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Zinc in PDB 1dk4: Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase

Enzymatic activity of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase

All present enzymatic activity of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase:
3.1.3.25;

Protein crystallography data

The structure of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase, PDB code: 1dk4 was solved by B.Stec, H.Yang, K.A.Johnson, L.Chen, M.F.Roberts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.870, 78.430, 129.720, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 33.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase (pdb code 1dk4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase, PDB code: 1dk4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1dk4

Go back to Zinc Binding Sites List in 1dk4
Zinc binding site 1 out of 6 in the Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn290

b:34.4
occ:1.00
OD1 A:ASP201 2.0 28.2 1.0
OD1 A:ASP84 2.0 16.1 1.0
OD1 A:ASP81 2.0 29.4 1.0
O1 A:PO4293 2.7 38.3 1.0
CG A:ASP201 3.1 33.3 1.0
O3 A:PO4293 3.2 57.7 1.0
CG A:ASP84 3.2 21.3 1.0
CG A:ASP81 3.2 27.0 1.0
OE2 A:GLU65 3.4 14.0 1.0
ZN A:ZN291 3.5 42.0 1.0
P A:PO4293 3.5 31.2 1.0
CB A:ASP201 3.7 30.8 1.0
CA A:ASP84 3.8 19.5 1.0
CA A:ASP201 3.8 37.8 1.0
OD2 A:ASP81 3.9 38.5 1.0
O A:ILE83 3.9 18.9 1.0
NH2 A:ARG198 4.0 69.4 1.0
CB A:ASP84 4.0 23.5 1.0
OD2 A:ASP84 4.1 10.2 1.0
N A:GLY85 4.1 14.7 1.0
OD2 A:ASP201 4.2 37.9 1.0
O2 A:PO4293 4.2 33.1 1.0
CB A:ASP81 4.4 27.4 1.0
C A:ASP84 4.5 13.3 1.0
N A:ASP201 4.6 40.7 1.0
CD A:GLU65 4.7 23.5 1.0
O4 A:PO4293 4.7 65.7 1.0
C A:ILE83 4.8 26.4 1.0
N A:ASP84 4.8 21.2 1.0
O A:ASP201 4.8 56.7 1.0
C A:ASP201 4.9 40.9 1.0

Zinc binding site 2 out of 6 in 1dk4

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Zinc binding site 2 out of 6 in the Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn291

b:42.0
occ:1.00
O1 A:PO4293 1.7 38.3 1.0
OE2 A:GLU65 1.9 14.0 1.0
O A:HOH633 2.0 6.3 1.0
O A:ILE83 2.1 18.9 1.0
OE1 A:GLU65 2.5 8.3 1.0
OD2 A:ASP81 2.5 38.5 1.0
CD A:GLU65 2.5 23.5 1.0
P A:PO4293 2.8 31.2 1.0
O2 A:PO4293 2.9 33.1 1.0
OD1 A:ASP81 3.2 29.4 1.0
CG A:ASP81 3.2 27.0 1.0
O A:HOH632 3.3 19.1 1.0
C A:ILE83 3.3 26.4 1.0
ZN A:ZN290 3.5 34.4 1.0
O4 A:PO4293 3.6 65.7 1.0
O3 A:PO4293 3.9 57.7 1.0
ZN A:ZN292 4.0 58.4 1.0
CG A:GLU65 4.0 20.9 1.0
N A:ILE83 4.1 13.8 1.0
CA A:ASP84 4.2 19.5 1.0
N A:GLY85 4.2 14.7 1.0
CA A:ILE83 4.2 22.1 1.0
N A:ASP84 4.3 21.2 1.0
CB A:ILE83 4.6 18.3 1.0
OD1 A:ASP84 4.6 16.1 1.0
NH2 A:ARG198 4.6 69.4 1.0
CB A:ASP81 4.6 27.4 1.0
CB A:GLU65 4.7 14.9 1.0
OD1 A:ASP201 4.7 28.2 1.0
C A:ASP84 4.7 13.3 1.0
N A:SER86 4.7 34.0 1.0
CG2 A:ILE83 4.8 20.2 1.0
OD1 A:ASP44 4.9 44.7 1.0

Zinc binding site 3 out of 6 in 1dk4

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Zinc binding site 3 out of 6 in the Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn292

b:58.4
occ:1.00
O A:HOH632 1.9 19.1 1.0
O2 A:PO4293 2.0 33.1 1.0
CD A:GLU65 3.2 23.5 1.0
P A:PO4293 3.4 31.2 1.0
OE2 A:GLU65 3.5 14.0 1.0
OE1 A:GLU65 3.5 8.3 1.0
CG A:GLU65 3.8 20.9 1.0
O4 A:PO4293 3.9 65.7 1.0
ZN A:ZN291 4.0 42.0 1.0
OD1 A:ASP38 4.1 83.5 1.0
NH2 A:ARG198 4.1 69.4 1.0
O1 A:PO4293 4.2 38.3 1.0
O3 A:PO4293 4.3 57.7 1.0
OE2 A:GLU66 4.4 4.0 1.0
OD2 A:ASP44 4.5 46.4 1.0
CB A:ASP38 4.6 60.2 1.0
CZ A:ARG198 4.7 55.5 1.0
NH1 A:ARG198 4.7 71.1 1.0
CG A:ASP38 4.8 71.4 1.0

Zinc binding site 4 out of 6 in 1dk4

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Zinc binding site 4 out of 6 in the Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn590

b:35.3
occ:1.00
OE2 B:GLU365 2.0 52.7 1.0
O B:ILE383 2.1 22.1 1.0
O2 B:PO4593 2.1 41.4 1.0
O B:HOH609 2.1 13.8 1.0
O4 B:PO4593 2.1 34.2 1.0
OD2 B:ASP381 2.2 43.6 1.0
P B:PO4593 2.6 37.3 1.0
CG B:ASP381 3.0 35.1 1.0
OD1 B:ASP381 3.1 33.6 1.0
CD B:GLU365 3.1 53.4 1.0
C B:ILE383 3.2 14.5 1.0
O B:HOH620 3.4 14.1 1.0
ZN B:ZN591 3.5 27.3 1.0
O3 B:PO4593 3.6 24.9 1.0
OE1 B:GLU365 3.7 56.6 1.0
O1 B:PO4593 3.7 26.0 1.0
ZN B:ZN592 3.7 46.5 1.0
N B:ILE383 3.9 11.1 1.0
CA B:ASP384 4.0 11.8 1.0
N B:ASP384 4.0 14.6 1.0
CA B:ILE383 4.1 12.5 1.0
OE1 B:GLU366 4.1 40.9 1.0
N B:GLY385 4.3 28.2 1.0
CG B:GLU365 4.4 45.7 1.0
OG B:SER386 4.4 56.0 1.0
CB B:ASP381 4.4 24.6 1.0
CD B:PRO382 4.4 4.4 1.0
OD1 B:ASP344 4.5 24.6 1.0
CB B:GLU365 4.6 35.1 1.0
N B:PRO382 4.6 14.3 1.0
NH2 B:ARG498 4.7 59.6 1.0
C B:ASP384 4.7 12.5 1.0
CB B:ILE383 4.7 15.9 1.0
C B:ASP381 4.8 21.6 1.0
CA B:ASP381 4.8 27.5 1.0
OD1 B:ASP501 4.8 31.7 1.0

Zinc binding site 5 out of 6 in 1dk4

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Zinc binding site 5 out of 6 in the Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn591

b:27.3
occ:1.00
OD1 B:ASP381 1.7 33.6 1.0
OD1 B:ASP384 1.9 6.0 1.0
OD1 B:ASP501 2.0 31.7 1.0
O2 B:PO4593 2.4 41.4 1.0
O B:HOH629 2.5 16.5 1.0
CG B:ASP381 2.8 35.1 1.0
CG B:ASP384 2.9 3.7 1.0
O1 B:PO4593 2.9 26.0 1.0
CG B:ASP501 3.1 32.3 1.0
P B:PO4593 3.2 37.3 1.0
CA B:ASP384 3.3 11.8 1.0
CB B:ASP384 3.4 1.2 1.0
OD2 B:ASP381 3.5 43.6 1.0
ZN B:ZN590 3.5 35.3 1.0
CB B:ASP501 3.7 32.9 1.0
CB B:ASP381 3.9 24.6 1.0
CA B:ASP501 3.9 35.3 1.0
O4 B:PO4593 3.9 34.2 1.0
OD2 B:ASP384 4.0 32.6 1.0
OD2 B:ASP501 4.1 39.0 1.0
O B:ILE383 4.1 22.1 1.0
C B:ASP384 4.2 12.5 1.0
N B:GLY385 4.2 28.2 1.0
NH2 B:ARG498 4.2 59.6 1.0
OE2 B:GLU365 4.3 52.7 1.0
N B:ASP384 4.3 14.6 1.0
O3 B:PO4593 4.4 24.9 1.0
C B:ILE383 4.6 14.5 1.0
N B:ASP501 4.7 35.5 1.0
O B:VAL500 5.0 36.8 1.0

Zinc binding site 6 out of 6 in 1dk4

Go back to Zinc Binding Sites List in 1dk4
Zinc binding site 6 out of 6 in the Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of MJ0109 Gene Product Inositol Monophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn592

b:46.5
occ:1.00
O3 B:PO4593 1.7 24.9 1.0
OE1 B:GLU365 2.1 56.6 1.0
O B:HOH620 2.2 14.1 1.0
P B:PO4593 2.7 37.3 1.0
CD B:GLU365 3.0 53.4 1.0
O4 B:PO4593 3.1 34.2 1.0
OD1 B:ASP338 3.2 87.5 1.0
O2 B:PO4593 3.2 41.4 1.0
OE2 B:GLU365 3.3 52.7 1.0
NH2 B:ARG498 3.7 59.6 1.0
ZN B:ZN590 3.7 35.3 1.0
OG B:SER386 3.9 56.0 1.0
O1 B:PO4593 4.0 26.0 1.0
CG B:ASP338 4.1 71.5 1.0
CB B:ASP338 4.1 64.8 1.0
OE1 B:GLU366 4.1 40.9 1.0
CG B:GLU365 4.3 45.7 1.0
O B:HOH609 4.5 13.8 1.0
OE2 B:GLU366 4.5 34.3 1.0
CB B:SER386 4.6 56.4 1.0
O B:GLU339 4.6 42.7 1.0
CZ B:ARG498 4.7 50.7 1.0
OD2 B:ASP344 4.7 48.4 1.0
NH1 B:ARG498 4.7 52.8 1.0
CD B:GLU366 4.8 27.7 1.0

Reference:

B.Stec, H.Yang, K.A.Johnson, L.Chen, M.F.Roberts. MJ0109 Is An Enzyme That Is Both An Inositol Monophosphatase and the 'Missing' Archaeal Fructose-1,6-Bisphosphatase. Nat.Struct.Biol. V. 7 1046 2000.
ISSN: ISSN 1072-8368
PubMed: 11062561
DOI: 10.1038/80968
Page generated: Mon Jan 25 16:08:42 2021

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