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Magnesium in PDB 5zwk: Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp

Protein crystallography data

The structure of Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp, PDB code: 5zwk was solved by H.Yunyuan, G.Zeyuan, Y.Junjie, Y.Ping, W.Jian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.13 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.006, 155.746, 76.082, 90.00, 115.54, 90.00
R / Rfree (%) 19.4 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp (pdb code 5zwk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp, PDB code: 5zwk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5zwk

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Magnesium binding site 1 out of 8 in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:56.9
occ:1.00
 OD1 A:ASP121 1.8 50.6 1.0
OD2 A:ASP118 2.2 51.7 1.0
OE2 A:GLU280 2.3 51.0 1.0
O3P A:FBP401 2.5 61.5 1.0
CG A:ASP118 2.7 42.6 1.0
CG A:ASP121 2.8 46.2 1.0
CD A:GLU280 3.1 41.7 1.0
OD1 A:ASP118 3.1 41.3 1.0
MG A:MG404 3.1 56.4 1.0
O1 A:FBP401 3.2 64.1 1.0
CB A:ASP121 3.3 39.0 1.0
P1 A:FBP401 3.4 66.1 1.0
CG A:GLU280 3.5 37.0 1.0
CA A:ASP121 3.6 38.8 1.0
CB A:ASP118 3.7 37.8 1.0
O2P A:FBP401 3.9 53.5 1.0
OD2 A:ASP121 3.9 45.2 1.0
C1 A:FBP401 4.0 51.7 1.0
OE1 A:GLU280 4.0 41.6 1.0
N A:GLY122 4.5 43.5 1.0
N A:ASP121 4.6 39.9 1.0
C A:ASP121 4.6 40.4 1.0
O1P A:FBP401 4.7 65.0 1.0
CD1 A:ILE135 4.8 35.9 1.0
CG A:GLU97 5.0 53.0 1.0
CB A:GLU280 5.0 36.4 1.0

Magnesium binding site 2 out of 8 in 5zwk

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Magnesium binding site 2 out of 8 in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:56.4
occ:1.00
 OD1 A:ASP118 2.2 41.3 1.0
O3P A:FBP401 2.4 61.5 1.0
O A:HOH554 2.7 41.5 1.0
O A:LEU120 2.8 46.6 1.0
O2P A:FBP401 2.9 53.5 1.0
CG A:ASP118 3.0 42.6 1.0
MG A:MG403 3.1 56.9 1.0
P1 A:FBP401 3.2 66.1 1.0
OD2 A:ASP118 3.2 51.7 1.0
CA A:ASP121 3.4 38.8 1.0
C A:LEU120 3.5 38.7 1.0
N A:ASP121 3.8 39.9 1.0
OD1 A:ASP121 4.1 50.6 1.0
OE1 A:GLU97 4.2 61.9 1.0
CB A:ASP121 4.3 39.0 1.0
O1P A:FBP401 4.3 65.0 1.0
O1 A:FBP401 4.3 64.1 1.0
N A:GLY122 4.3 43.5 1.0
CG A:GLU97 4.3 53.0 1.0
C A:ASP121 4.3 40.4 1.0
CD A:GLU97 4.4 61.4 1.0
CB A:ASP118 4.4 37.8 1.0
CG A:ASP121 4.6 46.2 1.0
N A:LEU120 4.7 31.7 1.0
CA A:LEU120 4.7 37.0 1.0
CB A:GLU97 4.7 44.9 1.0
CB A:SER123 4.8 55.1 1.0
N A:SER123 4.8 54.1 1.0

Magnesium binding site 3 out of 8 in 5zwk

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Magnesium binding site 3 out of 8 in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp


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 Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:37.4
occ:1.00
 O1P B:FBP401 2.2 54.9 1.0
OD1 B:ASP118 2.2 33.0 1.0
OE2 B:GLU97 2.4 57.5 1.0
O B:LEU120 2.6 37.6 1.0
O B:HOH516 2.7 35.8 1.0
OD2 B:ASP118 2.8 42.4 1.0
CG B:ASP118 2.8 34.9 1.0
MG B:MG404 3.1 50.7 1.0
C B:LEU120 3.4 35.0 1.0
CD B:GLU97 3.5 51.4 1.0
CA B:ASP121 3.6 34.3 1.0
P1 B:FBP401 3.7 55.4 1.0
N B:ASP121 3.8 34.3 1.0
O3P B:FBP401 4.2 51.4 1.0
CG B:GLU97 4.3 44.2 1.0
CB B:ASP118 4.4 35.7 1.0
OE1 B:GLU97 4.4 61.3 1.0
N B:LEU120 4.5 32.2 1.0
CB B:ASP121 4.5 39.7 1.0
O1 B:FBP401 4.5 47.3 1.0
CA B:LEU120 4.5 33.7 1.0
O2P B:FBP401 4.5 47.9 1.0
N B:GLY122 4.6 37.6 1.0
OE2 B:GLU98 4.6 52.8 1.0
C B:ASP121 4.6 38.6 1.0
CB B:GLU97 4.7 42.7 1.0
OD2 B:ASP74 4.7 65.6 1.0
OE2 B:GLU280 4.8 43.7 1.0

Magnesium binding site 4 out of 8 in 5zwk

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Magnesium binding site 4 out of 8 in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp


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 Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:50.7
occ:1.00
 OD2 B:ASP118 2.1 42.4 1.0
OE2 B:GLU280 2.1 43.7 1.0
O1P B:FBP401 2.4 54.9 1.0
O1 B:FBP401 2.5 47.3 1.0
OD1 B:ASP121 2.8 39.3 1.0
P1 B:FBP401 3.0 55.4 1.0
MG B:MG403 3.1 37.4 1.0
OE2 B:GLU97 3.1 57.5 1.0
CG B:ASP118 3.3 34.9 1.0
CD B:GLU280 3.3 41.2 1.0
CB B:ASP121 3.6 39.7 1.0
CG B:ASP121 3.6 37.6 1.0
CA B:ASP121 3.6 34.3 1.0
C1 B:FBP401 3.7 45.6 1.0
OD1 B:ASP118 3.9 33.0 1.0
O3P B:FBP401 3.9 51.4 1.0
CG B:GLU280 4.0 34.7 1.0
O2P B:FBP401 4.1 47.9 1.0
O B:HOH552 4.2 47.6 1.0
CD B:GLU97 4.2 51.4 1.0
N B:GLY122 4.2 37.6 1.0
OE1 B:GLU280 4.3 41.0 1.0
CB B:ASP118 4.4 35.7 1.0
O3 B:FBP401 4.5 38.5 1.0
OE1 B:GLU97 4.5 61.3 1.0
C B:ASP121 4.5 38.6 1.0
C2 B:FBP401 4.7 45.6 1.0
N B:ASP121 4.7 34.3 1.0
O B:LEU120 4.8 37.6 1.0
C3 B:FBP401 4.8 40.1 1.0
OD2 B:ASP121 4.8 46.6 1.0
O2 B:FBP401 5.0 43.5 1.0

Magnesium binding site 5 out of 8 in 5zwk

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Magnesium binding site 5 out of 8 in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp


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 Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:62.6
occ:1.00
 O C:HOH540 2.3 43.8 1.0
O2P C:FBP401 2.4 59.3 1.0
O C:LEU120 2.4 40.6 1.0
OD1 C:ASP118 3.0 48.4 1.0
C C:LEU120 3.2 37.7 1.0
OE1 C:GLU97 3.5 58.3 1.0
P1 C:FBP401 3.6 73.3 1.0
CA C:ASP121 3.7 41.8 1.0
O1P C:FBP401 3.8 59.7 1.0
N C:ASP121 3.8 42.1 1.0
OE2 C:GLU97 3.8 64.4 1.0
MG C:MG404 3.8 53.7 1.0
CG C:ASP118 3.9 44.0 1.0
CD C:GLU97 3.9 59.6 1.0
OD2 C:ASP118 3.9 53.2 1.0
CA C:LEU120 4.3 39.9 1.0
N C:LEU120 4.3 39.1 1.0
N C:GLY122 4.4 45.1 1.0
C C:ASP121 4.5 41.7 1.0
O3P C:FBP401 4.5 66.2 1.0
OE2 C:GLU98 4.5 62.2 1.0
CB C:ASP121 4.7 39.9 1.0
O1 C:FBP401 4.8 61.0 1.0
CB C:LEU120 4.8 35.5 1.0

Magnesium binding site 6 out of 8 in 5zwk

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Magnesium binding site 6 out of 8 in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp


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 Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:53.7
occ:1.00
 OE2 C:GLU280 2.0 56.2 1.0
O2P C:FBP401 2.1 59.3 1.0
OD2 C:ASP118 2.1 53.2 1.0
OD1 C:ASP121 2.4 50.5 1.0
O1 C:FBP401 2.4 61.0 1.0
P1 C:FBP401 2.8 73.3 1.0
OE1 C:GLU97 3.1 58.3 1.0
CG C:ASP118 3.3 44.0 1.0
CD C:GLU280 3.3 46.4 1.0
CG C:ASP121 3.3 51.1 1.0
CB C:ASP121 3.5 39.9 1.0
C1 C:FBP401 3.6 53.9 1.0
O3P C:FBP401 3.8 66.2 1.0
OD1 C:ASP118 3.8 48.4 1.0
CA C:ASP121 3.8 41.8 1.0
MG C:MG403 3.8 62.6 1.0
O1P C:FBP401 3.9 59.7 1.0
CG C:GLU280 4.0 40.2 1.0
OE1 C:GLU280 4.2 43.1 1.0
CD C:GLU97 4.3 59.6 1.0
CB C:ASP118 4.4 41.5 1.0
OD2 C:ASP121 4.5 46.5 1.0
N C:GLY122 4.5 45.1 1.0
C C:ASP121 4.7 41.7 1.0
C2 C:FBP401 4.7 53.3 1.0
O3 C:FBP401 4.8 45.3 1.0
N C:ASP121 4.8 42.1 1.0
C3 C:FBP401 4.9 48.5 1.0

Magnesium binding site 7 out of 8 in 5zwk

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Magnesium binding site 7 out of 8 in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp


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 Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:47.6
occ:1.00
 O1P D:FBP401 2.3 42.8 1.0
O D:LEU120 2.4 37.7 1.0
OD1 D:ASP118 2.4 35.5 1.0
OE1 D:GLU97 2.7 60.3 1.0
OE2 D:GLU97 2.8 67.1 1.0
CD D:GLU97 2.9 52.7 1.0
OD2 D:ASP118 3.0 38.3 1.0
CG D:ASP118 3.0 37.3 1.0
C D:LEU120 3.5 32.5 1.0
P1 D:FBP401 3.8 50.6 1.0
MG D:MG404 3.9 43.5 1.0
CG D:GLU97 4.1 50.9 1.0
CA D:ASP121 4.1 33.5 1.0
N D:ASP121 4.2 33.4 1.0
O3P D:FBP401 4.3 41.0 1.0
N D:LEU120 4.4 31.9 1.0
CB D:GLU97 4.4 41.5 1.0
CA D:LEU120 4.5 35.6 1.0
O2P D:FBP401 4.5 43.1 1.0
CB D:ASP118 4.5 29.5 1.0
OE2 D:GLU98 4.5 49.8 1.0
OD1 D:ASP74 4.7 54.2 1.0
CB D:ASP121 4.9 39.5 1.0
O1 D:FBP401 4.9 45.6 1.0

Magnesium binding site 8 out of 8 in 5zwk

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Magnesium binding site 8 out of 8 in the Crystal Structure of Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp


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 Human Liver Fructose-1,6-Bisphoaphatase Complex with Fructose-1,6-Bisphophate and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:43.5
occ:1.00
 OD1 D:ASP121 2.1 39.5 1.0
OD2 D:ASP118 2.2 38.3 1.0
OE2 D:GLU280 2.3 39.6 1.0
O1 D:FBP401 2.4 45.6 1.0
O1P D:FBP401 2.4 42.8 1.0
P1 D:FBP401 2.9 50.6 1.0
CG D:ASP121 3.0 41.0 1.0
CB D:ASP121 3.2 39.5 1.0
CD D:GLU280 3.4 36.0 1.0
CG D:ASP118 3.5 37.3 1.0
CA D:ASP121 3.5 33.5 1.0
OE2 D:GLU97 3.6 67.1 1.0
C1 D:FBP401 3.7 37.2 1.0
NH2 D:ARG276 3.8 47.4 1.0
O2P D:FBP401 3.9 43.1 1.0
MG D:MG403 3.9 47.6 1.0
CG D:GLU280 4.0 36.1 1.0
O3P D:FBP401 4.1 41.0 1.0
O3 D:FBP401 4.1 37.0 1.0
N D:GLY122 4.1 34.6 1.0
OD2 D:ASP121 4.2 40.0 1.0
OD1 D:ASP118 4.3 35.5 1.0
C D:ASP121 4.3 34.2 1.0
OE1 D:GLU280 4.4 41.4 1.0
CB D:ASP118 4.4 29.5 1.0
C3 D:FBP401 4.4 34.3 1.0
C2 D:FBP401 4.5 39.4 1.0
CD D:GLU97 4.6 52.7 1.0
N D:ASP121 4.6 33.4 1.0
O D:LEU120 4.7 37.7 1.0
O2 D:FBP401 4.8 40.0 1.0
OE1 D:GLU97 4.9 60.3 1.0
CD1 D:ILE135 5.0 34.2 1.0

Reference:

H.Yunyuan, G.Zeyuan, Y.Junjie, Y.Ping, W.Jian, R.Li. Location of Fbpase Catalytic Metal Binding Site: A Combined Experimental and Theoretical Study To Be Published.
Page generated: Mon Sep 30 18:44:26 2024

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