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Magnesium in PDB 5i0d: Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan

Protein crystallography data

The structure of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan, PDB code: 5i0d was solved by S.H.Light, G.Minasov, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.77
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.753, 101.233, 166.391, 90.00, 101.02, 90.00
R / Rfree (%) 14.4 / 17.1

Other elements in 5i0d:

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

Chlorine (Cl) 7 atoms
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan (pdb code 5i0d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan, PDB code: 5i0d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5i0d

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Magnesium binding site 1 out of 8 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


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 Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:14.6
occ:1.00
 O A:HOH1257 2.0 16.8 1.0
O A:HOH1372 2.0 16.3 1.0
O A:HOH1255 2.0 16.6 1.0
O A:HOH1621 2.1 16.7 1.0
O A:HOH2353 2.1 19.3 1.0
OD1 A:ASN377 2.1 15.6 1.0
CG A:ASN377 3.1 14.8 1.0
ND2 A:ASN377 3.5 14.6 1.0
O A:HOH1228 4.0 24.9 1.0
O A:HOH2375 4.1 25.5 1.0
OD1 A:ASP373 4.1 16.1 1.0
OD2 A:ASP380 4.1 19.9 1.0
OD2 A:ASP185 4.2 19.4 1.0
OD2 A:ASP183 4.2 19.7 1.0
OD2 A:ASP373 4.2 16.1 1.0
ND2 A:ASN376 4.3 15.9 1.0
OD1 A:ASP185 4.4 18.6 1.0
CB A:ASN377 4.5 14.3 1.0
CG A:ASP373 4.5 15.7 1.0
NZ A:LYS369 4.6 31.2 1.0
CG A:ASP185 4.7 18.9 1.0
CA A:ASN377 4.8 13.9 1.0

Magnesium binding site 2 out of 8 in 5i0d

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Magnesium binding site 2 out of 8 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


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 Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:25.2
occ:1.00
 O A:HOH2322 2.0 19.8 1.0
O A:HOH2401 2.1 24.9 1.0
O A:HOH2293 2.1 29.8 1.0
O A:HOH1330 2.1 16.7 1.0
O A:HOH2423 2.2 34.9 1.0
O A:HOH2604 2.3 33.8 1.0
O A:HOH1354 4.1 17.5 1.0
O A:HOH2340 4.2 32.9 1.0
ND2 A:ASN606 4.2 15.6 1.0
O A:HOH1448 4.3 40.8 1.0
OD1 A:ASP560 4.4 13.4 1.0
O A:GLY558 4.4 13.5 1.0
O A:HOH2004 4.4 31.4 1.0
O A:HOH2147 4.4 25.4 1.0
CG A:ASN606 4.5 15.7 1.0
O A:HOH2607 4.6 47.7 1.0
OD1 A:ASN606 4.6 15.5 1.0
CE1 A:HIS475 4.7 15.0 1.0
O A:HOH2390 4.7 54.4 1.0

Magnesium binding site 3 out of 8 in 5i0d

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Magnesium binding site 3 out of 8 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


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 Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:14.2
occ:1.00
 O A:HOH2102 2.0 31.6 1.0
O A:HOH1934 2.1 28.0 1.0
O A:HOH1980 2.2 24.4 1.0
OD1 A:ASP403 2.2 18.6 1.0
O A:GLU401 2.2 16.3 1.0
OD2 A:ASP407 2.2 18.2 1.0
CG A:ASP403 3.2 17.7 1.0
CG A:ASP407 3.3 17.4 1.0
C A:GLU401 3.4 15.2 1.0
OD1 A:ASP407 3.7 18.6 1.0
N A:ASP403 3.8 15.5 1.0
OD2 A:ASP403 3.9 19.0 1.0
NE A:ARG404 4.1 21.4 1.0
O A:HOH2089 4.1 46.5 1.0
CB A:ASP403 4.2 16.7 1.0
CA A:GLU401 4.3 15.1 1.0
N A:TRP402 4.3 14.7 1.0
CA A:TRP402 4.3 14.9 1.0
CB A:GLU401 4.4 15.5 1.0
NH2 A:ARG404 4.5 23.5 1.0
CA A:ASP403 4.5 16.0 1.0
C A:TRP402 4.5 15.0 1.0
CB A:ASP407 4.6 16.2 1.0
O A:SER693 4.6 18.9 1.0
O A:HOH1912 4.7 37.4 1.0
CZ A:ARG404 4.7 22.8 1.0
OD1 A:ASP694 4.8 25.4 1.0
O A:HOH1944 4.9 33.6 1.0
CD A:ARG404 4.9 20.4 1.0
CG A:GLU401 5.0 16.0 1.0

Magnesium binding site 4 out of 8 in 5i0d

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Magnesium binding site 4 out of 8 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


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 Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:33.1
occ:1.00
 O A:HOH2549 2.0 33.9 1.0
O A:HOH2304 2.0 31.7 1.0
O A:HOH1294 2.2 24.2 1.0
O A:HOH2611 2.2 35.3 1.0
O A:HOH2485 2.2 33.0 1.0
O A:HOH2297 2.3 37.0 1.0
O A:HOH1295 4.0 23.5 1.0
O A:HOH1454 4.1 26.7 1.0
O A:HOH1728 4.2 14.3 1.0
O A:HOH2448 4.3 47.2 1.0
O A:HOH2303 4.3 39.4 1.0
O A:HOH2234 4.3 20.8 1.0
NZ A:LYS643 4.4 13.8 1.0
O A:HOH2190 4.4 43.4 1.0
O A:HOH1389 4.4 31.5 1.0
OD2 A:ASP765 4.5 16.7 1.0
O A:HOH2612 5.0 47.7 1.0

Magnesium binding site 5 out of 8 in 5i0d

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Magnesium binding site 5 out of 8 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


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 Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:41.1
occ:1.00
 O A:HOH2372 2.0 26.6 1.0
O A:HOH2547 2.1 35.5 1.0
O A:HOH1623 2.1 28.7 1.0
O A:HOH2583 2.1 34.9 1.0
O A:HOH2605 2.2 35.2 1.0
O A:HOH2446 2.6 39.0 1.0
O A:HOH1589 4.2 24.3 1.0
O A:HOH2371 4.2 46.7 1.0
O A:HOH1487 4.2 15.2 1.0
O A:HOH1933 4.3 28.6 1.0
O A:GLY510 4.4 17.0 1.0
O A:HOH1770 4.4 30.5 1.0
O A:HOH2569 4.5 33.4 1.0
CB A:SER578 4.7 16.2 1.0
O A:HOH1537 4.7 30.4 1.0
CA A:SER578 4.8 16.2 1.0

Magnesium binding site 6 out of 8 in 5i0d

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Magnesium binding site 6 out of 8 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1101

b:15.1
occ:1.00
 O B:HOH1320 2.0 15.3 1.0
O B:HOH1247 2.0 16.6 1.0
O B:HOH1233 2.1 14.6 1.0
O B:HOH2318 2.1 19.6 1.0
OD1 B:ASN377 2.1 17.3 1.0
O B:HOH1373 2.2 16.2 1.0
CG B:ASN377 3.1 16.2 1.0
ND2 B:ASN377 3.5 16.6 1.0
O B:HOH1286 4.0 22.4 1.0
OD1 B:ASP373 4.1 15.4 1.0
O B:HOH2330 4.1 29.5 1.0
OD2 B:ASP185 4.1 19.0 1.0
OD2 B:ASP380 4.1 19.6 1.0
OD2 B:ASP373 4.2 16.0 1.0
OD2 B:ASP183 4.2 19.3 1.0
ND2 B:ASN376 4.3 16.6 1.0
O B:HOH2331 4.3 47.7 1.0
O B:HOH2547 4.4 44.9 1.0
OD1 B:ASP185 4.4 17.6 1.0
CB B:ASN377 4.5 15.5 1.0
CG B:ASP373 4.5 15.4 1.0
CG B:ASP185 4.7 17.6 1.0
NZ B:LYS369 4.8 30.5 1.0
CA B:ASN377 4.8 14.9 1.0
O B:ASP373 5.0 13.9 1.0

Magnesium binding site 7 out of 8 in 5i0d

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Magnesium binding site 7 out of 8 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:17.5
occ:1.00
 O B:HOH2226 2.0 35.3 1.0
O B:HOH2022 2.1 26.8 1.0
O B:GLU401 2.2 21.4 1.0
OD1 B:ASP403 2.2 24.2 1.0
OD2 B:ASP407 2.2 23.8 1.0
O B:HOH2075 2.3 33.3 1.0
CG B:ASP403 3.1 22.8 1.0
CG B:ASP407 3.3 22.7 1.0
C B:GLU401 3.4 19.6 1.0
OD1 B:ASP407 3.6 23.5 1.0
N B:ASP403 3.7 20.3 1.0
OD2 B:ASP403 3.8 23.9 1.0
CB B:ASP403 4.1 21.6 1.0
NE B:ARG404 4.1 24.7 1.0
N B:TRP402 4.3 19.1 1.0
CA B:TRP402 4.3 19.4 1.0
CA B:GLU401 4.3 19.0 1.0
NH2 B:ARG404 4.4 26.2 1.0
CB B:GLU401 4.4 19.3 1.0
CA B:ASP403 4.4 20.8 1.0
C B:TRP402 4.5 19.7 1.0
CZ B:ARG404 4.6 25.9 1.0
CB B:ASP407 4.6 21.9 1.0
O B:SER693 4.6 21.3 1.0
OD1 B:ASP694 4.6 26.8 1.0
O B:HOH1768 4.7 41.9 1.0
CD B:ARG404 4.9 24.3 1.0
CG B:GLU401 5.0 19.5 1.0
CG B:ARG404 5.0 23.2 1.0

Magnesium binding site 8 out of 8 in 5i0d

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Magnesium binding site 8 out of 8 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:32.8
occ:1.00
 O B:HOH2290 2.0 23.6 1.0
O B:HOH2027 2.1 30.5 1.0
O B:HOH2387 2.1 33.6 1.0
O B:HOH1290 2.1 21.3 1.0
O B:HOH2588 2.2 37.5 1.0
O B:HOH2422 2.3 35.8 1.0
ND2 B:ASN606 4.0 20.0 1.0
O B:HOH1350 4.2 22.2 1.0
O B:HOH1556 4.2 46.3 1.0
CG B:ASN606 4.3 19.9 1.0
OD1 B:ASN606 4.3 20.0 1.0
OD1 B:ASP560 4.3 17.6 1.0
O B:HOH2001 4.4 26.6 1.0
O B:GLY558 4.4 18.4 1.0
O B:HOH2062 4.5 29.5 1.0
O B:HOH2405 4.5 46.7 1.0
CE1 B:HIS475 4.8 18.5 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 16:37:53 2024

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