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Magnesium in PDB 5hxm: Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose

Enzymatic activity of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose

All present enzymatic activity of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose:
3.2.1.177;

Protein crystallography data

The structure of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose, PDB code: 5hxm was solved by A.S.Halavaty, S.H.Light, G.Minasov, J.Winsor, S.Grimshaw, L.Shuvalova, S.Peterson, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.74 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.157, 102.437, 74.011, 90.00, 103.78, 90.00
R / Rfree (%) 15.2 / 19.5

Other elements in 5hxm:

The structure of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose (pdb code 5hxm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose, PDB code: 5hxm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5hxm

Go back to Magnesium Binding Sites List in 5hxm
Magnesium binding site 1 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:42.2
occ:1.00
 O A:HOH1502 1.9 45.0 1.0
O A:HOH1300 2.0 37.8 1.0
O A:HOH1536 2.0 40.2 1.0
O A:HOH2067 2.1 40.9 1.0
OD1 A:ASN346 2.1 37.4 1.0
O A:HOH1231 2.1 40.9 1.0
CG A:ASN346 3.1 38.5 1.0
ND2 A:ASN346 3.5 37.8 1.0
O A:HOH1537 3.6 47.7 1.0
OD2 A:ASP349 4.0 48.9 1.0
OD2 A:ASP152 4.0 44.0 1.0
OD2 A:ASP154 4.0 43.2 1.0
OD1 A:ASP342 4.2 45.7 1.0
O A:HOH2053 4.3 55.8 1.0
ND2 A:ASN345 4.3 42.5 1.0
OD2 A:ASP342 4.3 40.8 1.0
OD1 A:ASP154 4.4 43.1 1.0
CB A:ASN346 4.4 35.1 1.0
CG A:ASP342 4.7 44.4 1.0
CG A:ASP154 4.7 43.0 1.0
CA A:ASN346 4.7 36.7 1.0

Magnesium binding site 2 out of 5 in 5hxm

Go back to Magnesium Binding Sites List in 5hxm
Magnesium binding site 2 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:49.0
occ:1.00
 O A:HOH1729 2.0 50.0 1.0
O A:HOH1849 2.0 71.2 1.0
OD2 A:ASP376 2.3 47.0 1.0
O A:GLU370 2.3 43.3 1.0
OD1 A:ASP372 2.4 51.0 1.0
O A:HOH1940 2.5 63.4 1.0
CG A:ASP372 3.2 52.0 1.0
CG A:ASP376 3.3 49.7 1.0
C A:GLU370 3.5 46.3 1.0
OD1 A:ASP376 3.7 51.4 1.0
OD2 A:ASP372 3.8 54.8 1.0
N A:ASP372 3.8 45.3 1.0
NE A:ARG373 4.1 56.4 1.0
CB A:ASP372 4.1 50.1 1.0
NH2 A:ARG373 4.3 61.6 1.0
CA A:GLU370 4.4 46.9 1.0
N A:TRP371 4.4 44.2 1.0
CA A:TRP371 4.5 44.8 1.0
CA A:ASP372 4.5 48.9 1.0
CB A:GLU370 4.5 45.0 1.0
O A:SER662 4.6 45.3 1.0
C A:TRP371 4.6 45.0 1.0
CZ A:ARG373 4.6 61.6 1.0
CB A:ASP376 4.6 47.7 1.0
OD1 A:ASP663 4.8 51.1 1.0

Magnesium binding site 3 out of 5 in 5hxm

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Magnesium binding site 3 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:67.2
occ:1.00
 O A:HOH2191 1.8 69.4 1.0
O A:HOH1412 2.2 51.5 1.0
O A:HOH1967 2.2 51.5 1.0
O A:HOH1976 2.3 59.8 1.0
O A:HOH2080 2.4 56.1 1.0
ND2 A:ASN575 4.2 50.6 1.0
OD1 A:ASP529 4.4 49.1 1.0
CG A:ASN575 4.4 50.0 1.0
O A:HOH1286 4.5 44.6 1.0
OD1 A:ASN575 4.5 46.9 1.0
O A:GLY527 4.6 50.7 1.0
CE1 A:HIS444 4.9 52.8 1.0

Magnesium binding site 4 out of 5 in 5hxm

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Magnesium binding site 4 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:69.4
occ:1.00
 O A:HOH2060 1.7 65.9 1.0
O A:HOH2114 2.1 65.7 1.0
O A:HOH2188 2.2 50.2 1.0
O A:HOH2121 2.2 62.9 1.0
O A:HOH1499 2.2 48.0 1.0
O A:HOH2224 2.4 63.3 1.0
O A:HOH1507 3.5 56.7 1.0
O A:HOH1275 4.0 42.6 1.0
O A:HOH2155 4.2 61.0 1.0
O A:HOH1509 4.3 38.2 1.0
O A:HOH1705 4.3 37.9 1.0
NZ A:LYS612 4.4 37.0 1.0
O A:HOH1246 4.6 53.8 1.0
OD2 A:ASP734 4.6 41.6 1.0

Magnesium binding site 5 out of 5 in 5hxm

Go back to Magnesium Binding Sites List in 5hxm
Magnesium binding site 5 out of 5 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:85.8
occ:1.00
 O A:HOH2150 1.9 69.7 1.0
O A:HOH2055 2.0 76.7 1.0
O A:HOH1325 2.3 55.4 1.0
OD1 A:ASP832 4.1 58.4 1.0
O A:GLU853 4.3 44.0 1.0
OD2 A:ASP832 4.4 64.8 1.0
O A:HOH1547 4.4 55.8 1.0
CG A:ASP832 4.5 56.4 1.0
CA A:GLY831 4.9 47.0 1.0

Reference:

S.H.Light, L.A.Cahoon, K.V.Mahasenan, M.Lee, B.Boggess, A.S.Halavaty, S.Mobashery, N.E.Freitag, W.F.Anderson. Transferase Versus Hydrolase: the Role of Conformational Flexibility in Reaction Specificity. Structure V. 25 295 2017.
ISSN: ISSN 1878-4186
PubMed: 28089449
DOI: 10.1016/J.STR.2016.12.007
Page generated: Sun Sep 29 16:36:39 2024

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