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Mercury in PDB 1yp2: Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase

Enzymatic activity of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase

All present enzymatic activity of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase:
2.7.7.27;

Protein crystallography data

The structure of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase, PDB code: 1yp2 was solved by X.Jin, M.A.Ballicora, J.Preiss, J.H.Geiger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.465, 137.551, 91.623, 90.00, 112.53, 90.00
R / Rfree (%) 17.2 / 22.9

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase (pdb code 1yp2). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase, PDB code: 1yp2:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 1yp2

Go back to Mercury Binding Sites List in 1yp2
Mercury binding site 1 out of 4 in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg3226

b:35.4
occ:1.00
HG A:PMB3226 0.0 35.4 1.0
O A:HOH3462 1.7 6.5 1.0
C4 A:PMB3226 1.8 39.3 1.0
SG A:CYS354 2.1 19.3 1.0
O A:VAL338 2.2 19.8 1.0
C3 A:PMB3226 2.7 37.5 1.0
C A:VAL338 2.9 22.2 1.0
C5 A:PMB3226 3.0 36.8 1.0
O A:ILE355 3.4 23.3 1.0
CG2 A:VAL338 3.4 24.1 1.0
N A:ILE355 3.6 23.1 1.0
CB A:VAL338 3.6 21.0 1.0
N A:ILE339 3.6 18.5 1.0
CB A:CYS354 3.6 12.3 1.0
O A:HOH3412 3.7 26.7 1.0
O A:HOH3415 3.8 46.9 1.0
CA A:CYS354 3.8 23.6 1.0
CG A:LYS340 3.8 35.4 1.0
CA A:VAL338 3.8 23.1 1.0
CA A:ILE339 3.9 19.6 1.0
C2 A:PMB3226 4.0 39.8 1.0
C A:ILE355 4.1 24.0 1.0
C A:CYS354 4.1 24.1 1.0
N A:LYS340 4.1 21.1 1.0
C A:ILE339 4.2 21.6 1.0
C6 A:PMB3226 4.2 40.2 1.0
CD A:LYS340 4.3 39.8 1.0
CA A:ILE355 4.6 22.4 1.0
C1 A:PMB3226 4.6 42.8 1.0
N A:VAL338 4.8 22.3 1.0
CE A:LYS340 4.8 41.8 1.0
O A:ILE339 4.9 20.5 1.0
N A:SER356 5.0 29.3 1.0
CB A:LYS340 5.0 31.5 1.0

Mercury binding site 2 out of 4 in 1yp2

Go back to Mercury Binding Sites List in 1yp2
Mercury binding site 2 out of 4 in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg3227

b:35.4
occ:1.00
HG B:PMB3227 0.0 35.4 1.0
C4 B:PMB3227 1.8 40.5 1.0
SG B:CYS354 2.0 40.5 1.0
O B:HOH3403 2.6 22.1 1.0
C3 B:PMB3227 2.7 26.4 1.0
CB B:CYS354 2.9 21.9 1.0
C5 B:PMB3227 2.9 36.4 1.0
CG2 B:VAL338 3.1 22.1 1.0
O B:HOH3251 3.2 16.5 1.0
O B:VAL338 3.2 15.6 1.0
O B:HOH3362 3.3 28.5 1.0
CA B:CYS354 3.4 24.1 1.0
CB B:VAL338 3.9 20.2 1.0
N B:ILE355 4.0 21.6 1.0
NH2 B:ARG378 4.0 65.3 1.0
C B:CYS354 4.1 23.1 1.0
C2 B:PMB3227 4.1 33.1 1.0
C B:VAL338 4.1 18.6 1.0
C6 B:PMB3227 4.2 34.2 1.0
CZ B:ARG378 4.4 62.5 1.0
O B:ILE355 4.6 22.2 1.0
CA B:VAL338 4.7 17.6 1.0
C1 B:PMB3227 4.7 38.5 1.0
NH1 B:ARG378 4.7 63.4 1.0
C B:ILE355 4.8 21.2 1.0
N B:CYS354 4.8 19.4 1.0

Mercury binding site 3 out of 4 in 1yp2

Go back to Mercury Binding Sites List in 1yp2
Mercury binding site 3 out of 4 in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg3228

b:35.4
occ:1.00
HG C:PMB3228 0.0 35.4 1.0
SG C:CYS354 1.7 44.4 1.0
C4 C:PMB3228 1.8 20.7 1.0
O C:HOH3428 2.7 16.5 1.0
C3 C:PMB3228 2.7 42.6 1.0
CB C:CYS354 2.7 25.3 1.0
C5 C:PMB3228 2.9 44.8 1.0
O C:HOH3249 3.0 20.2 1.0
CA C:CYS354 3.2 20.4 1.0
O C:VAL338 3.3 16.8 1.0
CG2 C:VAL338 3.3 23.3 1.0
NH1 C:ARG378 3.4 80.5 1.0
N C:ILE355 3.5 21.2 1.0
C C:CYS354 3.6 21.2 1.0
O C:HOH3386 3.7 31.9 1.0
O C:HOH3310 4.0 37.0 1.0
C2 C:PMB3228 4.1 46.6 1.0
CB C:VAL338 4.2 19.9 1.0
O C:ILE355 4.3 16.4 1.0
C C:VAL338 4.3 18.7 1.0
C6 C:PMB3228 4.3 47.9 1.0
C C:ILE355 4.3 20.3 1.0
CZ C:ARG378 4.4 80.5 1.0
CA C:ILE355 4.6 20.0 1.0
O C:CYS354 4.6 20.5 1.0
N C:CYS354 4.7 16.7 1.0
OG C:SER356 4.7 24.9 1.0
C1 C:PMB3228 4.8 49.1 1.0
N C:SER356 4.9 21.4 1.0
CA C:VAL338 4.9 18.8 1.0
NH2 C:ARG378 5.0 80.5 1.0

Mercury binding site 4 out of 4 in 1yp2

Go back to Mercury Binding Sites List in 1yp2
Mercury binding site 4 out of 4 in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg3229

b:35.4
occ:1.00
HG D:PMB3229 0.0 35.4 1.0
C4 D:PMB3229 1.8 19.2 1.0
NH1 D:ARG378 2.2 80.6 1.0
SG D:CYS354 2.5 38.6 1.0
C3 D:PMB3229 2.7 28.0 1.0
O D:HOH3234 2.8 23.1 1.0
C5 D:PMB3229 2.9 24.4 1.0
O D:HOH3423 3.1 38.9 1.0
CB D:CYS354 3.2 28.4 1.0
O D:VAL338 3.3 19.5 1.0
CZ D:ARG378 3.4 80.6 1.0
CG2 D:VAL338 3.5 17.1 1.0
CA D:CYS354 3.6 23.9 1.0
NH2 D:ARG378 3.8 80.6 1.0
N D:ILE355 4.0 23.6 1.0
C D:CYS354 4.1 25.6 1.0
CB D:VAL338 4.1 16.5 1.0
C2 D:PMB3229 4.1 32.8 1.0
C6 D:PMB3229 4.2 31.3 1.0
C D:VAL338 4.2 21.1 1.0
CE D:LYS340 4.3 32.8 1.0
O D:HOH3474 4.5 58.3 1.0
NE D:ARG378 4.5 80.6 1.0
O D:ILE355 4.6 20.8 1.0
C1 D:PMB3229 4.7 35.5 1.0
C D:ILE355 4.8 23.1 1.0
CA D:VAL338 4.8 20.6 1.0
CG D:LYS340 4.8 22.9 1.0

Reference:

X.Jin, M.A.Ballicora, J.Preiss, J.H.Geiger. Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase. Embo J. V. 24 694 2005.
ISSN: ISSN 0261-4189
PubMed: 15692569
DOI: 10.1038/SJ.EMBOJ.7600551
Page generated: Wed Oct 28 18:41:00 2020

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