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Sodium in PDB 6cni: Crystal Structure of H105A PGAM5 Dimer

Enzymatic activity of Crystal Structure of H105A PGAM5 Dimer

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

Protein crystallography data

The structure of Crystal Structure of H105A PGAM5 Dimer, PDB code: 6cni 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) 43.03 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.003, 72.018, 81.941, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of H105A PGAM5 Dimer (pdb code 6cni). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of H105A PGAM5 Dimer, PDB code: 6cni:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6cni

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Sodium binding site 1 out of 6 in the Crystal Structure of H105A PGAM5 Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of H105A PGAM5 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:25.1
occ:1.00
 OH A:TYR92 2.7 17.1 1.0
O A:ALA96 2.8 18.7 1.0
O A:ILE264 2.9 20.1 1.0
CB A:ALA94 3.2 18.7 1.0
O A:ARG265 3.4 18.6 1.0
CG A:ARG98 3.6 15.9 1.0
CZ A:TYR92 3.6 18.5 1.0
CD A:ARG98 3.6 21.3 1.0
CE1 A:TYR92 3.6 17.6 1.0
C A:ARG265 3.7 18.2 1.0
N A:ARG98 3.7 16.0 1.0
C A:ILE264 3.7 20.8 1.0
CG2 A:ILE264 3.8 18.3 1.0
C A:ALA96 3.9 16.8 1.0
CA A:PRO266 4.0 21.2 1.0
N A:PRO266 4.0 20.6 1.0
CB A:ARG98 4.0 16.5 1.0
CB A:ILE264 4.0 17.1 1.0
CA A:THR97 4.0 14.1 1.0
C A:THR97 4.1 18.8 1.0
N A:ARG265 4.3 17.1 1.0
CA A:ARG265 4.4 19.0 1.0
CA A:ARG98 4.5 19.0 1.0
N A:THR97 4.5 15.0 1.0
CA A:ILE264 4.5 17.5 1.0
CA A:ALA94 4.6 20.4 1.0
CD A:PRO266 4.8 20.1 1.0
C A:PRO266 4.8 22.4 1.0
CE2 A:TYR92 4.9 18.6 1.0
CD1 A:TYR92 4.9 17.6 1.0
NE A:ARG98 4.9 21.1 1.0
O A:PRO266 4.9 21.2 1.0
O A:THR97 5.0 18.2 1.0
OE1 A:GLN219 5.0 30.7 1.0

Sodium binding site 2 out of 6 in 6cni

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Sodium binding site 2 out of 6 in the Crystal Structure of H105A PGAM5 Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of H105A PGAM5 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:26.1
occ:1.00
 O A:ARG118 2.8 23.3 1.0
O A:HOH537 2.9 22.6 1.0
N A:ARG152 3.0 20.9 1.0
NH1 A:ARG152 3.0 22.0 1.0
CG A:ARG152 3.3 16.6 1.0
CB A:ARG118 3.4 26.9 1.0
CB A:ARG152 3.4 19.9 1.0
N A:THR151 3.6 19.8 1.0
CD A:ARG152 3.6 18.1 1.0
CB A:THR151 3.6 22.8 1.0
CA A:ARG152 3.8 21.4 1.0
C A:ARG118 3.8 25.7 1.0
C A:THR151 3.9 21.4 1.0
CA A:THR151 3.9 21.0 1.0
CZ A:ARG152 4.0 21.5 1.0
CB A:MET150 4.2 19.2 1.0
CA A:ARG118 4.2 23.9 1.0
NE A:ARG152 4.2 21.3 1.0
CD2 A:TYR108 4.2 20.2 1.0
C A:MET150 4.3 21.6 1.0
OG1 A:THR151 4.4 25.4 1.0
CE2 A:TYR108 4.4 22.2 1.0
CG A:ARG118 4.7 28.1 1.0
CG2 A:THR151 4.7 23.9 1.0
O A:GLU115 4.7 33.6 1.0
CA A:MET150 4.7 22.9 1.0
CD A:ARG118 4.8 35.2 1.0
O A:HOH505 4.8 37.9 1.0
O A:MET150 4.9 21.5 1.0
CG A:TYR108 4.9 16.1 1.0
C A:ARG152 5.0 21.7 1.0

Sodium binding site 3 out of 6 in 6cni

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Sodium binding site 3 out of 6 in the Crystal Structure of H105A PGAM5 Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of H105A PGAM5 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:25.8
occ:1.00
 O B:ARG273 2.8 22.3 1.0
O A:GLY276 2.8 17.4 1.0
N A:ASN255 2.8 14.8 1.0
CA A:GLY276 3.2 18.1 1.0
CG A:ASN255 3.3 20.6 1.0
ND2 A:ASN255 3.3 20.9 1.0
O A:SER253 3.3 28.7 1.0
C A:GLY276 3.4 15.2 1.0
CA A:LEU254 3.5 14.2 1.0
CB A:ASN255 3.6 17.6 1.0
C A:LEU254 3.6 18.9 1.0
NH2 B:ARG273 3.7 33.4 1.0
OD1 A:ASN255 3.7 20.9 1.0
CA A:ASN255 3.8 16.7 1.0
C B:ARG273 4.0 17.6 1.0
C A:SER253 4.2 23.2 1.0
CB A:SER258 4.2 14.9 1.0
N A:LEU254 4.3 17.7 1.0
OG A:SER258 4.4 16.1 1.0
N A:GLY276 4.6 15.6 1.0
CB A:LEU254 4.6 17.1 1.0
N A:ASP277 4.7 17.4 1.0
CD2 A:LEU254 4.7 19.2 1.0
O A:LEU254 4.8 18.4 1.0
CA B:ARG273 4.8 17.4 1.0
CZ B:ARG273 4.9 42.8 1.0
CB B:THR274 4.9 29.3 1.0
C A:ASN255 4.9 17.0 1.0
N B:THR274 4.9 15.7 1.0
O A:LEU275 4.9 16.2 1.0
CA B:THR274 4.9 17.7 1.0
O A:ASN255 5.0 15.2 1.0
OG1 B:THR274 5.0 38.2 1.0

Sodium binding site 4 out of 6 in 6cni

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Sodium binding site 4 out of 6 in the Crystal Structure of H105A PGAM5 Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of H105A PGAM5 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:25.6
occ:1.00
 O B:ASN256 2.7 17.7 1.0
N B:THR287 3.1 17.7 1.0
CA B:ILE286 3.3 21.9 1.0
O B:THR287 3.4 20.8 1.0
SD B:MET281 3.6 20.8 1.0
CG2 B:ILE286 3.6 20.5 1.0
CB B:ASN255 3.7 17.1 1.0
NE2 B:GLN127 3.7 19.2 1.0
C B:ILE286 3.7 22.0 1.0
C B:ASN256 3.8 16.9 1.0
N B:ASN256 3.8 15.8 1.0
CG2 B:THR278 3.8 21.1 1.0
CB B:ILE286 3.8 18.9 1.0
O B:LYS285 4.0 21.6 1.0
CE B:MET281 4.1 20.7 1.0
CG1 B:ILE286 4.1 21.8 1.0
CA B:ASN256 4.1 16.7 1.0
CB B:ASN256 4.1 15.7 1.0
CA B:THR287 4.2 18.7 1.0
CD B:GLN127 4.2 19.2 1.0
C B:THR287 4.2 20.6 1.0
C B:ASN255 4.3 15.1 1.0
N B:ILE286 4.4 19.2 1.0
CB B:THR278 4.4 21.0 1.0
CG B:ASN255 4.4 22.3 1.0
CA B:ASN255 4.5 17.5 1.0
OG1 B:THR287 4.6 23.1 1.0
C B:LYS285 4.6 23.8 1.0
CG B:GLN127 4.6 18.4 1.0
OG1 B:THR278 4.7 21.7 1.0
ND2 B:ASN255 4.8 20.7 1.0
OE1 B:GLN127 4.9 18.5 1.0
O B:ILE286 5.0 23.2 1.0
N B:GLY257 5.0 14.5 1.0

Sodium binding site 5 out of 6 in 6cni

Go back to Sodium Binding Sites List in 6cni
Sodium binding site 5 out of 6 in the Crystal Structure of H105A PGAM5 Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of H105A PGAM5 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:32.8
occ:1.00
 O B:ARG118 2.7 24.7 1.0
NH2 B:ARG152 3.0 27.9 1.0
N B:ARG152 3.0 23.3 1.0
O B:HOH501 3.1 31.4 1.0
CG B:ARG152 3.3 19.9 1.0
CB B:ARG152 3.3 23.9 1.0
CB B:ARG118 3.4 30.1 1.0
CD B:ARG152 3.5 23.3 1.0
N B:THR151 3.7 24.4 1.0
CA B:ARG152 3.7 27.5 1.0
CB B:THR151 3.8 26.9 1.0
C B:ARG118 3.8 27.3 1.0
C B:THR151 3.9 25.2 1.0
CZ B:ARG152 4.0 25.1 1.0
CA B:THR151 4.0 24.9 1.0
NE B:ARG152 4.2 22.4 1.0
CA B:ARG118 4.2 28.8 1.0
CD2 B:TYR108 4.2 22.6 1.0
CB B:MET150 4.4 30.6 1.0
C B:MET150 4.4 25.1 1.0
CE2 B:TYR108 4.4 24.4 1.0
O B:GLU115 4.5 43.0 1.0
OG1 B:THR151 4.5 30.3 1.0
CG B:ARG118 4.7 31.0 1.0
O B:HOH491 4.7 40.2 1.0
CG2 B:THR151 4.8 27.8 1.0
CD B:ARG118 4.8 33.6 1.0
CG B:TYR108 4.8 20.2 1.0
CA B:MET150 4.9 26.1 1.0
C B:ARG152 5.0 24.9 1.0
N B:THR119 5.0 26.5 1.0

Sodium binding site 6 out of 6 in 6cni

Go back to Sodium Binding Sites List in 6cni
Sodium binding site 6 out of 6 in the Crystal Structure of H105A PGAM5 Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of H105A PGAM5 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:25.7
occ:1.00
 O A:ARG273 2.7 20.9 1.0
O B:GLY276 2.8 19.1 1.0
N B:ASN255 2.8 17.8 1.0
CA B:GLY276 3.3 18.2 1.0
O B:SER253 3.3 26.3 1.0
CG B:ASN255 3.4 22.3 1.0
ND2 B:ASN255 3.4 20.7 1.0
C B:GLY276 3.4 17.3 1.0
CA B:LEU254 3.5 16.2 1.0
C B:LEU254 3.6 17.1 1.0
CB B:ASN255 3.6 17.1 1.0
CA B:ASN255 3.8 17.5 1.0
OD1 B:ASN255 3.9 20.2 1.0
C A:ARG273 3.9 16.0 1.0
CG2 A:THR274 4.1 17.6 0.4
CD A:ARG273 4.1 26.5 1.0
C B:SER253 4.2 24.8 1.0
CB B:SER258 4.3 17.0 1.0
N B:LEU254 4.4 18.0 1.0
OG B:SER258 4.4 17.5 1.0
CG A:ARG273 4.5 20.6 1.0
CB B:LEU254 4.6 18.6 1.0
N B:GLY276 4.6 16.6 1.0
CD2 B:LEU254 4.6 24.8 1.0
CA A:ARG273 4.7 15.5 1.0
N B:ASP277 4.7 17.8 1.0
O B:LEU254 4.8 20.5 1.0
C B:ASN255 4.9 15.1 1.0
N A:THR274 4.9 17.3 1.0
O B:ASN255 4.9 16.8 1.0
CA A:THR274 5.0 16.6 0.6
CA A:THR274 5.0 17.0 0.4
CB A:THR274 5.0 21.0 0.6
O B:LEU275 5.0 16.6 1.0
OG1 A:THR274 5.0 23.5 0.6

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: Tue Dec 15 12:03:52 2020

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