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Magnesium in PDB 6cnl: Crystal Structure of H105A PGAM5 Dodecamer

Enzymatic activity of Crystal Structure of H105A PGAM5 Dodecamer

All present enzymatic activity of Crystal Structure of H105A PGAM5 Dodecamer:
3.1.3.16;

Protein crystallography data

The structure of Crystal Structure of H105A PGAM5 Dodecamer, PDB code: 6cnl was solved by K.Ruiz, C.Agnew, N.Jura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.372, 242.538, 272.458, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26.4

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 31;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of H105A PGAM5 Dodecamer (pdb code 6cnl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 31 binding sites of Magnesium where determined in the Crystal Structure of H105A PGAM5 Dodecamer, PDB code: 6cnl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 31 in 6cnl

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Magnesium binding site 1 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:15.8
occ:1.00
 NH1 A:ARG104 2.5 49.6 1.0
ND1 A:HIS230 3.1 25.7 1.0
CB A:HIS230 3.3 16.6 1.0
CA A:HIS230 3.4 20.8 1.0
NE A:ARG152 3.4 32.1 1.0
NH2 A:ARG152 3.5 34.1 1.0
N A:ALA231 3.6 28.1 1.0
CG A:HIS230 3.6 29.9 1.0
CZ A:ARG104 3.7 30.0 1.0
O A:HOH405 3.8 25.5 1.0
CB A:ALA105 3.9 29.5 1.0
CZ A:ARG152 3.9 29.0 1.0
C A:HIS230 4.1 26.1 1.0
CG A:ARG104 4.2 23.8 1.0
O A:CYS229 4.2 22.1 1.0
CE1 A:HIS230 4.3 29.6 1.0
N A:ALA105 4.3 29.4 1.0
CE1 A:TYR108 4.4 34.5 1.0
NH2 A:ARG104 4.4 31.2 1.0
OE2 A:GLU177 4.5 26.3 1.0
CD A:ARG152 4.5 32.2 1.0
NE A:ARG104 4.6 28.5 1.0
OH A:TYR108 4.6 58.1 1.0
N A:HIS230 4.6 22.4 1.0
CA A:ALA105 4.6 25.8 1.0
O A:ALA105 4.6 26.5 1.0
CD A:ARG104 4.7 36.1 1.0
CB A:ALA231 4.7 21.9 1.0
CA A:ALA231 4.8 28.0 1.0
C A:CYS229 4.8 22.4 1.0
CZ A:TYR108 4.8 45.4 1.0
CD2 A:HIS230 4.9 26.8 1.0
C A:ALA105 5.0 23.1 1.0

Magnesium binding site 2 out of 31 in 6cnl

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Magnesium binding site 2 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:58.8
occ:1.00
 O C:HOH401 2.1 52.0 1.0
OD2 C:ASP200 3.7 42.5 1.0
O C:GLU177 4.4 21.9 1.0
NE2 C:GLN196 4.4 42.8 1.0
CG C:ASP200 4.5 37.1 1.0
OD1 C:ASP200 4.5 43.7 1.0
CA C:GLY178 4.7 21.2 1.0
O C:HOH409 4.9 25.3 1.0

Magnesium binding site 3 out of 31 in 6cnl

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Magnesium binding site 3 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:27.7
occ:1.00
 N C:ARG152 3.1 27.8 1.0
O C:ARG118 3.2 43.2 1.0
NH1 C:ARG152 3.3 34.8 1.0
CG C:ARG152 3.4 23.9 1.0
CB C:ARG118 3.4 56.4 1.0
CB C:ARG152 3.6 28.6 1.0
N C:THR151 3.7 28.0 1.0
CB C:THR151 3.8 26.2 1.0
CD C:ARG152 3.8 26.0 1.0
CA C:ARG152 4.0 29.6 1.0
CA C:THR151 4.0 21.9 1.0
C C:THR151 4.0 31.6 1.0
C C:ARG118 4.2 44.3 1.0
CB C:MET150 4.2 32.2 1.0
CZ C:ARG152 4.2 34.0 1.0
C C:MET150 4.4 25.8 1.0
NE C:ARG152 4.4 31.8 1.0
CA C:ARG118 4.4 55.5 1.0
CG C:ARG118 4.5 45.0 1.0
OG1 C:THR151 4.6 47.4 1.0
CG2 C:THR151 4.7 36.3 1.0
CD2 C:TYR108 4.8 43.9 1.0
CA C:MET150 4.8 23.3 1.0
SD C:MET150 4.9 31.8 1.0
CG C:MET150 4.9 28.0 1.0
CE2 C:TYR108 4.9 35.0 1.0

Magnesium binding site 4 out of 31 in 6cnl

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Magnesium binding site 4 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:13.4
occ:1.00
 ND1 C:HIS230 3.3 21.9 1.0
CA C:HIS230 3.4 24.1 1.0
NE C:ARG152 3.4 31.8 1.0
CB C:HIS230 3.4 26.8 1.0
NE C:ARG104 3.5 31.4 1.0
N C:ALA231 3.5 20.9 1.0
NH2 C:ARG152 3.7 35.5 1.0
CG C:HIS230 3.8 21.9 1.0
C C:HIS230 4.0 20.5 1.0
CZ C:ARG152 4.0 34.0 1.0
CG C:ARG104 4.0 23.6 1.0
NH2 C:ARG104 4.0 28.7 1.0
CZ C:ARG104 4.2 22.4 1.0
O C:CYS229 4.2 27.5 1.0
CB C:ALA105 4.2 25.8 1.0
CD C:ARG104 4.3 26.5 1.0
OE2 C:GLU177 4.4 28.0 1.0
CD C:ARG152 4.4 26.0 1.0
CE1 C:HIS230 4.5 31.2 1.0
N C:ALA105 4.5 35.6 1.0
CB C:ALA231 4.6 18.3 1.0
N C:HIS230 4.6 18.8 1.0
CA C:ALA231 4.6 24.8 1.0
O C:ALA105 4.7 28.6 1.0
C C:CYS229 4.8 21.2 1.0
CA C:ALA105 4.9 33.7 1.0
CE1 C:TYR108 4.9 35.5 1.0

Magnesium binding site 5 out of 31 in 6cnl

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Magnesium binding site 5 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:36.8
occ:1.00
 O C:ALA96 2.7 29.5 1.0
N C:ALA215 2.7 40.7 1.0
O C:ILE264 2.9 29.0 1.0
CB C:ALA215 3.3 30.2 1.0
O C:ARG265 3.5 24.9 1.0
C C:ARG265 3.5 24.8 1.0
CA C:ALA215 3.6 31.3 1.0
N C:ARG98 3.6 29.8 1.0
CA C:ARG214 3.6 29.9 1.0
N C:PRO266 3.6 29.8 1.0
C C:ARG214 3.6 27.8 1.0
CA C:THR97 3.6 33.8 1.0
C C:ALA96 3.7 25.2 1.0
CA C:PRO266 3.7 37.9 1.0
C C:ILE264 3.7 29.8 1.0
CB C:ARG214 3.8 32.5 1.0
CG C:ARG98 3.9 31.2 1.0
C C:THR97 4.0 26.6 1.0
N C:THR97 4.1 27.7 1.0
CA C:ARG265 4.2 23.9 1.0
N C:ARG265 4.3 33.3 1.0
CB C:ARG98 4.4 35.4 1.0
CD C:PRO266 4.4 31.8 1.0
CG2 C:ILE264 4.5 27.7 1.0
CB C:ILE264 4.5 34.6 1.0
CB C:PRO266 4.6 26.0 1.0
CA C:ARG98 4.6 34.7 1.0
CD C:ARG98 4.6 27.3 1.0
C C:ALA215 4.8 29.3 1.0
CA C:ILE264 4.8 28.2 1.0
C C:PRO266 4.8 29.8 1.0
CG C:ARG214 4.8 31.9 1.0
O C:ARG214 4.8 25.6 1.0
CB C:THR97 4.8 25.4 1.0
O C:ALA215 4.9 32.3 1.0
N C:ARG214 4.9 32.9 1.0
CA C:ALA96 5.0 32.2 1.0
O C:HIS213 5.0 24.0 1.0
O C:THR97 5.0 27.6 1.0

Magnesium binding site 6 out of 31 in 6cnl

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Magnesium binding site 6 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:31.0
occ:1.00
 O C:ALA241 2.5 19.6 1.0
CD2 O:TRP62 3.2 20.9 1.0
NE2 C:GLN243 3.2 25.9 1.0
CG C:GLN243 3.2 22.4 1.0
CH2 O:TRP58 3.3 32.9 1.0
CE2 O:TRP62 3.4 28.6 1.0
C C:ALA241 3.4 21.9 1.0
CG O:TRP62 3.5 27.1 1.0
CE3 O:TRP62 3.5 23.1 1.0
O C:ARG240 3.6 24.5 1.0
CD C:GLN243 3.7 23.5 1.0
CZ2 O:TRP58 3.8 25.9 1.0
NE1 O:TRP62 3.8 33.1 1.0
CD1 O:TRP62 3.8 25.9 1.0
CA C:ALA241 3.8 20.4 1.0
CZ2 O:TRP62 3.9 30.4 1.0
CZ3 O:TRP58 4.0 31.4 1.0
CZ3 O:TRP62 4.0 28.5 1.0
CG2 C:VAL270 4.1 37.8 1.0
CB O:TRP62 4.2 30.6 1.0
CH2 O:TRP62 4.2 27.3 1.0
N C:GLN243 4.3 22.3 1.0
N C:LEU242 4.4 24.0 1.0
CB C:GLN243 4.5 17.3 1.0
C C:ARG240 4.6 18.4 1.0
N C:ALA241 4.7 21.2 1.0
C C:LEU242 4.8 26.8 1.0
CE2 O:TRP58 4.8 25.4 1.0
CB C:VAL270 4.8 31.5 1.0
CA C:GLN243 4.9 21.4 1.0
CA C:LEU242 4.9 31.3 1.0
OE1 C:GLN243 4.9 29.7 1.0
CE3 O:TRP58 4.9 30.5 1.0
CB C:ALA241 5.0 16.4 1.0

Magnesium binding site 7 out of 31 in 6cnl

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Magnesium binding site 7 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:21.6
occ:1.00
 NE L:ARG104 3.3 33.1 1.0
NE L:ARG152 3.4 27.3 1.0
N L:ALA231 3.4 32.2 1.0
CB L:HIS230 3.5 30.8 1.0
ND1 L:HIS230 3.5 30.4 1.0
NH2 L:ARG152 3.5 38.9 1.0
CA L:HIS230 3.5 25.0 1.0
NH2 L:ARG104 3.6 26.7 1.0
O L:HOH411 3.7 34.2 1.0
CZ L:ARG104 3.8 32.4 1.0
CZ L:ARG152 3.9 25.8 1.0
CG L:HIS230 3.9 31.6 1.0
CG L:ARG104 4.0 32.7 1.0
C L:HIS230 4.0 31.1 1.0
OE2 L:GLU177 4.2 24.4 1.0
CD L:ARG104 4.2 29.2 1.0
CB L:ALA231 4.4 24.8 1.0
CB L:ALA105 4.4 37.4 1.0
CD L:ARG152 4.5 32.7 1.0
O L:CYS229 4.5 32.2 1.0
CA L:ALA231 4.5 27.9 1.0
CE1 L:TYR108 4.6 47.6 1.0
N L:ALA105 4.7 31.2 1.0
CE1 L:HIS230 4.7 34.2 1.0
N L:HIS230 4.8 24.9 1.0
O L:ALA105 4.8 28.9 1.0
OH L:TYR108 5.0 45.9 1.0
CD L:GLU177 5.0 29.6 1.0

Magnesium binding site 8 out of 31 in 6cnl

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Magnesium binding site 8 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg302

b:26.1
occ:1.00
 NH1 L:ARG162 3.4 50.3 1.0
NH2 L:ARG162 3.5 58.1 1.0
CD L:ARG125 3.8 33.4 1.0
CG L:ARG125 3.9 36.0 1.0
CZ L:ARG162 3.9 60.0 1.0
CD1 L:ILE159 4.2 46.4 1.0
CG1 L:ILE159 4.2 34.3 1.0
OE2 L:GLU129 4.7 64.9 1.0
NH1 L:ARG125 4.8 41.4 1.0

Magnesium binding site 9 out of 31 in 6cnl

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Magnesium binding site 9 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:20.7
occ:1.00
 CA J:HIS230 3.3 40.2 1.0
NE J:ARG104 3.3 24.6 1.0
CB J:HIS230 3.3 39.9 1.0
ND1 J:HIS230 3.4 32.0 1.0
N J:ALA231 3.4 39.7 1.0
NE J:ARG152 3.6 35.8 1.0
NH2 J:ARG152 3.7 41.8 1.0
CG J:HIS230 3.8 31.6 1.0
C J:HIS230 3.9 36.9 1.0
CG J:ARG104 3.9 41.1 1.0
NH2 J:ARG104 3.9 37.6 1.0
CZ J:ARG104 4.1 29.2 1.0
CZ J:ARG152 4.1 40.6 1.0
OE2 J:GLU177 4.2 40.6 1.0
CD J:ARG104 4.2 32.1 1.0
CB J:ALA105 4.3 39.0 1.0
O J:CYS229 4.4 29.4 1.0
N J:HIS230 4.5 28.3 1.0
N J:ALA105 4.6 27.8 1.0
CA J:ALA231 4.6 36.8 1.0
O J:ALA105 4.6 37.8 1.0
CB J:ALA231 4.6 37.2 1.0
CE1 J:HIS230 4.6 43.7 1.0
CD J:ARG152 4.7 41.7 1.0
CA J:ALA105 4.9 41.2 1.0
C J:CYS229 4.9 30.5 1.0
CD J:GLU177 4.9 39.7 1.0

Magnesium binding site 10 out of 31 in 6cnl

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Magnesium binding site 10 out of 31 in the Crystal Structure of H105A PGAM5 Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of H105A PGAM5 Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg302

b:39.5
occ:1.00
 O J:HOH402 2.5 29.2 1.0
N J:LEU250 2.9 25.3 1.0
C J:GLY248 3.1 39.0 1.0
CA J:GLY248 3.1 32.0 1.0
O J:GLU247 3.1 47.8 1.0
CB J:LEU250 3.2 43.0 1.0
CA J:LEU250 3.3 31.7 1.0
N J:ARG251 3.3 23.9 1.0
O J:ASP184 3.4 37.5 1.0
O J:GLY248 3.4 30.4 1.0
N J:TRP249 3.5 41.3 1.0
C J:LEU250 3.5 33.0 1.0
N J:ASP184 3.6 42.6 1.0
CG J:ARG251 3.7 30.3 1.0
CB J:PRO183 3.7 46.4 1.0
C J:ASP184 3.8 40.5 1.0
C J:GLU247 3.9 36.4 1.0
C J:TRP249 3.9 30.6 1.0
N J:GLY248 4.0 40.1 1.0
CA J:PRO183 4.0 40.4 1.0
NE J:ARG251 4.0 35.5 1.0
C J:PRO183 4.2 43.7 1.0
CA J:TRP249 4.3 34.3 1.0
CA J:ASP184 4.4 40.4 1.0
CD J:ARG251 4.4 32.3 1.0
CA J:ARG251 4.4 33.7 1.0
O J:LEU250 4.5 31.7 1.0
N J:PRO185 4.5 38.7 1.0
CB J:ARG251 4.5 37.3 1.0
CG J:LEU250 4.6 40.5 1.0
O J:PRO185 4.6 40.5 1.0
CD J:PRO185 4.6 41.7 1.0
CD1 J:TRP249 5.0 38.2 1.0
O J:TRP249 5.0 29.8 1.0
CZ J:ARG251 5.0 34.0 1.0
CG J:TRP249 5.0 32.3 1.0

Reference:

K.Ruiz, T.M.Thaker, C.Agnew, L.Miller-Vedam, R.Trenker, C.Herrera, M.Ingaramo, D.Toso, A.Frost, N.Jura. Functional Role of PGAM5 Multimeric Assemblies and Their Polymerization Into Filaments. Nat Commun V. 10 531 2019.
ISSN: ESSN 2041-1723
PubMed: 30705304
DOI: 10.1038/S41467-019-08393-W
Page generated: Mon Sep 30 22:27:57 2024

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