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Zinc in PDB 5ldz: Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase

Enzymatic activity of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase

All present enzymatic activity of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase:
3.1.3.11;

Protein crystallography data

The structure of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase, PDB code: 5ldz was solved by A.Ruf, T.Tetaz, B.Schott, C.Joseph, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.80 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.519, 121.519, 316.580, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.9

Other elements in 5ldz:

The structure of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase (pdb code 5ldz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase, PDB code: 5ldz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5ldz

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Zinc binding site 1 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:50.0
occ:1.00
 OE2 A:GLU281 2.0 49.0 1.0
OD2 A:ASP119 2.0 40.9 1.0
OD1 A:ASP122 2.1 34.2 1.0
O A:HOH501 2.1 40.0 1.0
OE1 A:GLU98 2.3 70.3 1.0
CG A:ASP119 2.8 37.0 1.0
OD1 A:ASP119 3.0 36.9 1.0
CD A:GLU281 3.0 45.7 1.0
CG A:ASP122 3.1 41.6 1.0
CD A:GLU98 3.3 87.5 1.0
CB A:ASP122 3.6 38.9 1.0
CG A:GLU281 3.6 33.9 1.0
OE2 A:GLU98 3.6 92.3 1.0
CA A:ASP122 4.0 37.8 1.0
OE1 A:GLU281 4.1 43.6 1.0
O4 A:SO4403 4.1 54.9 1.0
CB A:ASP119 4.2 28.7 1.0
OD2 A:ASP122 4.3 49.3 1.0
O A:HOH515 4.6 43.8 1.0
CG A:GLU98 4.6 53.2 1.0
N A:ASP122 4.8 38.3 1.0

Zinc binding site 2 out of 9 in 5ldz

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Zinc binding site 2 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:38.6
occ:1.00
 NE2 A:HIS335 1.9 45.3 1.0
OE2 A:GLU226 2.0 39.2 1.0
O A:HOH570 2.2 18.4 1.0
CD A:GLU226 2.7 48.6 1.0
OE1 A:GLU226 2.7 38.8 1.0
CE1 A:HIS335 2.8 43.7 1.0
CD2 A:HIS335 3.0 45.9 1.0
ND1 A:HIS335 4.0 43.9 1.0
CG A:HIS335 4.0 43.1 1.0
CG A:GLU226 4.1 32.1 1.0
O A:HOH531 4.4 39.5 1.0
CB A:PRO222 4.5 39.9 1.0
O A:HOH532 5.0 46.2 1.0

Zinc binding site 3 out of 9 in 5ldz

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Zinc binding site 3 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:48.9
occ:1.00
 OD2 B:ASP119 1.9 49.9 1.0
OE2 B:GLU281 2.0 51.3 1.0
O B:HOH505 2.0 39.5 1.0
OD1 B:ASP122 2.1 30.1 1.0
OE1 B:GLU98 2.3 43.7 1.0
CG B:ASP119 2.7 42.9 1.0
OD1 B:ASP119 2.9 43.0 1.0
CD B:GLU281 3.0 51.6 1.0
CG B:ASP122 3.1 37.3 1.0
CD B:GLU98 3.3 77.9 1.0
CG B:GLU281 3.5 38.3 1.0
CB B:ASP122 3.6 29.7 1.0
OE2 B:GLU98 3.6 82.1 1.0
CA B:ASP122 4.0 29.8 1.0
OE1 B:GLU281 4.1 36.5 1.0
CB B:ASP119 4.1 32.4 1.0
O3 B:SO4402 4.2 56.9 1.0
OD2 B:ASP122 4.3 45.5 1.0
CG B:GLU98 4.6 52.9 1.0
O B:HOH534 4.7 37.1 1.0
N B:ASP122 4.8 29.1 1.0
CD1 B:ILE136 4.9 33.2 1.0
CB B:GLU281 4.9 33.3 1.0

Zinc binding site 4 out of 9 in 5ldz

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Zinc binding site 4 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:50.0
occ:1.00
 OD2 C:ASP119 1.9 58.1 1.0
OE2 C:GLU281 2.0 44.8 1.0
O C:HOH504 2.1 31.8 1.0
OD1 C:ASP122 2.1 34.5 1.0
OE1 C:GLU98 2.3 55.0 1.0
CG C:ASP119 2.7 46.9 1.0
OD1 C:ASP119 2.9 45.9 1.0
CD C:GLU281 3.1 46.0 1.0
CG C:ASP122 3.2 42.3 1.0
CD C:GLU98 3.2 77.4 1.0
O C:HOH542 3.5 57.7 1.0
CG C:GLU281 3.5 40.1 1.0
CB C:ASP122 3.6 36.1 1.0
OE2 C:GLU98 3.6 83.0 1.0
CA C:ASP122 4.0 36.3 1.0
CB C:ASP119 4.1 35.1 1.0
OE1 C:GLU281 4.2 44.1 1.0
O1 C:SO4402 4.2 55.7 1.0
OD2 C:ASP122 4.3 47.8 1.0
CG C:GLU98 4.6 52.1 1.0
N C:ASP122 4.8 35.5 1.0
O C:HOH516 4.8 53.1 1.0
CD1 C:ILE136 5.0 32.6 1.0
CB C:GLU281 5.0 33.4 1.0

Zinc binding site 5 out of 9 in 5ldz

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Zinc binding site 5 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:47.3
occ:1.00
 OE2 D:GLU281 2.0 56.4 1.0
OD2 D:ASP119 2.0 50.2 1.0
OD1 D:ASP122 2.0 34.0 1.0
O D:HOH502 2.1 39.4 1.0
OE1 D:GLU98 2.3 83.1 1.0
CG D:ASP119 2.8 40.4 1.0
OD1 D:ASP119 3.0 39.4 1.0
CD D:GLU281 3.1 47.8 1.0
CG D:ASP122 3.1 38.4 1.0
CD D:GLU98 3.3 89.7 1.0
CB D:ASP122 3.5 34.8 1.0
CG D:GLU281 3.5 37.6 1.0
OE2 D:GLU98 3.7 94.0 1.0
CA D:ASP122 3.9 34.1 1.0
O2 D:SO4403 4.0 50.3 1.0
OE1 D:GLU281 4.1 45.6 1.0
OD2 D:ASP122 4.2 45.4 1.0
CB D:ASP119 4.2 32.8 1.0
CG D:GLU98 4.7 55.6 1.0
O D:HOH514 4.8 46.6 1.0
N D:ASP122 4.8 34.6 1.0
CD1 D:ILE136 5.0 41.9 1.0

Zinc binding site 6 out of 9 in 5ldz

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Zinc binding site 6 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:41.3
occ:1.00
 OE2 D:GLU226 2.0 52.3 1.0
NE2 D:HIS335 2.0 44.5 1.0
O D:HOH578 2.3 16.5 1.0
CD D:GLU226 2.7 55.3 1.0
OE1 D:GLU226 2.8 36.6 1.0
CE1 D:HIS335 2.9 43.6 1.0
CD2 D:HIS335 3.1 45.3 1.0
ND1 D:HIS335 4.0 44.5 1.0
CG D:HIS335 4.1 43.3 1.0
CG D:GLU226 4.2 39.3 1.0
NZ D:LYS334 4.4 70.9 1.0
O D:HOH563 4.6 48.5 1.0
CB D:PRO222 4.6 40.0 1.0
O D:HOH531 4.8 46.4 1.0

Zinc binding site 7 out of 9 in 5ldz

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Zinc binding site 7 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:50.8
occ:1.00
 OE2 E:GLU281 2.1 48.0 1.0
OD1 E:ASP122 2.1 37.4 1.0
OD2 E:ASP119 2.1 55.6 1.0
OE1 E:GLU98 2.2 54.9 1.0
O E:HOH501 2.3 35.9 1.0
CG E:ASP119 2.9 47.2 1.0
OD1 E:ASP119 3.0 46.2 1.0
CD E:GLU281 3.1 54.5 1.0
CG E:ASP122 3.2 41.4 1.0
CD E:GLU98 3.3 77.2 1.0
O E:HOH554 3.6 63.0 1.0
CB E:ASP122 3.6 33.0 1.0
CG E:GLU281 3.7 41.3 1.0
OE2 E:GLU98 3.7 78.8 1.0
CA E:ASP122 4.0 32.3 1.0
O4 E:SO4403 4.0 57.7 1.0
OE1 E:GLU281 4.2 48.9 1.0
OD2 E:ASP122 4.3 47.3 1.0
CB E:ASP119 4.3 34.3 1.0
O E:HOH508 4.5 41.1 1.0
CG E:GLU98 4.6 52.0 1.0
N E:ASP122 4.9 32.3 1.0

Zinc binding site 8 out of 9 in 5ldz

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Zinc binding site 8 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:38.1
occ:1.00
 OE2 E:GLU226 2.0 44.5 1.0
NE2 E:HIS335 2.1 43.6 1.0
O E:HOH577 2.2 15.3 1.0
CD E:GLU226 2.7 48.8 1.0
OE1 E:GLU226 2.8 33.8 1.0
CE1 E:HIS335 2.9 42.0 1.0
CD2 E:HIS335 3.1 44.4 1.0
ND1 E:HIS335 4.1 42.9 1.0
CG E:HIS335 4.2 42.5 1.0
CG E:GLU226 4.2 39.5 1.0
CB E:PRO222 4.5 44.0 1.0
O E:HOH569 4.8 38.3 1.0
O E:HOH506 4.8 47.5 1.0

Zinc binding site 9 out of 9 in 5ldz

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Zinc binding site 9 out of 9 in the Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Quadruple Space Group Ambiguity Due to Rotational and Translational Non-Crystallographic Symmetry in Human Liver Fructose-1,6- Bisphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:50.4
occ:1.00
 OD2 F:ASP119 1.9 50.9 1.0
OE2 F:GLU281 1.9 64.9 1.0
OD1 F:ASP122 2.1 32.8 1.0
O F:HOH502 2.1 39.7 1.0
OE1 F:GLU98 2.3 63.6 1.0
CG F:ASP119 2.7 41.4 1.0
CD F:GLU281 3.0 58.8 1.0
OD1 F:ASP119 3.0 40.8 1.0
CG F:ASP122 3.1 38.8 1.0
CD F:GLU98 3.3 86.5 1.0
CG F:GLU281 3.4 41.2 1.0
CB F:ASP122 3.6 34.7 1.0
OE2 F:GLU98 3.7 94.7 1.0
CA F:ASP122 4.0 34.2 1.0
OE1 F:GLU281 4.0 41.2 1.0
CB F:ASP119 4.1 34.2 1.0
O3 F:SO4402 4.1 55.0 1.0
OD2 F:ASP122 4.2 44.0 1.0
CG F:GLU98 4.6 57.5 1.0
O F:HOH530 4.8 49.7 1.0
N F:ASP122 4.8 33.6 1.0
CB F:GLU281 4.9 29.9 1.0
CD1 F:ILE136 4.9 25.9 1.0

Reference:

A.Ruf, T.Tetaz, B.Schott, C.Joseph, M.G.Rudolph. Quadruple Space-Group Ambiguity Owing to Rotational and Translational Noncrystallographic Symmetry in Human Liver Fructose-1,6-Bisphosphatase. Acta Crystallogr D Struct V. 72 1212 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27841754
DOI: 10.1107/S2059798316016715
Page generated: Sun Oct 27 20:59:31 2024

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