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Magnesium in PDB 5m7y: Crystal Structure of GH125 1,6-Alpha-Mannosidase Mutant From Clostridium Perfringens in Complex with 1,6-Alpha-Mannotriose

Protein crystallography data

The structure of Crystal Structure of GH125 1,6-Alpha-Mannosidase Mutant From Clostridium Perfringens in Complex with 1,6-Alpha-Mannotriose, PDB code: 5m7y was solved by A.Males, S.Alonso-Gil, P.Fernandes, S.J.Williams, C.Rovira, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.82 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.414, 44.016, 85.079, 90.00, 96.59, 90.00
R / Rfree (%) 14.7 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of GH125 1,6-Alpha-Mannosidase Mutant From Clostridium Perfringens in Complex with 1,6-Alpha-Mannotriose (pdb code 5m7y). 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 GH125 1,6-Alpha-Mannosidase Mutant From Clostridium Perfringens in Complex with 1,6-Alpha-Mannotriose, PDB code: 5m7y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5m7y

Go back to Magnesium Binding Sites List in 5m7y
Magnesium binding site 1 out of 2 in the Crystal Structure of GH125 1,6-Alpha-Mannosidase Mutant From Clostridium Perfringens in Complex with 1,6-Alpha-Mannotriose


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 GH125 1,6-Alpha-Mannosidase Mutant From Clostridium Perfringens in Complex with 1,6-Alpha-Mannotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:29.4
occ:1.00
O A:HOH853 1.9 30.1 1.0
O A:HOH628 2.0 36.3 1.0
O A:HOH844 2.2 34.4 1.0
O A:GLY152 2.3 29.8 1.0
C A:GLY152 3.4 22.3 1.0
CA A:GLY152 3.7 22.9 1.0
O A:HOH675 4.2 37.0 1.0
OE1 A:GLU154 4.2 22.9 1.0
O A:HOH833 4.4 30.4 1.0
CD A:GLU154 4.4 22.1 1.0
CG A:GLU154 4.4 20.4 1.0
O A:HOH830 4.5 35.3 1.0
N A:ASP153 4.6 23.3 1.0
O A:HOH719 4.7 32.3 1.0
CA A:ASP153 5.0 21.8 0.4

Magnesium binding site 2 out of 2 in 5m7y

Go back to Magnesium Binding Sites List in 5m7y
Magnesium binding site 2 out of 2 in the Crystal Structure of GH125 1,6-Alpha-Mannosidase Mutant From Clostridium Perfringens in Complex with 1,6-Alpha-Mannotriose


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 GH125 1,6-Alpha-Mannosidase Mutant From Clostridium Perfringens in Complex with 1,6-Alpha-Mannotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:46.0
occ:1.00
O A:HOH610 2.1 44.4 1.0
O A:HOH892 2.1 40.3 1.0
O A:HOH888 2.2 46.7 1.0
O A:HOH638 4.0 35.3 1.0
O A:ARG179 4.0 21.4 1.0
O A:HOH770 4.6 36.7 1.0
O A:HOH699 4.7 29.5 1.0
O A:GLU180 4.8 23.6 1.0
CA A:GLU180 5.0 19.8 1.0

Reference:

S.Alonso-Gil, A.Males, P.Z.Fernandes, S.J.Williams, G.J.Davies, C.Rovira. Computational Design of Experiment Unveils the Conformational Reaction Coordinate of GH125 Alpha-Mannosidases. J. Am. Chem. Soc. V. 139 1085 2017.
ISSN: ESSN 1520-5126
PubMed: 28026180
DOI: 10.1021/JACS.6B11247
Page generated: Mon Dec 14 20:50:51 2020

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