Atomistry » Magnesium » PDB 5hr6-5i8q » 5i0d
Atomistry »
  Magnesium »
    PDB 5hr6-5i8q »
      5i0d »

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

Go back to Magnesium Binding Sites List in 5i0d
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

Go back to Magnesium Binding Sites List in 5i0d
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

Go back to Magnesium Binding Sites List in 5i0d
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

Go back to Magnesium Binding Sites List in 5i0d
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

Go back to Magnesium Binding Sites List in 5i0d
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

Go back to Magnesium Binding Sites List in 5i0d
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

Go back to Magnesium Binding Sites List in 5i0d
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

Go back to Magnesium Binding Sites List in 5i0d
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy