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Zinc 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:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Characteristics of Alkaline Phosphatase From A Moderately Halophilic Bacteria Halomonas Sp.593, PDB code: 3wbh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3wbh

Go back to Zinc Binding Sites List in 3wbh
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn504

b:35.9
occ:1.00
 NE2 A:HIS273 2.2 10.7 1.0
OD2 A:ASP269 2.2 12.6 1.0
NE2 A:HIS461 2.3 9.7 1.0
O B:HOH633 2.5 22.1 1.0
CL A:CL506 2.5 34.9 1.0
OD1 A:ASP269 2.6 12.0 1.0
O A:HOH636 2.6 14.5 1.0
CG A:ASP269 2.8 11.6 1.0
CD2 A:HIS273 3.1 10.6 1.0
CE1 A:HIS461 3.2 10.3 1.0
CE1 A:HIS273 3.2 10.7 1.0
CD2 A:HIS461 3.3 10.2 1.0
O A:HOH629 4.0 12.9 1.0
CE1 A:HIS312 4.2 9.7 1.0
OG A:SER65 4.2 11.6 1.0
CB A:ASP269 4.2 10.9 1.0
CG A:HIS273 4.3 10.6 1.0
ND1 A:HIS273 4.3 11.0 1.0
ND1 A:HIS461 4.3 10.5 1.0
NE2 A:HIS312 4.4 10.1 1.0
CG A:HIS461 4.4 10.4 1.0
ZN A:ZN505 4.5 13.6 1.0
O A:HOH635 4.5 22.4 1.0
OG1 A:THR314 4.6 16.7 1.0
OH B:TYR321 4.7 10.2 1.0
OD1 A:ASP12 4.9 12.6 1.0

Zinc binding site 2 out of 4 in 3wbh

Go back to Zinc Binding Sites List in 3wbh
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn505

b:13.6
occ:1.00
 OG A:SER65 1.7 11.6 1.0
NE2 A:HIS312 2.0 10.1 1.0
OD2 A:ASP311 2.1 9.2 1.0
OD1 A:ASP12 2.1 12.6 1.0
CG A:ASP12 2.7 11.9 1.0
OD2 A:ASP12 2.7 10.6 1.0
CB A:SER65 2.9 11.6 1.0
CD2 A:HIS312 2.9 9.7 1.0
CG A:ASP311 3.0 10.0 1.0
CE1 A:HIS312 3.0 9.7 1.0
OD1 A:ASP311 3.4 10.2 1.0
CA A:SER65 3.4 11.4 1.0
CL A:CL506 3.7 34.9 1.0
O A:HOH639 3.8 9.7 1.0
N A:SER65 4.0 11.4 1.0
CG A:HIS312 4.0 9.9 1.0
ND1 A:HIS312 4.0 10.1 1.0
CB A:ASP12 4.1 12.1 1.0
O A:HOH604 4.1 11.4 1.0
CE1 A:HIS461 4.1 10.3 1.0
OD1 A:ASP269 4.3 12.0 1.0
CB A:ASP311 4.3 9.7 1.0
CG A:ASP269 4.3 11.6 1.0
N A:GLY13 4.4 12.5 1.0
OD2 A:ASP269 4.5 12.6 1.0
MG A:MG501 4.5 10.4 1.0
ZN A:ZN504 4.5 35.9 1.0
NE2 A:HIS461 4.5 9.7 1.0
CA A:ASP12 4.5 12.5 1.0
C A:ASP12 4.7 12.5 1.0
O A:HOH629 4.7 12.9 1.0
C A:SER65 4.8 11.2 1.0
CB A:ASP269 4.8 10.9 1.0
ND1 A:HIS461 4.8 10.5 1.0
C A:ASP64 4.9 12.0 1.0
OG1 A:THR118 4.9 11.7 1.0
O A:HOH640 5.0 9.5 1.0

Zinc binding site 3 out of 4 in 3wbh

Go back to Zinc Binding Sites List in 3wbh
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
B:Zn504

b:33.4
occ:1.00
 OD2 B:ASP269 2.0 15.8 1.0
NE2 B:HIS461 2.3 11.2 1.0
NE2 B:HIS273 2.3 11.4 1.0
O B:HOH634 2.4 20.9 1.0
CL B:CL506 2.4 29.1 1.0
O A:HOH637 2.5 18.3 1.0
CG B:ASP269 2.7 14.3 1.0
OD1 B:ASP269 2.8 15.3 1.0
CD2 B:HIS273 3.2 10.9 1.0
CE1 B:HIS461 3.2 11.3 1.0
CD2 B:HIS461 3.3 10.9 1.0
CE1 B:HIS273 3.3 11.6 1.0
O B:HOH610 3.9 11.5 1.0
CB B:ASP269 4.2 13.2 1.0
CE1 B:HIS312 4.2 11.4 1.0
OG B:SER65 4.2 12.4 1.0
ND1 B:HIS461 4.3 11.9 1.0
CG B:HIS273 4.4 11.1 1.0
ND1 B:HIS273 4.4 12.7 1.0
NE2 B:HIS312 4.4 11.9 1.0
CG B:HIS461 4.4 11.4 1.0
OH A:TYR321 4.5 13.1 1.0
ZN B:ZN505 4.5 13.2 1.0
OG1 B:THR314 4.6 17.0 1.0
OD1 B:ASP12 4.9 9.9 1.0

Zinc binding site 4 out of 4 in 3wbh

Go back to Zinc Binding Sites List in 3wbh
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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:Zn505

b:13.2
occ:1.00
 OG B:SER65 1.9 12.4 1.0
OD2 B:ASP311 1.9 10.4 1.0
NE2 B:HIS312 2.1 11.9 1.0
OD1 B:ASP12 2.1 9.9 1.0
CG B:ASP12 2.7 9.5 1.0
OD2 B:ASP12 2.8 8.7 1.0
CG B:ASP311 2.8 10.9 1.0
CD2 B:HIS312 2.9 11.7 1.0
CE1 B:HIS312 3.1 11.4 1.0
CB B:SER65 3.1 11.9 1.0
OD1 B:ASP311 3.1 11.4 1.0
CA B:SER65 3.5 11.8 1.0
CL B:CL506 3.7 29.1 1.0
O B:HOH638 3.9 7.8 1.0
CG B:HIS312 4.1 11.4 1.0
O B:HOH612 4.1 10.3 1.0
ND1 B:HIS312 4.1 11.6 1.0
CB B:ASP12 4.1 10.2 1.0
N B:SER65 4.2 12.5 1.0
CB B:ASP311 4.2 10.9 1.0
OD2 B:ASP269 4.2 15.8 1.0
CE1 B:HIS461 4.3 11.3 1.0
N B:GLY13 4.3 11.3 1.0
CG B:ASP269 4.3 14.3 1.0
CA B:ASP12 4.5 10.3 1.0
MG B:MG501 4.5 11.7 1.0
OD1 B:ASP269 4.5 15.3 1.0
NE2 B:HIS461 4.5 11.2 1.0
ZN B:ZN504 4.5 33.4 1.0
C B:ASP12 4.6 11.0 1.0
CB B:ASP269 4.8 13.2 1.0
O B:HOH610 4.8 11.5 1.0
C B:SER65 4.8 11.3 1.0
OG1 B:THR118 4.9 10.0 1.0
O B:HOH636 4.9 10.2 1.0
C B:ASP64 5.0 13.1 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: Sat Oct 26 18:01:06 2024

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