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Manganese in PDB 1ypp: Acid Anhydride Hydrolase

Enzymatic activity of Acid Anhydride Hydrolase

All present enzymatic activity of Acid Anhydride Hydrolase:
3.6.1.1;

Protein crystallography data

The structure of Acid Anhydride Hydrolase, PDB code: 1ypp was solved by E.H.Harutyunyan, I.P.Kuranova, V.S.Lamzin, Z.Dauter, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.000, 106.200, 56.100, 90.00, 90.00, 90.00
R / Rfree (%) 19 / n/a

Manganese Binding Sites:

The binding sites of Manganese atom in the Acid Anhydride Hydrolase (pdb code 1ypp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Acid Anhydride Hydrolase, PDB code: 1ypp:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1ypp

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Manganese binding site 1 out of 8 in the Acid Anhydride Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Acid Anhydride Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:15.9
occ:1.00
 OD1 A:ASP152 1.9 10.1 1.0
O A:HOH407 1.9 8.8 1.0
OD2 A:ASP120 2.1 25.5 1.0
OD2 A:ASP115 2.2 36.2 1.0
O A:HOH418 2.3 17.0 1.0
O3 A:PO4302 2.7 23.4 1.0
CG A:ASP152 3.0 19.4 1.0
CG A:ASP120 3.2 15.1 1.0
CG A:ASP115 3.2 22.1 1.0
OD2 A:ASP152 3.3 29.8 1.0
OD1 A:ASP120 3.3 15.0 1.0
O1 A:PO4302 3.3 31.7 1.0
P A:PO4302 3.5 22.8 1.0
OD1 A:ASP115 3.5 26.8 1.0
O A:HOH424 3.7 20.2 1.0
MN A:MN403 3.8 23.3 1.0
MN A:MN402 3.8 21.6 1.0
NZ A:LYS154 4.0 7.0 1.0
O2 A:PO4302 4.1 23.7 1.0
O A:HOH421 4.2 18.5 1.0
OD2 A:ASP117 4.3 27.3 1.0
CB A:ASP152 4.3 15.1 1.0
CB A:ASP120 4.4 14.8 1.0
CB A:ASP115 4.5 15.5 1.0
CB A:ASP117 4.6 24.9 1.0
CA A:ASP152 4.7 23.5 1.0
O A:PRO118 4.7 21.4 1.0
O4 A:PO4302 4.8 28.6 1.0
OH A:TYR93 4.9 11.1 1.0
CG A:ASP117 5.0 24.8 1.0

Manganese binding site 2 out of 8 in 1ypp

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Manganese binding site 2 out of 8 in the Acid Anhydride Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Acid Anhydride Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:21.6
occ:1.00
 OD1 A:ASP120 1.9 15.0 1.0
O A:HOH476 2.0 37.9 1.0
O1 A:PO4302 2.1 31.7 1.0
O A:HOH474 2.1 37.3 1.0
O A:HOH478 2.5 39.0 1.0
O A:HOH407 2.6 8.8 1.0
CG A:ASP120 3.1 15.1 1.0
P A:PO4302 3.4 22.8 1.0
O2 A:PO4302 3.5 23.7 1.0
OD2 A:ASP120 3.6 25.5 1.0
MN A:MN401 3.8 15.9 1.0
OD2 A:ASP117 4.0 27.3 1.0
OE1 A:GLU48 4.2 6.6 1.0
O3 A:PO4302 4.3 23.4 1.0
CB A:ASP120 4.3 14.8 1.0
O A:PRO118 4.3 21.4 1.0
O A:HOH418 4.4 17.0 1.0
CG A:ASP117 4.4 24.8 1.0
CE2 A:TYR93 4.4 11.3 1.0
OH A:TYR93 4.4 11.1 1.0
O4 A:PO4302 4.5 28.6 1.0
CB A:ASP117 4.6 24.9 1.0
O A:HOH412 4.8 14.1 1.0
CZ A:TYR93 4.9 13.8 1.0
CB A:ALA95 4.9 17.4 1.0
CA A:ASP120 4.9 15.6 1.0
O A:GLY94 5.0 13.1 1.0

Manganese binding site 3 out of 8 in 1ypp

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Manganese binding site 3 out of 8 in the Acid Anhydride Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Acid Anhydride Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:23.3
occ:1.00
 O A:HOH424 1.8 20.2 1.0
OD2 A:ASP152 1.9 29.8 1.0
O3 A:PO4302 2.1 23.4 1.0
OD2 A:ASP147 2.1 14.1 1.0
O3 A:PO4301 2.3 23.5 1.0
CG A:ASP152 3.1 19.4 1.0
CG A:ASP147 3.1 13.5 1.0
CB A:ASP147 3.5 16.4 1.0
P A:PO4302 3.5 22.8 1.0
OD1 A:ASP152 3.6 10.1 1.0
P A:PO4301 3.7 20.9 1.0
MN A:MN401 3.8 15.9 1.0
OD2 A:ASP115 3.9 36.2 1.0
O4 A:PO4302 3.9 28.6 1.0
O4 A:PO4301 3.9 17.9 1.0
O A:HOH426 4.1 20.2 1.0
OH A:TYR192 4.2 13.5 1.0
OD1 A:ASP147 4.2 15.0 1.0
O A:HOH411 4.2 13.1 1.0
CB A:ASP152 4.2 15.1 1.0
O2 A:PO4302 4.3 23.7 1.0
O A:HOH463 4.4 33.8 1.0
NZ A:LYS154 4.4 7.0 1.0
O2 A:PO4301 4.4 25.8 1.0
O1 A:PO4302 4.7 31.7 1.0
O1 A:PO4301 4.7 13.1 1.0
NZ A:LYS193 4.8 11.0 1.0
O A:HOH407 4.8 8.8 1.0
OD2 A:ASP120 4.8 25.5 1.0
CA A:ASP147 5.0 18.5 1.0

Manganese binding site 4 out of 8 in 1ypp

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Manganese binding site 4 out of 8 in the Acid Anhydride Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Acid Anhydride Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:27.3
occ:1.00
 O A:HOH419 1.8 17.3 1.0
O A:HOH426 1.9 20.2 1.0
OE2 A:GLU58 2.0 5.1 1.0
O1 A:PO4301 2.1 13.1 1.0
O2 A:PO4302 2.2 23.7 1.0
CD A:GLU58 3.0 6.7 1.0
P A:PO4301 3.4 20.9 1.0
OE1 A:GLU58 3.5 9.6 1.0
O3 A:PO4301 3.5 23.5 1.0
P A:PO4302 3.6 22.8 1.0
NZ A:LYS56 3.8 10.8 1.0
OD2 A:ASP117 4.2 27.3 1.0
O4 A:PO4302 4.2 28.6 1.0
O3 A:PO4302 4.2 23.4 1.0
NH1 A:ARG78 4.2 9.4 1.0
O4 A:PO4301 4.3 17.9 1.0
O A:HOH478 4.3 39.0 1.0
CG A:GLU58 4.3 14.5 1.0
O A:HOH457 4.5 32.0 1.0
O2 A:PO4301 4.6 25.8 1.0
O A:HOH424 4.6 20.2 1.0
OD2 A:ASP71 4.6 9.8 1.0
O A:HOH472 4.6 36.4 1.0
O1 A:PO4302 4.7 31.7 1.0
CE A:LYS56 4.8 11.0 1.0
O A:HOH407 4.8 8.8 1.0

Manganese binding site 5 out of 8 in 1ypp

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Manganese binding site 5 out of 8 in the Acid Anhydride Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Acid Anhydride Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:25.5
occ:1.00
 OD1 B:ASP152 2.0 8.8 1.0
OD2 B:ASP120 2.3 22.1 1.0
OD2 B:ASP115 2.5 29.8 1.0
O3 B:PO4302 2.8 30.2 1.0
O1 B:PO4302 2.9 41.1 1.0
CG B:ASP152 3.1 20.2 1.0
CG B:ASP115 3.3 24.9 1.0
CG B:ASP120 3.3 20.6 1.0
OD1 B:ASP115 3.4 29.9 1.0
P B:PO4302 3.5 31.7 1.0
OD2 B:ASP152 3.5 27.4 1.0
OD1 B:ASP120 3.5 18.7 1.0
MN B:MN402 3.8 25.9 1.0
O B:HOH417 3.9 17.1 1.0
MN B:MN403 3.9 27.3 1.0
O B:HOH448 4.2 28.9 1.0
NZ B:LYS154 4.2 3.5 1.0
O2 B:PO4302 4.4 36.2 1.0
CB B:ASP152 4.4 21.5 1.0
CB B:ASP115 4.6 27.4 1.0
CB B:ASP120 4.6 18.7 1.0
OD2 B:ASP117 4.6 26.3 1.0
CB B:ASP117 4.6 18.6 1.0
O B:PRO118 4.6 25.0 1.0
O4 B:PO4302 4.7 34.4 1.0
O B:HOH445 4.7 28.2 1.0
OH B:TYR93 4.8 6.9 1.0
O B:HOH406 4.8 11.2 1.0
CA B:ASP152 4.8 25.0 1.0
O B:HOH455 4.9 32.3 1.0

Manganese binding site 6 out of 8 in 1ypp

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Manganese binding site 6 out of 8 in the Acid Anhydride Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Acid Anhydride Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:25.9
occ:1.00
 OD1 B:ASP120 2.0 18.7 1.0
O1 B:PO4302 2.2 41.1 1.0
O B:HOH458 2.2 33.0 1.0
O B:HOH425 3.2 20.5 1.0
CG B:ASP120 3.2 20.6 1.0
OD2 B:ASP120 3.6 22.1 1.0
P B:PO4302 3.6 31.7 1.0
O2 B:PO4302 3.7 36.2 1.0
MN B:MN401 3.8 25.5 1.0
OE1 B:GLU48 4.1 15.3 1.0
OH B:TYR93 4.2 6.9 1.0
O B:PRO118 4.3 25.0 1.0
CE1 B:TYR93 4.4 4.0 1.0
O B:HOH432 4.5 24.0 1.0
OD2 B:ASP117 4.5 26.3 1.0
CB B:ASP120 4.5 18.7 1.0
O3 B:PO4302 4.5 30.2 1.0
CG B:ASP117 4.6 16.3 1.0
O4 B:PO4302 4.6 34.4 1.0
CB B:ASP117 4.7 18.6 1.0
OE2 B:GLU48 4.8 24.6 1.0
CZ B:TYR93 4.8 7.5 1.0
CB B:ALA95 4.9 11.2 1.0
CD B:GLU48 4.9 18.6 1.0
O B:GLY94 5.0 12.1 1.0
OD1 B:ASP117 5.0 24.1 1.0

Manganese binding site 7 out of 8 in 1ypp

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Manganese binding site 7 out of 8 in the Acid Anhydride Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Acid Anhydride Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:27.3
occ:1.00
 O3 B:PO4302 1.9 30.2 1.0
OD2 B:ASP147 2.2 17.8 1.0
O B:HOH445 2.2 28.2 1.0
O B:HOH417 2.3 17.1 1.0
O3 B:PO4301 2.3 28.6 1.0
OD2 B:ASP152 2.4 27.4 1.0
CG B:ASP147 3.3 12.2 1.0
P B:PO4302 3.3 31.7 1.0
CG B:ASP152 3.4 20.2 1.0
O4 B:PO4301 3.5 30.2 1.0
P B:PO4301 3.5 23.4 1.0
O4 B:PO4302 3.6 34.4 1.0
CB B:ASP147 3.7 20.9 1.0
OD1 B:ASP152 3.8 8.8 1.0
MN B:MN401 3.9 25.5 1.0
O B:HOH406 4.0 11.2 1.0
OH B:TYR192 4.0 14.7 1.0
NZ B:LYS154 4.2 3.5 1.0
O B:HOH436 4.2 25.6 1.0
O2 B:PO4302 4.2 36.2 1.0
O1 B:PO4302 4.3 41.1 1.0
O B:HOH429 4.4 22.8 1.0
OD1 B:ASP147 4.4 23.8 1.0
OD2 B:ASP115 4.4 29.8 1.0
O2 B:PO4301 4.4 29.9 1.0
CB B:ASP152 4.5 21.5 1.0
O1 B:PO4301 4.6 17.4 1.0
NZ B:LYS193 4.9 14.7 1.0
CE B:LYS154 4.9 10.5 1.0
OD2 B:ASP120 4.9 22.1 1.0
CD2 B:LEU145 4.9 19.7 1.0

Manganese binding site 8 out of 8 in 1ypp

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Manganese binding site 8 out of 8 in the Acid Anhydride Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Acid Anhydride Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:23.8
occ:1.00
 OE2 B:GLU58 1.8 22.8 1.0
O1 B:PO4301 2.1 17.4 1.0
O B:HOH447 2.2 28.7 1.0
O B:HOH406 2.2 11.2 1.0
O2 B:PO4302 2.4 36.2 1.0
CD B:GLU58 2.9 29.8 1.0
P B:PO4301 3.3 23.4 1.0
OE1 B:GLU58 3.4 38.1 1.0
O3 B:PO4301 3.5 28.6 1.0
P B:PO4302 3.8 31.7 1.0
NZ B:LYS56 3.8 30.7 1.0
O3 B:PO4302 4.2 30.2 1.0
CG B:GLU58 4.2 29.5 1.0
O B:HOH455 4.3 32.3 1.0
O4 B:PO4301 4.3 30.2 1.0
O B:HOH458 4.3 33.0 1.0
OD2 B:ASP117 4.4 26.3 1.0
NH1 B:ARG78 4.4 20.8 1.0
O2 B:PO4301 4.5 29.9 1.0
OD2 B:ASP71 4.6 22.9 1.0
O4 B:PO4302 4.7 34.4 1.0
O1 B:PO4302 4.7 41.1 1.0
CE B:LYS56 4.8 15.3 1.0
O B:HOH503 4.8 50.9 1.0

Reference:

E.H.Harutyunyan, I.P.Kuranova, B.K.Vainshtein, W.E.Hohne, V.S.Lamzin, Z.Dauter, A.V.Teplyakov, K.S.Wilson. X-Ray Structure of Yeast Inorganic Pyrophosphatase Complexed with Manganese and Phosphate. Eur.J.Biochem. V. 239 220 1996.
ISSN: ISSN 0014-2956
PubMed: 8706712
DOI: 10.1111/J.1432-1033.1996.0220U.X
Page generated: Sat Oct 5 13:13:20 2024

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