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Magnesium in PDB 4ak6: BPGH117_H302E Mutant Glycoside Hydrolase

Protein crystallography data

The structure of BPGH117_H302E Mutant Glycoside Hydrolase, PDB code: 4ak6 was solved by J.H.Hehemann, L.Smyth, A.Yadav, D.J.Vocadlo, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.28 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.260, 96.550, 103.440, 90.00, 90.00, 90.00
R / Rfree (%) 21.555 / 25.234

Magnesium Binding Sites:

The binding sites of Magnesium atom in the BPGH117_H302E Mutant Glycoside Hydrolase (pdb code 4ak6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the BPGH117_H302E Mutant Glycoside Hydrolase, PDB code: 4ak6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4ak6

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Magnesium binding site 1 out of 5 in the BPGH117_H302E Mutant Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of BPGH117_H302E Mutant Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1399

b:17.9
occ:1.00
O A:HOH2222 2.0 23.8 1.0
O A:HOH2061 2.1 25.1 1.0
O A:HOH2059 2.2 21.5 1.0
O A:HOH2060 2.3 18.6 1.0
O A:HOH2063 2.3 20.6 1.0
O A:HOH2172 2.4 31.7 1.0
O A:PRO91 3.7 17.9 1.0
O A:HOH2105 3.9 34.0 1.0
O A:ALA348 4.3 19.0 1.0
O A:HOH2102 4.3 23.5 1.0
OD1 A:ASP245 4.4 29.2 1.0
O A:ILE349 4.4 17.6 1.0
O A:PRO166 4.4 21.9 1.0
OD1 A:ASP90 4.4 21.6 1.0
O A:ASP90 4.5 16.5 1.0
C A:ASP90 4.5 17.2 1.0
OE2 A:GLU167 4.5 24.6 1.0
C A:ALA348 4.5 18.6 1.0
CG2 A:THR165 4.5 22.7 1.0
CA A:ALA348 4.6 19.5 1.0
CB A:ASP90 4.6 22.5 1.0
C A:PRO91 4.6 19.1 1.0
CA A:ASP90 4.7 20.4 1.0
CB A:ALA348 4.7 17.1 1.0
O A:VAL304 4.7 22.5 1.0
CG A:GLU167 4.8 21.8 1.0

Magnesium binding site 2 out of 5 in 4ak6

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Magnesium binding site 2 out of 5 in the BPGH117_H302E Mutant Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of BPGH117_H302E Mutant Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1402

b:35.9
occ:1.00
O A:HOH2116 2.5 35.1 1.0
OG1 A:THR165 3.0 23.7 1.0
NE2 A:GLN180 3.4 26.8 1.0
OE1 A:GLN180 3.7 26.9 1.0
CD A:GLN180 3.9 23.8 1.0
CD2 A:PHE164 4.0 30.7 1.0
CE2 A:PHE164 4.0 30.3 1.0
O A:HOH2062 4.0 24.6 1.0
CB A:THR165 4.1 22.6 1.0
CG2 A:THR165 4.3 22.7 1.0
O A:HOH2058 4.3 20.6 1.0
OD2 A:ASP90 4.4 25.1 1.0
CD1 A:TRP127 4.5 31.1 1.0
CD2 A:TRP127 4.6 25.0 1.0
CG A:TRP127 4.6 29.6 1.0
NE1 A:TRP127 4.6 30.3 1.0
CE2 A:TRP127 4.7 30.5 1.0
ND1 A:HIS244 4.8 40.7 1.0
CG A:HIS244 4.9 34.3 1.0
CG A:ASP90 4.9 22.7 1.0
CE1 A:HIS244 4.9 42.8 1.0
OD1 A:ASP245 4.9 29.2 1.0
OD1 A:ASP90 5.0 21.6 1.0

Magnesium binding site 3 out of 5 in 4ak6

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Magnesium binding site 3 out of 5 in the BPGH117_H302E Mutant Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of BPGH117_H302E Mutant Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1398

b:40.5
occ:1.00
O B:HOH2184 2.5 37.6 1.0
O B:HOH2113 2.8 26.2 1.0
OG1 B:THR165 3.1 21.4 1.0
NE2 B:GLN180 3.2 20.9 1.0
OE1 B:GLN180 3.6 20.1 1.0
CD B:GLN180 3.8 17.9 1.0
CE2 B:PHE164 4.0 19.6 1.0
CD2 B:PHE164 4.1 24.9 1.0
CB B:THR165 4.1 20.7 1.0
O B:HOH2032 4.2 20.5 1.0
CG2 B:THR165 4.2 19.1 1.0
ND1 B:HIS244 4.3 30.5 1.0
O B:HOH2028 4.4 23.5 1.0
OD2 B:ASP90 4.5 23.1 1.0
CE1 B:HIS244 4.5 26.8 1.0
CG B:TRP127 4.6 17.0 1.0
CD2 B:TRP127 4.6 23.0 1.0
CG B:HIS244 4.7 24.8 1.0
CD1 B:TRP127 4.8 25.8 1.0
OD1 B:ASP245 4.8 20.6 1.0
CE2 B:TRP127 4.9 27.3 1.0
NE1 B:TRP127 4.9 26.7 1.0
CG B:ASP90 4.9 20.1 1.0
NE2 B:HIS244 5.0 20.8 1.0

Magnesium binding site 4 out of 5 in 4ak6

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Magnesium binding site 4 out of 5 in the BPGH117_H302E Mutant Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of BPGH117_H302E Mutant Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1399

b:17.7
occ:1.00
O B:HOH2185 2.0 20.2 1.0
O B:HOH2031 2.3 17.2 1.0
O B:HOH2033 2.3 22.3 1.0
O B:HOH2029 2.3 25.2 1.0
O B:HOH2030 2.3 18.1 1.0
O B:HOH2150 2.4 22.6 1.0
O B:HOH2072 3.8 27.1 1.0
O B:PRO91 3.9 18.7 1.0
O B:HOH2069 4.2 21.6 1.0
O B:ILE349 4.2 18.3 1.0
O B:ALA348 4.3 19.1 1.0
O B:PRO166 4.4 20.1 1.0
CG2 B:THR165 4.4 19.1 1.0
OE2 B:GLU167 4.5 23.8 1.0
O B:ASP90 4.5 19.6 1.0
OD1 B:ASP90 4.5 19.5 1.0
OD1 B:ASP245 4.5 20.6 1.0
O B:VAL304 4.6 17.1 1.0
C B:ASP90 4.6 19.1 1.0
C B:ALA348 4.6 17.8 1.0
CA B:ALA348 4.7 17.4 1.0
C B:PRO91 4.7 19.8 1.0
CG B:GLU167 4.7 15.9 1.0
CA B:ASP90 4.8 19.3 1.0
CB B:ALA348 4.8 16.0 1.0
CB B:ASP90 4.8 19.7 1.0
CD B:GLU167 4.9 22.2 1.0
CB B:GLU303 5.0 18.7 1.0

Magnesium binding site 5 out of 5 in 4ak6

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Magnesium binding site 5 out of 5 in the BPGH117_H302E Mutant Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of BPGH117_H302E Mutant Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1400

b:50.5
occ:1.00
O B:HOH2186 3.7 44.9 1.0
O B:PRO322 3.8 21.0 1.0
C B:PRO322 4.3 19.7 1.0
CG B:GLU323 4.4 19.5 1.0
CB B:PRO322 4.4 18.2 1.0
CH2 B:TRP270 4.4 27.5 1.0
O A:HOH2089 4.6 42.6 1.0
NE1 A:TRP60 4.7 35.1 1.0
CG2 A:VAL341 4.8 20.6 1.0
CA B:PRO322 4.9 19.2 1.0
N B:GLU323 5.0 19.9 1.0
CZ3 B:TRP270 5.0 29.2 1.0

Reference:

J.H.Hehemann, L.Smyth, A.Yadav, D.J.Vocadlo, A.B.Boraston. Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight Into the Degradation (of A Polysaccharide From) Red Seaweeds. J.Biol.Chem. V. 287 13985 2012.
ISSN: ISSN 0021-9258
PubMed: 22393053
DOI: 10.1074/JBC.M112.345645
Page generated: Mon Dec 14 09:07:59 2020

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