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Magnesium in PDB 3wbh: Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593

Enzymatic activity of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593

All present enzymatic activity of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593:
3.1.3.1;

Protein crystallography data

The structure of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593, PDB code: 3wbh was solved by S.Arai, Y.Yonezawa, M.Ishibashi, F.Matsumoto, T.Tamada, H.Tokunaga, M.Tokunaga, R.Kuroki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.29 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.713, 146.974, 58.280, 90.00, 105.21, 90.00
R / Rfree (%) 17.7 / 22.5

Other elements in 3wbh:

The structure of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593 (pdb code 3wbh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593, PDB code: 3wbh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3wbh

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Magnesium binding site 1 out of 6 in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:10.4
occ:1.00
 OE2 A:GLU264 1.9 13.1 1.0
OD2 A:ASP12 2.0 10.6 1.0
O A:HOH638 2.1 10.7 1.0
OG1 A:THR118 2.1 11.7 1.0
O A:HOH640 2.2 9.5 1.0
O A:HOH639 2.2 9.7 1.0
CG A:ASP12 3.0 11.9 1.0
CD A:GLU264 3.0 13.8 1.0
CB A:THR118 3.2 11.7 1.0
OE1 A:GLU264 3.5 14.0 1.0
CB A:ASP12 3.5 12.1 1.0
OD1 A:ASP12 4.0 12.6 1.0
ND1 A:HIS116 4.0 15.2 1.0
O A:HOH629 4.0 12.9 1.0
N A:THR118 4.1 11.9 1.0
CG2 A:THR118 4.1 11.9 1.0
OG A:SER65 4.3 11.6 1.0
CG A:GLU264 4.3 13.7 1.0
CA A:THR118 4.3 12.2 1.0
O A:HOH604 4.3 11.4 1.0
CA A:GLY266 4.4 11.9 1.0
ZN A:ZN505 4.5 13.6 1.0
CE1 A:HIS116 4.5 15.8 1.0
CB A:SER65 4.5 11.6 1.0
O A:GLY266 4.6 12.6 1.0
OD2 A:ASP311 4.8 9.2 1.0
CA A:ASP12 5.0 12.5 1.0
OG1 A:THR112 5.0 11.4 1.0
CG2 A:THR112 5.0 11.2 1.0

Magnesium binding site 2 out of 6 in 3wbh

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Magnesium binding site 2 out of 6 in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:21.4
occ:1.00
 O A:ALA45 2.2 15.2 1.0
O A:GLY48 2.2 14.3 1.0
O B:SER481 2.4 17.9 1.0
O A:LYS46 2.4 18.7 1.0
OG B:SER482 2.5 18.0 1.0
O B:HOH637 2.5 16.8 1.0
C A:LYS46 3.1 19.1 1.0
C A:GLY48 3.2 15.2 1.0
C A:ALA45 3.3 16.7 1.0
C B:SER481 3.4 17.9 1.0
CA A:LYS46 3.5 18.5 1.0
O A:HOH615 3.5 14.5 1.0
CB B:SER482 3.6 18.1 1.0
CA B:SER482 3.8 16.2 1.0
N A:LYS46 3.8 17.6 1.0
N A:GLY48 3.9 16.0 1.0
N B:SER482 4.0 17.8 1.0
N A:VAL49 4.1 15.0 1.0
CA A:VAL49 4.1 14.6 1.0
N A:GLU47 4.2 18.9 1.0
C A:GLU47 4.2 18.0 1.0
CA A:GLY48 4.2 15.4 1.0
CA A:ALA45 4.6 17.3 1.0
O A:GLU47 4.6 15.9 1.0
CA B:SER481 4.6 18.4 1.0
CA A:GLU47 4.6 19.7 1.0
O B:LEU478 4.7 16.7 1.0
CB B:SER481 4.8 18.1 1.0
CG1 A:VAL49 4.9 16.6 1.0
CB A:LYS46 4.9 19.5 1.0

Magnesium binding site 3 out of 6 in 3wbh

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Magnesium binding site 3 out of 6 in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:32.5
occ:1.00
 O A:HOH646 2.0 30.8 1.0
OD1 A:ASP255 2.4 29.6 1.0
O A:GLY103 2.5 20.1 1.0
OD2 A:ASP257 2.5 31.9 1.0
O A:HOH634 2.7 26.8 1.0
OD2 A:ASP255 2.8 28.1 1.0
CG A:ASP255 3.0 27.2 1.0
OE2 A:GLU256 3.2 44.3 1.0
CG A:ASP257 3.4 31.7 1.0
CB A:ASP257 3.6 28.0 1.0
C A:GLY103 3.7 19.7 1.0
N A:ASP257 4.1 25.3 1.0
CD A:GLU256 4.2 41.6 1.0
CA A:GLY103 4.4 20.2 1.0
CB A:ASP255 4.4 26.6 1.0
CG A:GLU256 4.5 36.2 1.0
CA A:ASP257 4.5 26.2 1.0
OD1 A:ASP257 4.6 32.0 1.0
N A:GLU256 4.6 26.9 1.0
N A:LYS104 4.7 18.9 1.0
CA A:LYS104 4.9 20.6 1.0

Magnesium binding site 4 out of 6 in 3wbh

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Magnesium binding site 4 out of 6 in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:11.7
occ:1.00
 OD2 B:ASP12 1.9 8.7 1.0
OE2 B:GLU264 1.9 13.9 1.0
O B:HOH635 2.1 11.5 1.0
O B:HOH638 2.1 7.8 1.0
OG1 B:THR118 2.2 10.0 1.0
O B:HOH636 2.2 10.2 1.0
CG B:ASP12 2.9 9.5 1.0
CD B:GLU264 3.0 12.8 1.0
CB B:THR118 3.2 10.7 1.0
OE1 B:GLU264 3.3 12.1 1.0
CB B:ASP12 3.5 10.2 1.0
OD1 B:ASP12 4.0 9.9 1.0
ND1 B:HIS116 4.0 18.6 1.0
CG2 B:THR118 4.1 10.8 1.0
N B:THR118 4.1 11.3 1.0
O B:HOH612 4.2 10.3 1.0
CA B:THR118 4.3 11.3 1.0
CG B:GLU264 4.3 13.5 1.0
O B:HOH610 4.3 11.5 1.0
OG B:SER65 4.4 12.4 1.0
CA B:GLY266 4.5 13.6 1.0
ZN B:ZN505 4.5 13.2 1.0
CE1 B:HIS116 4.5 19.4 1.0
O B:GLY266 4.6 13.8 1.0
CB B:SER65 4.7 11.9 1.0
OD2 B:ASP311 4.8 10.4 1.0
CA B:ASP12 4.9 10.3 1.0
OG1 B:THR112 5.0 14.1 1.0

Magnesium binding site 5 out of 6 in 3wbh

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Magnesium binding site 5 out of 6 in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:17.1
occ:1.00
 OG A:SER482 2.2 17.2 1.0
O A:SER481 2.2 15.0 1.0
O B:ALA45 2.2 19.3 1.0
O B:GLY48 2.5 16.7 1.0
O A:HOH623 2.6 15.0 1.0
O B:LYS46 2.7 18.6 1.0
C A:SER481 3.2 17.0 1.0
C B:LYS46 3.3 21.8 1.0
CB A:SER482 3.3 16.9 1.0
C B:ALA45 3.4 20.4 1.0
C B:GLY48 3.4 16.9 1.0
CA B:LYS46 3.5 22.8 1.0
CA A:SER482 3.6 16.5 1.0
O B:HOH614 3.8 14.7 1.0
N A:SER482 3.8 16.6 1.0
N B:LYS46 3.9 20.2 1.0
CA B:VAL49 4.1 16.5 1.0
N B:VAL49 4.1 16.2 1.0
N B:GLY48 4.3 18.6 1.0
N B:GLU47 4.3 23.1 1.0
CA A:SER481 4.4 16.7 1.0
C B:GLU47 4.5 21.2 1.0
CA B:GLY48 4.5 17.0 1.0
CB A:SER481 4.6 17.3 1.0
O A:LEU478 4.6 16.9 1.0
CA B:ALA45 4.7 21.7 1.0
O B:GLU47 4.8 19.9 1.0
CA B:GLU47 4.9 23.7 1.0
CG1 B:VAL49 4.9 17.8 1.0
CB B:LYS46 4.9 25.4 1.0
N A:SER481 4.9 16.8 1.0
C B:VAL49 5.0 16.3 1.0

Magnesium binding site 6 out of 6 in 3wbh

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Magnesium binding site 6 out of 6 in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:24.6
occ:1.00
 O B:HOH641 2.0 20.7 1.0
OD1 B:ASP255 2.1 23.6 1.0
O B:HOH642 2.2 23.8 1.0
O B:GLY103 2.2 16.5 1.0
OD1 B:ASP257 2.3 27.4 1.0
OD2 B:ASP255 2.7 24.9 1.0
CG B:ASP255 2.8 24.2 1.0
CG B:ASP257 3.3 27.1 1.0
C B:GLY103 3.4 16.7 1.0
CB B:ASP257 3.9 25.2 1.0
CA B:GLY103 4.1 17.1 1.0
N B:ASP257 4.1 24.3 1.0
CB B:ASP255 4.3 25.1 1.0
OD2 B:ASP257 4.4 26.6 1.0
N B:LYS104 4.4 15.8 1.0
OE2 B:GLU256 4.5 21.4 1.0
N B:GLU256 4.6 28.8 1.0
CA B:LYS104 4.7 16.5 1.0
CA B:ASP257 4.7 24.7 1.0
C B:LYS104 4.9 15.2 1.0
CA B:ASP255 5.0 25.3 1.0

Reference:

S.Arai, Y.Yonezawa, M.Ishibashi, F.Matsumoto, M.Adachi, T.Tamada, H.Tokunaga, M.Blaber, M.Tokunaga, R.Kuroki. Structural Characteristics of Alkaline Phosphatase From the Moderately Halophilic Bacterium Halomonas Sp. 593. Acta Crystallogr.,Sect.D V. 70 811 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004713033609
Page generated: Mon Dec 14 09:00:28 2020

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