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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

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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

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