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Zinc in PDB 3e2d: The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase

Enzymatic activity of The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase

All present enzymatic activity of The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase:
3.1.3.1;

Protein crystallography data

The structure of The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase, PDB code: 3e2d was solved by R.Helland, R.L.Larsen, B.Asgeirsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.70 / 1.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.240, 165.980, 57.480, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 16.6

Other elements in 3e2d:

The structure of The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase (pdb code 3e2d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase, PDB code: 3e2d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3e2d

Go back to Zinc Binding Sites List in 3e2d
Zinc binding site 1 out of 4 in the The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:3.2
occ:1.00
 O4 A:SO4610 2.0 7.5 1.0
NE2 A:HIS277 2.0 3.1 1.0
NE2 A:HIS465 2.1 3.3 1.0
OD1 A:ASP273 2.2 4.4 1.0
OD2 A:ASP273 2.5 4.4 1.0
O2 A:SO4610 2.6 7.5 1.0
CG A:ASP273 2.7 3.6 1.0
S A:SO4610 2.9 5.8 1.0
CE1 A:HIS277 3.0 2.5 1.0
CE1 A:HIS465 3.0 2.0 1.0
CD2 A:HIS277 3.0 2.6 1.0
CD2 A:HIS465 3.1 2.5 1.0
O3 A:SO4610 3.7 5.1 1.0
CE1 A:HIS316 4.0 3.2 1.0
O1 A:SO4610 4.0 4.7 1.0
ZN A:ZN602 4.1 4.8 1.0
ND1 A:HIS277 4.1 2.9 1.0
ND1 A:HIS465 4.1 2.3 1.0
CG A:HIS277 4.1 3.0 1.0
CB A:ASP273 4.2 2.6 1.0
CG A:HIS465 4.2 2.5 1.0
O A:HOH624 4.2 3.6 1.0
NE2 A:HIS316 4.2 3.4 1.0
OG1 A:THR318 4.3 4.0 1.0
O A:HOH705 4.4 7.1 1.0
OD1 A:ASP12 4.6 3.0 1.0
OH B:TYR325 4.7 4.5 1.0
CG2 A:THR318 4.8 4.0 1.0
O A:ASP273 4.9 3.5 1.0
C2 A:EDO621 4.9 25.4 1.0

Zinc binding site 2 out of 4 in 3e2d

Go back to Zinc Binding Sites List in 3e2d
Zinc binding site 2 out of 4 in the The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:4.8
occ:1.00
 OD1 A:ASP12 1.9 3.0 1.0
O2 A:SO4610 2.0 7.5 1.0
NE2 A:HIS316 2.0 3.4 1.0
OD2 A:ASP315 2.1 3.7 1.0
OG A:SER65 2.2 6.3 0.5
CG A:ASP12 2.7 3.4 1.0
OD2 A:ASP12 2.9 3.6 1.0
CG A:ASP315 2.9 2.9 1.0
CE1 A:HIS316 3.0 3.2 1.0
CD2 A:HIS316 3.0 3.7 1.0
OD1 A:ASP315 3.2 3.4 1.0
CB A:SER65 3.2 4.7 0.5
S A:SO4610 3.3 5.8 1.0
CB A:SER65 3.5 4.4 0.5
OG A:SER65 3.6 7.9 0.5
OD1 A:ASP273 3.8 4.4 1.0
O3 A:SO4610 3.9 5.1 1.0
CA A:SER65 3.9 4.2 0.5
CA A:SER65 3.9 4.0 0.5
CE1 A:HIS465 4.0 2.0 1.0
O1 A:SO4610 4.0 4.7 1.0
CG A:ASP273 4.0 3.6 1.0
ND1 A:HIS316 4.1 3.5 1.0
ZN A:ZN601 4.1 3.2 1.0
CG A:HIS316 4.1 2.2 1.0
N A:SER65 4.1 3.3 0.5
CB A:ASP12 4.1 2.9 1.0
N A:SER65 4.1 3.4 0.5
NE2 A:HIS465 4.2 3.3 1.0
N A:GLY13 4.3 2.3 1.0
O4 A:SO4610 4.3 7.5 1.0
CB A:ASP315 4.3 3.1 1.0
O A:HOH836 4.4 10.9 1.0
CB A:ASP273 4.5 2.6 1.0
CA A:ASP12 4.5 2.4 1.0
OD2 A:ASP273 4.5 4.4 1.0
O A:HOH629 4.5 3.0 1.0
C A:ASP12 4.6 2.4 1.0
MG A:MG603 4.7 3.0 1.0
O A:HOH624 4.7 3.6 1.0
ND1 A:HIS465 4.8 2.3 1.0

Zinc binding site 3 out of 4 in 3e2d

Go back to Zinc Binding Sites List in 3e2d
Zinc binding site 3 out of 4 in the The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:3.8
occ:1.00
 O4 B:SO4610 1.9 8.7 1.0
NE2 B:HIS277 2.0 2.9 1.0
NE2 B:HIS465 2.1 3.3 1.0
OD1 B:ASP273 2.2 4.0 1.0
OD2 B:ASP273 2.5 5.5 1.0
O2 B:SO4610 2.5 9.0 1.0
CG B:ASP273 2.7 4.0 1.0
S B:SO4610 2.8 7.3 1.0
CE1 B:HIS277 3.0 2.4 1.0
CE1 B:HIS465 3.0 3.0 1.0
CD2 B:HIS277 3.0 3.0 1.0
CD2 B:HIS465 3.1 2.7 1.0
O3 B:SO4610 3.7 7.0 1.0
O1 B:SO4610 4.0 6.7 1.0
CE1 B:HIS316 4.0 2.5 1.0
ND1 B:HIS277 4.1 3.0 1.0
ZN B:ZN602 4.1 5.0 1.0
CG B:HIS277 4.2 2.8 1.0
ND1 B:HIS465 4.2 3.3 1.0
CB B:ASP273 4.2 3.9 1.0
O B:HOH921 4.2 3.9 1.0
CG B:HIS465 4.2 3.0 1.0
NE2 B:HIS316 4.3 3.4 1.0
OG1 B:THR318 4.3 4.3 1.0
O A:HOH677 4.4 8.4 1.0
OD1 B:ASP12 4.6 2.2 1.0
OH A:TYR325 4.7 4.4 1.0
CG2 B:THR318 4.8 4.9 1.0
OG B:SER65 4.8 6.8 0.5
O B:ASP273 4.9 3.2 1.0

Zinc binding site 4 out of 4 in 3e2d

Go back to Zinc Binding Sites List in 3e2d
Zinc binding site 4 out of 4 in the The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:5.0
occ:1.00
 OD1 B:ASP12 1.9 2.2 1.0
NE2 B:HIS316 2.0 3.4 1.0
O2 B:SO4610 2.0 9.0 1.0
OD2 B:ASP315 2.1 4.0 1.0
OG B:SER65 2.1 6.8 0.5
CG B:ASP12 2.7 2.8 1.0
OD2 B:ASP12 2.9 3.4 1.0
CG B:ASP315 2.9 2.8 1.0
CE1 B:HIS316 3.0 2.5 1.0
CD2 B:HIS316 3.0 3.0 1.0
CB B:SER65 3.1 5.3 0.5
OD1 B:ASP315 3.2 3.1 1.0
S B:SO4610 3.3 7.3 1.0
CB B:SER65 3.4 5.0 0.5
OG B:SER65 3.5 8.6 0.5
CA B:SER65 3.8 4.5 0.5
CA B:SER65 3.8 4.3 0.5
OD1 B:ASP273 3.8 4.0 1.0
O3 B:SO4610 3.9 7.0 1.0
O1 B:SO4610 4.0 6.7 1.0
CE1 B:HIS465 4.0 3.0 1.0
ND1 B:HIS316 4.0 2.8 1.0
CG B:ASP273 4.1 4.0 1.0
N B:SER65 4.1 3.7 0.5
CG B:HIS316 4.1 2.0 1.0
CB B:ASP12 4.1 3.5 1.0
N B:SER65 4.1 3.8 0.5
ZN B:ZN601 4.1 3.8 1.0
NE2 B:HIS465 4.3 3.3 1.0
N B:GLY13 4.3 2.9 1.0
CB B:ASP315 4.3 3.0 1.0
O4 B:SO4610 4.3 8.7 1.0
O B:HOH1326 4.4 12.0 1.0
O B:HOH937 4.5 3.8 1.0
CA B:ASP12 4.5 2.9 1.0
CB B:ASP273 4.5 3.9 1.0
OD2 B:ASP273 4.5 5.5 1.0
C B:ASP12 4.6 2.8 1.0
MG B:MG603 4.7 3.2 1.0
O B:HOH921 4.8 3.9 1.0
ND1 B:HIS465 4.8 3.3 1.0

Reference:

R.Helland, R.L.Larsen, B.Asgeirsson. The 1.4 A Crystal Structure of the Large and Cold-Active Vibrio Sp. Alkaline Phosphatase. Biochim.Biophys.Acta V.1794 297 2009.
ISSN: ISSN 0006-3002
PubMed: 18977465
DOI: 10.1016/J.BBAPAP.2008.09.020
Page generated: Thu Oct 24 12:33:39 2024

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