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Magnesium in PDB 6ech: Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp

Enzymatic activity of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp

All present enzymatic activity of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp:
2.7.1.40;

Protein crystallography data

The structure of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp, PDB code: 6ech was solved by A.Padyana, S.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.52 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.550, 108.900, 296.840, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.8

Other elements in 6ech:

The structure of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp (pdb code 6ech). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp, PDB code: 6ech:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 6ech

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Magnesium binding site 1 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:34.6
occ:1.00
 OD2 A:ASP308 2.0 37.0 1.0
O3G A:ATP606 2.2 32.1 1.0
O3 A:OXL607 2.2 37.3 1.0
OE2 A:GLU284 2.3 33.8 1.0
O4 A:OXL607 2.4 35.7 1.0
C1 A:OXL607 3.1 35.8 1.0
CG A:ASP308 3.1 38.5 1.0
C2 A:OXL607 3.2 33.0 1.0
CD A:GLU284 3.2 34.4 1.0
PG A:ATP606 3.3 32.7 1.0
OE1 A:GLU284 3.5 35.0 1.0
O2G A:ATP606 3.8 33.4 1.0
CB A:ASP308 3.8 36.9 1.0
MG A:MG605 3.9 69.5 1.0
O1G A:ATP606 4.0 34.6 1.0
NZ A:LYS282 4.1 42.7 1.0
OD1 A:ASP308 4.2 40.9 1.0
O1 A:OXL607 4.2 41.1 1.0
CE2 A:PHE256 4.3 42.7 1.0
O2 A:OXL607 4.4 32.8 1.0
N A:ASP308 4.5 33.1 1.0
O3B A:ATP606 4.5 36.2 1.0
CE A:LYS282 4.5 41.6 1.0
O A:HOH740 4.5 46.0 1.0
CG A:GLU284 4.6 37.9 1.0
CA A:ASP308 4.7 35.4 1.0
CB A:ALA305 4.8 31.8 1.0
CD2 A:PHE256 4.9 44.8 1.0
OD1 A:ASP190 5.0 32.7 1.0

Magnesium binding site 2 out of 13 in 6ech

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Magnesium binding site 2 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:49.8
occ:1.00
 O1A A:ATP606 2.1 34.8 1.0
O1G A:ATP606 2.1 34.6 1.0
O1B A:ATP606 2.3 31.0 1.0
PG A:ATP606 3.3 32.7 1.0
PB A:ATP606 3.4 33.8 1.0
PA A:ATP606 3.4 32.5 1.0
O3G A:ATP606 3.6 32.1 1.0
O3B A:ATP606 3.7 36.2 1.0
O3A A:ATP606 3.7 30.6 1.0
OD2 A:ASP190 3.8 37.8 1.0
C1 A:OXL607 4.0 35.8 1.0
C2 A:OXL607 4.1 33.0 1.0
O1 A:OXL607 4.1 41.1 1.0
CG2 A:THR340 4.1 33.7 1.0
O A:HOH725 4.2 37.9 1.0
OG1 A:THR340 4.3 30.9 1.0
O2 A:OXL607 4.3 32.8 1.0
OG A:SER374 4.4 34.9 1.0
O4 A:OXL607 4.4 35.7 1.0
CB A:SER374 4.5 33.9 1.0
O3 A:OXL607 4.5 37.3 1.0
O A:HOH731 4.5 40.0 1.0
O2A A:ATP606 4.5 28.1 1.0
O5' A:ATP606 4.6 31.4 1.0
O2G A:ATP606 4.6 33.4 1.0
O A:HOH781 4.7 35.1 1.0
NH1 A:ARG85 4.7 38.6 1.0
O2B A:ATP606 4.8 38.5 1.0
C5' A:ATP606 4.8 31.6 1.0
CG A:ASP190 4.8 40.0 1.0
CB A:THR340 4.9 30.5 1.0

Magnesium binding site 3 out of 13 in 6ech

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Magnesium binding site 3 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:25.0
occ:1.00
 OD1 A:ASP125 2.4 35.5 1.0
O A:HOH740 2.7 46.0 1.0
O A:THR126 2.7 31.1 1.0
O2G A:ATP606 2.7 33.4 1.0
OD1 A:ASN87 2.8 34.3 1.0
OG A:SER89 2.8 39.2 1.0
OG A:SER255 3.3 35.0 1.0
CG A:ASN87 3.6 33.1 1.0
CG A:ASP125 3.6 35.5 1.0
ND2 A:ASN87 3.7 30.9 1.0
CB A:SER89 3.8 39.3 1.0
C A:THR126 3.8 31.0 1.0
NZ A:LYS282 4.0 42.7 1.0
PG A:ATP606 4.2 32.7 1.0
O A:ASP125 4.3 33.2 1.0
N A:SER89 4.4 34.2 1.0
OD2 A:ASP125 4.4 32.2 1.0
CA A:LYS127 4.4 36.9 1.0
CB A:SER255 4.4 35.3 1.0
C A:ASP125 4.4 33.8 1.0
N A:LYS127 4.5 34.0 1.0
N A:THR126 4.5 34.7 1.0
CB A:ASP125 4.5 34.5 1.0
OE1 A:GLU130 4.6 41.6 1.0
OE2 A:GLU130 4.6 44.4 1.0
NH2 A:ARG132 4.6 37.8 1.0
O A:LYS127 4.7 37.2 1.0
CA A:SER89 4.7 36.1 1.0
O3B A:ATP606 4.7 36.2 1.0
NH1 A:ARG85 4.7 38.6 1.0
CA A:THR126 4.8 32.4 1.0
CB A:ASN87 4.9 31.5 1.0
CD A:GLU130 4.9 42.0 1.0
C A:LYS127 5.0 38.6 1.0

Magnesium binding site 4 out of 13 in 6ech

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Magnesium binding site 4 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:69.5
occ:1.00
 O A:HOH934 2.5 44.6 1.0
OD2 A:ASP308 2.6 37.0 1.0
O A:HOH766 2.7 32.0 1.0
OD1 A:ASP308 2.7 40.9 1.0
CG A:ASP308 3.0 38.5 1.0
O3G A:ATP606 3.4 32.1 1.0
OD1 A:ASP190 3.4 32.7 1.0
NH2 A:ARG132 3.5 37.8 1.0
CA A:GLY220 3.6 43.6 1.0
MG A:MG602 3.9 34.6 1.0
O A:HOH861 4.1 38.6 1.0
CZ A:ARG132 4.3 39.4 1.0
N A:GLY220 4.4 46.1 1.0
O3B A:ATP606 4.4 36.2 1.0
OE2 A:GLU130 4.4 44.4 1.0
CB A:ASP308 4.5 36.9 1.0
PG A:ATP606 4.6 32.7 1.0
CG A:ASP190 4.6 40.0 1.0
C A:GLY220 4.6 39.9 1.0
ND2 A:ASN222 4.7 31.2 1.0
CE2 A:PHE256 4.8 42.7 1.0
NH1 A:ARG132 4.8 35.4 1.0
O A:HOH862 4.9 37.6 1.0

Magnesium binding site 5 out of 13 in 6ech

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Magnesium binding site 5 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:38.6
occ:1.00
 O1 B:OXL607 2.0 37.0 1.0
O2 B:OXL607 2.1 33.6 1.0
OD2 B:ASP308 2.1 33.3 1.0
O2G B:ATP606 2.2 25.1 1.0
OE2 B:GLU284 2.2 38.5 1.0
C1 B:OXL607 2.9 45.3 1.0
C2 B:OXL607 2.9 41.0 1.0
CG B:ASP308 3.2 33.3 1.0
CD B:GLU284 3.3 39.9 1.0
PG B:ATP606 3.3 31.5 1.0
OE1 B:GLU284 3.6 39.1 1.0
CB B:ASP308 3.7 32.7 1.0
O1G B:ATP606 3.8 31.1 1.0
O B:HOH753 4.0 32.5 1.0
NZ B:LYS282 4.1 41.8 1.0
O3G B:ATP606 4.1 33.2 1.0
O3 B:OXL607 4.1 44.6 1.0
O4 B:OXL607 4.2 36.4 1.0
MG B:MG605 4.3 44.4 1.0
OD1 B:ASP308 4.3 31.8 1.0
N B:ASP308 4.4 31.0 1.0
CE2 B:PHE256 4.4 49.1 1.0
CE B:LYS282 4.4 38.1 1.0
O3B B:ATP606 4.5 33.8 1.0
CG B:GLU284 4.6 38.9 1.0
CA B:ASP308 4.7 31.5 1.0
O B:HOH837 4.7 36.6 1.0
CB B:ALA305 4.8 37.2 1.0
CZ B:PHE256 4.8 46.8 1.0
OD1 B:ASP190 5.0 34.0 1.0
CB B:GLU284 5.0 39.8 1.0

Magnesium binding site 6 out of 13 in 6ech

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Magnesium binding site 6 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:25.9
occ:1.00
 O B:HOH837 2.5 36.6 1.0
OD1 B:ASN87 2.5 40.2 1.0
OD1 B:ASP125 2.5 36.4 1.0
O1G B:ATP606 2.6 31.1 1.0
O B:THR126 2.8 37.8 1.0
OG B:SER89 3.0 39.0 1.0
CG B:ASN87 3.4 37.9 1.0
OG B:SER255 3.4 34.4 1.0
CG B:ASP125 3.7 37.4 1.0
CB B:SER89 3.7 39.0 1.0
ND2 B:ASN87 3.8 38.5 1.0
C B:THR126 3.8 39.9 1.0
NZ B:LYS282 4.1 41.8 1.0
PG B:ATP606 4.1 31.5 1.0
O B:ASP125 4.2 40.0 1.0
NH2 B:ARG132 4.3 42.0 1.0
N B:SER89 4.4 41.2 1.0
OD2 B:ASP125 4.4 40.4 1.0
CB B:SER255 4.4 36.9 1.0
CA B:LYS127 4.5 42.0 1.0
C B:ASP125 4.5 36.0 1.0
N B:LYS127 4.5 39.8 1.0
NH1 B:ARG85 4.5 31.9 1.0
CB B:ASP125 4.6 38.1 1.0
CA B:SER89 4.6 38.1 1.0
O3B B:ATP606 4.6 33.8 1.0
N B:THR126 4.7 39.4 1.0
OE2 B:GLU130 4.7 48.8 1.0
OE1 B:GLU130 4.7 41.2 1.0
O B:LYS127 4.7 36.6 1.0
CB B:ASN87 4.7 36.7 1.0
O2G B:ATP606 4.8 25.1 1.0
CA B:THR126 4.9 38.1 1.0
N B:PHE88 4.9 40.5 1.0

Magnesium binding site 7 out of 13 in 6ech

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Magnesium binding site 7 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:35.8
occ:1.00
 O3G B:ATP606 2.0 33.2 1.0
O2A B:ATP606 2.0 37.0 1.0
O1B B:ATP606 2.2 28.2 1.0
O B:HOH714 2.3 25.4 1.0
PB B:ATP606 3.2 37.4 1.0
PG B:ATP606 3.2 31.5 1.0
PA B:ATP606 3.3 36.0 1.0
O3B B:ATP606 3.5 33.8 1.0
O3A B:ATP606 3.5 33.7 1.0
O2G B:ATP606 3.6 25.1 1.0
OD2 B:ASP190 3.8 35.5 1.0
C1 B:OXL607 4.1 45.3 1.0
OG B:SER374 4.1 32.4 1.0
C2 B:OXL607 4.1 41.0 1.0
O B:HOH746 4.1 38.4 1.0
O3 B:OXL607 4.2 44.6 1.0
O B:HOH721 4.2 38.9 1.0
CG2 B:THR340 4.3 35.1 1.0
O4 B:OXL607 4.4 36.4 1.0
O1A B:ATP606 4.4 33.6 1.0
O2 B:OXL607 4.4 33.6 1.0
CB B:SER374 4.5 35.1 1.0
OG1 B:THR340 4.5 35.7 1.0
O5' B:ATP606 4.5 35.0 1.0
O1 B:OXL607 4.5 37.0 1.0
C5' B:ATP606 4.5 36.6 1.0
O B:HOH753 4.6 32.5 1.0
O B:HOH828 4.6 32.2 1.0
O1G B:ATP606 4.6 31.1 1.0
O2B B:ATP606 4.6 35.0 1.0
NH1 B:ARG85 4.8 31.9 1.0
CG B:ASP190 4.9 35.4 1.0

Magnesium binding site 8 out of 13 in 6ech

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Magnesium binding site 8 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:44.4
occ:1.00
 OD1 B:ASP308 2.4 31.8 1.0
O B:HOH753 2.4 32.5 1.0
O B:HOH726 2.6 35.4 1.0
OD2 B:ASP308 2.6 33.3 1.0
CG B:ASP308 2.8 33.3 1.0
CA B:GLY220 3.6 32.6 1.0
OD1 B:ASP190 3.7 34.0 1.0
NH2 B:ARG132 4.0 42.0 1.0
O2G B:ATP606 4.0 25.1 1.0
ND2 B:ASN222 4.3 32.2 1.0
CZ B:PHE256 4.3 46.8 1.0
MG B:MG602 4.3 38.6 1.0
O B:HOH831 4.3 40.1 1.0
CE2 B:PHE256 4.3 49.1 1.0
CB B:ASP308 4.4 32.7 1.0
OE2 B:GLU130 4.4 48.8 1.0
C B:GLY220 4.4 32.8 1.0
O B:HOH865 4.4 33.8 1.0
N B:GLY220 4.5 35.4 1.0
OD1 B:ASN222 4.5 45.4 1.0
CZ B:ARG132 4.5 39.6 1.0
N B:VAL221 4.8 32.5 1.0
CG B:ASN222 4.8 36.6 1.0
NE B:ARG132 4.9 38.9 1.0
CG B:ASP190 4.9 35.4 1.0
O3B B:ATP606 5.0 33.8 1.0

Magnesium binding site 9 out of 13 in 6ech

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Magnesium binding site 9 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:47.7
occ:1.00
 OD2 C:ASP308 2.0 36.1 1.0
OE2 C:GLU284 2.1 32.6 1.0
O1 C:OXL604 2.3 33.5 1.0
O2 C:OXL604 2.3 44.2 1.0
CD C:GLU284 3.1 32.4 1.0
C1 C:OXL604 3.1 43.7 1.0
C2 C:OXL604 3.2 43.0 1.0
CG C:ASP308 3.2 37.8 1.0
OE1 C:GLU284 3.4 34.0 1.0
O C:HOH851 3.6 43.4 1.0
CB C:ASP308 3.8 39.0 1.0
O C:HOH800 3.8 48.4 1.0
CZ C:PHE256 4.0 57.3 1.0
NZ C:LYS282 4.1 39.3 1.0
OD1 C:ASP308 4.2 40.2 1.0
CE2 C:PHE256 4.3 55.5 1.0
O C:HOH806 4.4 49.7 1.0
O3 C:OXL604 4.4 50.2 1.0
O4 C:OXL604 4.4 37.7 1.0
CG C:GLU284 4.5 38.6 1.0
N C:ASP308 4.6 32.7 1.0
CE C:LYS282 4.6 37.5 1.0
CE1 C:PHE256 4.7 51.0 1.0
CA C:ASP308 4.8 36.9 1.0
O C:HOH764 4.9 44.2 1.0
CB C:ALA305 5.0 34.4 1.0
O C:HOH971 5.0 51.4 1.0

Magnesium binding site 10 out of 13 in 6ech

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Magnesium binding site 10 out of 13 in the Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Pyruvate Kinase Isoform L-Type with Phosphorylated SER12 (PS12) in Complex with Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:26.8
occ:1.00
 O C:HOH806 2.6 49.7 1.0
O C:THR126 2.6 36.1 1.0
OD1 C:ASN87 2.6 33.4 1.0
O C:HOH851 2.7 43.4 1.0
OD1 C:ASP125 2.7 41.7 1.0
OG C:SER89 2.8 42.0 1.0
C C:THR126 3.6 38.7 1.0
OG C:SER255 3.6 29.0 1.0
CG C:ASP125 3.7 39.6 1.0
CG C:ASN87 3.7 29.7 1.0
CB C:SER89 3.7 42.4 1.0
O C:ASP125 3.9 36.6 1.0
NZ C:LYS282 4.0 39.3 1.0
N C:SER89 4.1 39.8 1.0
CA C:LYS127 4.1 41.9 1.0
O C:HOH865 4.2 48.5 1.0
N C:LYS127 4.2 40.2 1.0
C C:ASP125 4.2 35.1 1.0
ND2 C:ASN87 4.3 30.6 1.0
OD2 C:ASP125 4.4 42.2 1.0
NH2 C:ARG85 4.4 29.6 1.0
CA C:SER89 4.5 39.2 1.0
O C:LYS127 4.5 38.5 1.0
CB C:ASP125 4.5 34.9 1.0
N C:THR126 4.5 35.3 1.0
C C:LYS127 4.7 37.4 1.0
N C:PHE88 4.7 34.1 1.0
CA C:THR126 4.7 38.0 1.0
OE2 C:GLU130 4.7 53.5 1.0
CB C:SER255 4.8 32.9 1.0
CB C:ASN87 4.9 28.2 1.0
CA C:ASN87 4.9 29.1 1.0
C C:PHE88 4.9 35.7 1.0
CA C:ASP125 5.0 32.8 1.0

Reference:

B.M.Gassaway, R.L.Cardone, A.K.Padyana, M.C.Petersen, E.T.Judd, S.Hayes, S.Tong, K.W.Barber, M.Apostolidi, A.Abulizi, J.B.Sheetz, G.Kshitiz, H.R.Aerni, S.Gross, C.Kung, V.T.Samuel, G.I.Shulman, R.G.Kibbey, J.Rinehart. Distinct Hepatic Pka and Cdk Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production. Cell Rep 2019.
ISSN: ESSN 2211-1247
Page generated: Mon Sep 30 23:52:22 2024

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