Atomistry » Zinc » PDB 3w52-3wnq » 3wbh
Atomistry »
  Zinc »
    PDB 3w52-3wnq »
      3wbh »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy