42.1 1.0
ND1 A:HIS1181 4.4 39.7 1.0
CG A:HIS1181 4.4 38.2 1.0
CD1 A:TYR1267 4.4 50.0 1.0
C5 A:GLC1472 4.5 56.0 1.0
CE1 A:TYR1267 4.5 53.2 1.0
CA A:ASP1183 4.5 42.1 1.0
N A:ASP1183 4.6 40.3 1.0
O6 A:GLC1472 4.8 57.6 1.0
O A:HOH2462 4.8 43.3 1.0
C1 A:GLC1472 4.9 61.5 1.0
C A:SER1182 4.9 38.9 1.0

Nickel binding site 3 out of 4 in 5x7r

Go back to Nickel Binding Sites List in 5x7r
Nickel binding site 3 out of 4 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 Nickel with other atoms in the Ni 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
B:Ni1501

b:30.5
occ:1.00
 O B:HOH2421 2.1 26.6 1.0
O B:HOH2127 2.1 26.6 1.0
NE2 B:HIS187 2.2 27.9 1.0
OD2 B:ASP196 2.2 25.1 1.0
O B:HOH2332 2.2 26.3 1.0
NE2 B:HIS190 2.3 31.8 1.0
CD2 B:HIS187 3.1 28.5 1.0
CG B:ASP196 3.1 26.2 1.0
CE1 B:HIS187 3.2 28.3 1.0
CD2 B:HIS190 3.2 31.2 1.0
CE1 B:HIS190 3.3 31.8 1.0
OD1 B:ASP196 3.4 25.7 1.0
O B:HOH2117 3.9 27.6 1.0
OE2 B:GLU175 4.1 37.0 1.0
O B:HOH2095 4.3 23.3 1.0
ND1 B:HIS187 4.3 28.3 1.0
CG B:HIS187 4.3 29.4 1.0
OE1 B:GLU175 4.4 34.6 1.0
ND1 B:HIS190 4.4 31.2 1.0
CG B:HIS190 4.4 30.6 1.0
O B:SER170 4.4 26.0 1.0
NH2 B:ARG169 4.5 27.8 1.0
CB B:ASP196 4.5 25.4 1.0
O B:HOH2795 4.6 41.7 1.0
CD B:GLU175 4.7 37.6 1.0
CB B:ARG169 4.9 25.8 1.0
NE B:ARG169 4.9 27.1 1.0

Nickel binding site 4 out of 4 in 5x7r

Go back to Nickel Binding Sites List in 5x7r
Nickel binding site 4 out of 4 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 Nickel with other atoms in the Ni 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
B:Ni1502

b:54.5
occ:1.00
 O B:HOH2008 1.6 37.9 1.0
O B:HOH2726 2.1 33.3 1.0
OD1 B:ASP1183 2.2 42.3 1.0
NE2 B:HIS1181 2.3 34.4 1.0
CE1 B:HIS1181 3.1 32.8 1.0
MG B:MG1608 3.3 50.1 1.0
CG B:ASP1183 3.3 43.6 1.0
CD2 B:HIS1181 3.4 32.8 1.0
O B:HOH2027 3.4 54.6 1.0
C6 B:GLC1472 3.7 64.1 1.0
OD2 B:ASP1183 3.8 47.5 1.0
O5 B:GLC1472 3.8 68.3 1.0
O B:HOH2709 4.1 53.3 1.0
CD1 B:TYR1267 4.2 49.2 1.0
CE1 B:TYR1267 4.3 52.1 1.0
ND1 B:HIS1181 4.3 34.0 1.0
C5 B:GLC1472 4.4 63.2 1.0
CG B:HIS1181 4.4 32.0 1.0
OD2 B:ASP376 4.4 43.5 1.0
CB B:ASP1183 4.6 39.1 1.0
N B:ASP1183 4.7 35.6 1.0
CA B:ASP1183 4.7 37.6 1.0
O6 B:GLC1472 4.8 67.0 1.0
O B:HOH2595 4.9 50.5 1.0
C1 B:GLC1472 4.9 67.4 1.0
C B:SER1182 5.0 34.3 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: Thu Oct 10 08:12:56 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