Calcium in PDB 6bzi: Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury

Enzymatic activity of Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury

All present enzymatic activity of Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury:
3.8.1.1;

Protein crystallography data

The structure of Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury, PDB code: 6bzi was solved by A.H.Pang, S.Garneau-Tsodikova, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.722, 156.338, 216.134, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.6

Other elements in 6bzi:

The structure of Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury also contains other interesting chemical elements:

Mercury (Hg) 33 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury (pdb code 6bzi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury, PDB code: 6bzi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6bzi

Go back to Calcium Binding Sites List in 6bzi
Calcium binding site 1 out of 4 in the Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:24.5
occ:1.00
OD2 A:ASP5 2.3 24.1 1.0
O A:HOH820 2.3 23.6 1.0
OD1 A:ASP5 2.9 25.2 1.0
CG A:ASP5 2.9 23.4 1.0
CB A:ASP5 4.4 22.2 1.0
CB A:ASN28 4.5 22.7 1.0
N A:ASN28 4.6 19.8 1.0
N A:ASP5 5.0 21.7 1.0

Calcium binding site 2 out of 4 in 6bzi

Go back to Calcium Binding Sites List in 6bzi
Calcium binding site 2 out of 4 in the Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:25.2
occ:1.00
OD2 B:ASP5 2.3 23.5 1.0
CG B:ASP5 3.0 22.6 1.0
OD1 B:ASP5 3.0 23.7 1.0
CB B:ASN28 4.4 24.7 1.0
CB B:ASP5 4.4 21.8 1.0
N B:ASN28 4.6 21.9 1.0
N B:ASP5 5.0 22.4 1.0

Calcium binding site 3 out of 4 in 6bzi

Go back to Calcium Binding Sites List in 6bzi
Calcium binding site 3 out of 4 in the Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:23.6
occ:1.00
O C:HOH798 2.3 23.1 1.0
OD1 C:ASN98 2.4 21.2 1.0
CG C:ASN98 3.6 21.7 1.0
ND2 C:ASN98 4.1 22.2 1.0
O C:HOH702 4.2 15.5 1.0
OE2 C:GLU97 4.7 29.1 1.0
CG C:GLU97 4.8 26.3 1.0
CB C:ASN98 4.8 21.2 1.0

Calcium binding site 4 out of 4 in 6bzi

Go back to Calcium Binding Sites List in 6bzi
Calcium binding site 4 out of 4 in the Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Halogenase Pltm in Complex with Ethyl Mercury and Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:26.2
occ:1.00
O D:HOH762 2.3 26.1 1.0
OD2 D:ASP5 2.3 25.3 1.0
O D:HOH783 2.3 26.9 1.0
O D:HOH772 2.3 23.4 1.0
OD1 D:ASP5 2.9 26.1 1.0
CG D:ASP5 2.9 25.1 1.0
CB D:ASN28 4.3 23.5 1.0
CB D:ASP5 4.4 24.2 1.0
N D:ASN28 4.5 21.6 1.0
O D:GLY26 4.9 19.0 1.0

Reference:

S.Mori, A.H.Pang, N.Thamban Chandrika, S.Garneau-Tsodikova, O.V.Tsodikov. Unusual Substrate and Halide Versatility of Phenolic Halogenase Pltm. Nat Commun V. 10 1255 2019.
ISSN: ESSN 2041-1723
PubMed: 30890712
DOI: 10.1038/S41467-019-09215-9
Page generated: Sat Dec 12 06:00:50 2020

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