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Magnesium in PDB 2x98: H.Salinarum Alkaline Phosphatase

Enzymatic activity of H.Salinarum Alkaline Phosphatase

All present enzymatic activity of H.Salinarum Alkaline Phosphatase:
3.1.3.1;

Protein crystallography data

The structure of H.Salinarum Alkaline Phosphatase, PDB code: 2x98 was solved by A.Wende, P.Johansson, M.Grininger, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.143, 152.524, 86.799, 90.00, 110.00, 90.00
R / Rfree (%) 16.042 / 19.771

Other elements in 2x98:

The structure of H.Salinarum Alkaline Phosphatase also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 13 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the H.Salinarum Alkaline Phosphatase (pdb code 2x98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the H.Salinarum Alkaline Phosphatase, PDB code: 2x98:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 2x98

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Magnesium binding site 1 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1477

b:7.4
occ:1.00
 OE2 A:GLU299 2.0 8.1 1.0
OD2 A:ASP56 2.0 8.3 1.0
O A:HOH2138 2.1 10.9 1.0
O A:HOH2285 2.2 11.7 1.0
O A:HOH2287 2.2 10.1 1.0
OG1 A:THR172 2.2 8.6 1.0
CG A:ASP56 3.1 8.4 1.0
CD A:GLU299 3.1 11.6 1.0
CB A:THR172 3.3 7.2 1.0
OE1 A:GLU299 3.5 10.7 1.0
CB A:ASP56 3.6 4.7 1.0
ND1 A:HIS170 3.9 14.0 1.0
OD1 A:ASP56 4.1 7.5 1.0
O A:HOH2463 4.1 15.1 1.0
N A:THR172 4.1 6.6 1.0
CG2 A:THR172 4.2 8.2 1.0
CB A:SER115 4.3 6.4 0.5
CB A:SER115 4.3 8.0 0.5
CA A:THR172 4.3 7.0 1.0
OG A:SER115 4.3 5.6 0.5
CG A:GLU299 4.4 8.1 1.0
O A:HOH2087 4.4 15.5 1.0
O4 A:PO41474 4.4 10.2 1.0
CG2 A:THR166 4.5 8.7 1.0
CE1 A:HIS170 4.6 12.1 1.0
CA A:GLY301 4.6 7.9 1.0
OG A:SER115 4.6 11.9 0.5
O A:GLY301 4.7 9.4 1.0
ZN A:ZN1476 4.8 9.6 1.0
OD2 A:ASP346 4.9 12.8 1.0

Magnesium binding site 2 out of 11 in 2x98

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Magnesium binding site 2 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1478

b:5.5
occ:1.00
 O A:HOH2273 1.7 23.8 1.0
O A:SER285 2.2 20.4 1.0
O A:ASP282 2.4 12.3 1.0
OD1 A:ASP282 2.4 16.9 1.0
O B:HOH2247 2.4 31.6 1.0
OD2 B:ASP239 2.5 15.4 1.0
OD1 B:ASP239 2.6 16.7 1.0
O A:HOH2269 2.8 27.5 1.0
CG B:ASP239 2.9 14.3 1.0
C A:ASP282 3.4 11.6 1.0
C A:SER285 3.4 20.0 1.0
CG A:ASP282 3.6 17.6 1.0
MG B:MG1481 3.6 11.2 1.0
CA A:ASP282 3.9 12.3 1.0
O A:HOH2271 4.2 36.3 1.0
CB A:SER285 4.2 19.0 1.0
CA A:SER285 4.2 18.0 1.0
CB A:ASP282 4.3 12.4 1.0
N A:SER285 4.4 14.5 1.0
O B:HOH2245 4.4 20.6 1.0
N A:SER286 4.4 22.3 1.0
CB B:ASP239 4.4 12.8 1.0
OD2 A:ASP282 4.5 20.4 1.0
O B:HOH2246 4.5 27.9 1.0
N A:LEU283 4.5 10.1 1.0
CA A:SER286 4.6 24.7 1.0
OG A:SER286 4.8 28.9 1.0
O A:VAL281 4.9 11.6 1.0
CA A:LEU283 4.9 10.2 1.0
O B:ASP239 4.9 13.3 1.0

Magnesium binding site 3 out of 11 in 2x98

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Magnesium binding site 3 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1479

b:3.0
occ:1.00
 O A:HOH2345 2.3 18.7 1.0
OE1 A:GLU361 2.3 14.1 1.0
OE1 A:GLU363 2.4 13.4 1.0
O A:HOH2344 2.5 16.4 1.0
OE2 A:GLU363 2.7 13.6 1.0
CD A:GLU363 2.9 12.2 1.0
CD A:GLU361 3.5 11.0 1.0
CB A:GLU361 4.2 8.3 1.0
CG A:GLU361 4.3 11.7 1.0
O A:HOH2346 4.4 16.4 1.0
CG A:GLU363 4.4 9.4 1.0
OE2 A:GLU361 4.5 12.1 1.0
O A:VAL362 4.8 6.6 1.0

Magnesium binding site 4 out of 11 in 2x98

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Magnesium binding site 4 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1480

b:5.7
occ:1.00
 O A:HOH2423 2.2 29.1 1.0
OD1 A:ASP433 2.5 14.6 1.0
O A:HOH2422 2.5 28.9 1.0
OD2 A:ASP433 2.8 19.4 1.0
CG A:ASP433 3.0 13.5 1.0
O A:HOH2421 4.3 55.1 1.0
CB A:ASP433 4.4 8.1 1.0
O A:ASP433 4.5 9.0 1.0
C A:ASP433 4.7 7.5 1.0

Magnesium binding site 5 out of 11 in 2x98

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Magnesium binding site 5 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1481

b:11.0
occ:1.00
 OG A:SER45 2.4 6.9 1.0
O A:ASP291 2.4 12.9 1.0
O A:HOH2003 2.4 10.2 1.0
OH A:TYR158 2.5 7.1 1.0
O A:ALA47 2.6 7.7 1.0
CL A:CL1487 2.8 14.4 1.0
CZ A:TYR158 3.5 7.2 1.0
C A:ASP291 3.5 15.6 1.0
C A:ALA47 3.5 7.8 1.0
CB A:SER45 3.6 6.2 1.0
CA A:ALA48 3.8 8.6 1.0
CE1 A:TYR158 3.8 7.0 1.0
N A:SER45 4.0 8.3 1.0
N A:ALA48 4.1 7.8 1.0
CB A:ASP291 4.1 17.6 1.0
CA A:ASP291 4.2 17.1 1.0
O A:LEU469 4.3 5.6 1.0
CA A:SER45 4.3 7.5 1.0
O A:SER45 4.3 8.1 1.0
C A:SER45 4.5 7.5 1.0
CD A:LYS292 4.6 14.2 1.0
N A:LYS292 4.6 14.5 1.0
C A:ALA48 4.6 8.2 1.0
N A:ALA47 4.7 7.4 1.0
CE2 A:TYR158 4.7 5.9 1.0
CA A:ALA47 4.7 7.2 1.0
O A:ALA48 4.8 7.9 1.0
O A:ALA468 4.8 6.0 1.0
CB A:ALA48 4.8 10.0 1.0
C A:LEU469 4.8 6.5 1.0
CA A:LYS292 4.9 13.4 1.0
NZ A:LYS292 4.9 23.9 1.0
CA A:LEU469 4.9 7.3 1.0
O A:HOH2281 4.9 30.7 1.0

Magnesium binding site 6 out of 11 in 2x98

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Magnesium binding site 6 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1477

b:8.7
occ:1.00
 OE2 B:GLU299 2.1 9.6 1.0
OD2 B:ASP56 2.1 9.9 1.0
O B:HOH2480 2.1 12.4 1.0
O B:HOH2304 2.2 11.8 1.0
OG1 B:THR172 2.2 8.7 1.0
O B:HOH2305 2.3 10.3 1.0
CG B:ASP56 3.1 7.7 1.0
CD B:GLU299 3.1 12.0 1.0
CB B:THR172 3.2 7.5 1.0
OE1 B:GLU299 3.4 11.5 1.0
CB B:ASP56 3.6 5.5 1.0
ND1 B:HIS170 4.0 13.8 1.0
OD1 B:ASP56 4.1 5.1 1.0
N B:THR172 4.1 7.8 1.0
O B:HOH2307 4.1 16.3 1.0
CB B:SER115 4.2 8.4 0.5
CG2 B:THR172 4.2 8.3 1.0
CB B:SER115 4.2 6.6 0.5
O B:HOH2150 4.3 17.1 1.0
CA B:THR172 4.3 7.6 1.0
OG B:SER115 4.3 4.7 0.5
O4 B:PO41474 4.4 9.9 1.0
CG B:GLU299 4.4 8.5 1.0
OG B:SER115 4.4 12.9 0.5
CG2 B:THR166 4.5 8.5 1.0
CE1 B:HIS170 4.6 12.1 1.0
CA B:GLY301 4.7 8.1 1.0
ZN B:ZN1476 4.7 10.2 1.0
O B:GLY301 4.8 9.9 1.0
OD2 B:ASP346 4.9 11.2 1.0
CA B:ASP56 5.0 5.9 1.0

Magnesium binding site 7 out of 11 in 2x98

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Magnesium binding site 7 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1478

b:16.9
occ:1.00
 O B:HOH2147 2.1 27.2 1.0
O B:HOH2200 2.2 22.7 1.0
O B:HOH2148 2.2 25.9 1.0
O B:HOH2073 2.3 42.1 1.0
OE2 B:GLU167 2.3 14.8 1.0
O B:HOH2173 2.6 22.9 1.0
CD B:GLU167 3.3 16.8 1.0
OE1 B:GLU167 3.5 14.9 1.0
NE2 B:GLN206 4.2 11.3 1.0
O B:HOH2149 4.4 45.3 1.0
OE1 B:GLN206 4.5 16.1 1.0
OG B:SER254 4.6 15.1 1.0
O B:HOH2095 4.6 33.2 1.0
CG B:GLU167 4.7 9.8 1.0
NE2 B:GLN186 4.7 10.6 1.0
CA B:SER254 4.8 10.3 1.0
CD B:GLN206 4.8 12.4 1.0
CB B:SER254 4.9 10.5 1.0

Magnesium binding site 8 out of 11 in 2x98

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Magnesium binding site 8 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1479

b:3.5
occ:1.00
 O B:HOH2361 1.9 90.6 1.0
O B:HOH2360 2.2 18.8 1.0
OE1 B:GLU361 2.3 12.5 1.0
O B:HOH2357 2.5 15.3 1.0
OE1 B:GLU363 2.5 14.0 1.0
OE2 B:GLU363 2.7 15.1 1.0
CD B:GLU363 3.0 9.8 1.0
CD B:GLU361 3.5 13.5 1.0
CG B:GLU361 4.3 11.6 1.0
CB B:GLU361 4.3 9.9 1.0
O B:HOH2359 4.3 17.0 1.0
OE2 B:GLU361 4.4 12.4 1.0
CG B:GLU363 4.5 8.3 1.0
O B:VAL362 4.8 8.3 1.0

Magnesium binding site 9 out of 11 in 2x98

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Magnesium binding site 9 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1480

b:7.4
occ:1.00
 O B:HOH2442 2.2 32.5 1.0
OD1 B:ASP433 2.5 12.8 1.0
O B:HOH2441 2.5 24.6 1.0
OD2 B:ASP433 2.9 20.2 1.0
CG B:ASP433 3.0 14.1 1.0
O B:HOH2443 4.1 40.5 1.0
CB B:ASP433 4.5 8.9 1.0
O B:ASP433 4.5 8.1 1.0
C B:ASP433 4.7 8.8 1.0

Magnesium binding site 10 out of 11 in 2x98

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Magnesium binding site 10 out of 11 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1481

b:11.2
occ:1.00
 O B:HOH2245 2.0 20.6 1.0
O A:HOH2270 2.2 28.0 1.0
OD1 B:ASP239 2.3 16.7 1.0
OD1 A:ASP282 2.5 16.9 1.0
O A:HOH2269 2.5 27.5 1.0
O B:ASP239 2.6 13.3 1.0
OD2 A:ASP282 2.6 20.4 1.0
CG A:ASP282 2.9 17.6 1.0
CG B:ASP239 3.4 14.3 1.0
C B:ASP239 3.6 12.7 1.0
O B:HOH2291 3.6 38.9 1.0
MG A:MG1478 3.6 5.5 1.0
O B:HOH2244 3.7 25.7 1.0
CA B:ASP239 3.9 12.3 1.0
O B:HOH2247 4.1 31.6 1.0
OD2 B:ASP239 4.2 15.4 1.0
CB B:ASP239 4.3 12.8 1.0
O A:HOH2273 4.3 23.8 1.0
CB A:ASP282 4.5 12.4 1.0
O B:HOH2109 4.7 44.4 1.0
O A:ASP282 4.7 12.3 1.0
N B:ALA240 4.8 13.7 1.0
O B:VAL241 4.9 21.8 1.0

Reference:

A.Wende, P.Johansson, R.Vollrath, M.Dyall-Smith, D.Oesterhelt, M.Grininger. Structural and Biochemical Characterization of A Halophilic Archaeal Alkaline Phosphatase. J.Mol.Biol. V. 400 52 2010.
ISSN: ISSN 0022-2836
PubMed: 20438737
DOI: 10.1016/J.JMB.2010.04.057
Page generated: Wed Aug 14 07:01:36 2024

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