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Magnesium in PDB 4ak7: Crystal Structure of BPGH117_E303Q in Complex with Neoagarobiose

Protein crystallography data

The structure of Crystal Structure of BPGH117_E303Q in Complex with Neoagarobiose, PDB code: 4ak7 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) 69.84 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.900, 93.550, 104.960, 90.00, 90.00, 90.00
R / Rfree (%) 15.544 / 20.854

Other elements in 4ak7:

The structure of Crystal Structure of BPGH117_E303Q in Complex with Neoagarobiose also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of BPGH117_E303Q in Complex with Neoagarobiose (pdb code 4ak7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of BPGH117_E303Q in Complex with Neoagarobiose, PDB code: 4ak7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4ak7

Go back to Magnesium Binding Sites List in 4ak7
Magnesium binding site 1 out of 2 in the Crystal Structure of BPGH117_E303Q in Complex with Neoagarobiose


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 BPGH117_E303Q in Complex with Neoagarobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1407

b:13.3
occ:1.00
O A:HOH2095 2.1 8.2 1.0
O A:HOH2099 2.1 9.6 1.0
O A:HOH4001 2.1 7.6 1.0
O A:HOH2324 2.2 16.5 1.0
O A:HOH2096 2.2 4.8 1.0
O A:HOH2097 2.2 10.3 1.0
O A:PRO91 3.7 8.1 1.0
O A:HOH2204 3.9 11.4 1.0
O A:HOH2200 4.1 5.8 1.0
O A:ALA348 4.2 10.9 1.0
O A:ASP90 4.2 8.8 1.0
O A:ILE349 4.3 7.8 1.0
O A:PRO166 4.3 5.5 1.0
OD1 A:ASP245 4.4 9.0 1.0
OE2 A:GLU167 4.4 13.5 1.0
CG2 A:THR165 4.5 7.6 1.0
OD1 A:ASP90 4.5 11.4 1.0
C A:ASP90 4.5 8.2 1.0
C A:ALA348 4.5 9.3 1.0
CB A:ASP90 4.5 5.4 1.0
C A:PRO91 4.6 9.2 1.0
CA A:ALA348 4.6 10.5 1.0
CA A:ASP90 4.6 4.8 1.0
CB A:ALA348 4.8 5.5 1.0
O A:VAL304 4.8 11.1 1.0
CG A:GLU167 4.9 7.8 1.0
CD A:GLU167 5.0 11.3 1.0

Magnesium binding site 2 out of 2 in 4ak7

Go back to Magnesium Binding Sites List in 4ak7
Magnesium binding site 2 out of 2 in the Crystal Structure of BPGH117_E303Q in Complex with Neoagarobiose


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 BPGH117_E303Q in Complex with Neoagarobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1405

b:13.7
occ:1.00
O B:HOH2088 2.1 7.5 1.0
O B:HOH2089 2.1 12.5 1.0
O B:HOH2290 2.1 10.4 1.0
O B:HOH2091 2.1 8.3 1.0
O B:HOH4001 2.1 10.7 1.0
O B:HOH2087 2.2 7.2 1.0
O B:PRO91 3.7 6.5 1.0
O B:HOH2191 4.0 12.9 1.0
O B:ALA348 4.2 9.3 1.0
O B:HOH2188 4.2 6.5 1.0
O B:ILE349 4.2 9.0 1.0
O B:ASP90 4.3 10.2 1.0
OD1 B:ASP245 4.3 12.4 1.0
OD1 B:ASP90 4.4 8.2 1.0
C B:ASP90 4.4 8.7 1.0
O B:PRO166 4.4 5.9 1.0
OE2 B:GLU167 4.4 13.0 1.0
C B:ALA348 4.5 9.5 1.0
CG2 B:THR165 4.5 8.4 1.0
CA B:ALA348 4.5 10.4 1.0
CB B:ASP90 4.5 5.7 1.0
C B:PRO91 4.6 7.4 1.0
CA B:ASP90 4.6 10.3 1.0
CB B:ALA348 4.6 6.5 1.0
O B:VAL304 4.7 14.2 1.0
CG B:GLU167 4.9 9.8 1.0
N B:PRO91 5.0 6.8 1.0
C B:ILE349 5.0 8.9 1.0
CG B:ASP90 5.0 13.9 1.0
CD B:GLU167 5.0 9.0 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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