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Mercury in PDB 5l9w: Crystal Structure of the Apc Core Complex

Enzymatic activity of Crystal Structure of the Apc Core Complex

All present enzymatic activity of Crystal Structure of the Apc Core Complex:
6.4.1.8;

Protein crystallography data

The structure of Crystal Structure of the Apc Core Complex, PDB code: 5l9w was solved by E.Warkentin, S.Weidenweber, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 240.080, 240.080, 336.640, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 23.5

Other elements in 5l9w:

The structure of Crystal Structure of the Apc Core Complex also contains other interesting chemical elements:

Potassium (K) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of the Apc Core Complex (pdb code 5l9w). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Crystal Structure of the Apc Core Complex, PDB code: 5l9w:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 5l9w

Go back to Mercury Binding Sites List in 5l9w
Mercury binding site 1 out of 4 in the Crystal Structure of the Apc Core Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of the Apc Core Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg701

b:0.7
occ:0.62
OD2 A:ASP65 2.3 93.3 1.0
OD1 A:ASP126 2.3 0.8 1.0
OD2 A:ASP126 2.3 83.1 1.0
O A:HOH803 2.3 55.7 1.0
CE1 A:HIS123 2.3 0.5 1.0
ND1 A:HIS148 2.4 70.3 1.0
NE2 A:HIS123 2.5 88.1 1.0
CG A:ASP126 2.7 93.0 1.0
CE1 A:HIS148 3.2 76.7 1.0
CG A:ASP65 3.4 90.6 1.0
CG A:HIS148 3.5 69.8 1.0
ND1 A:HIS123 3.6 98.4 1.0
CD2 A:HIS123 3.8 72.7 1.0
CB A:HIS148 3.9 62.3 1.0
OD1 A:ASP65 4.0 100.0 1.0
CB A:ASP126 4.3 65.5 1.0
CG A:HIS123 4.4 81.9 1.0
NE2 A:HIS148 4.4 83.3 1.0
CB A:ASP65 4.4 75.6 1.0
CG1 A:VAL62 4.6 48.8 1.0
CD2 A:HIS148 4.6 76.4 1.0
N A:ASP126 4.9 65.0 1.0
CA A:HIS148 4.9 61.0 1.0
CG1 A:VAL361 4.9 75.2 1.0
CE A:MET160 5.0 95.5 1.0

Mercury binding site 2 out of 4 in 5l9w

Go back to Mercury Binding Sites List in 5l9w
Mercury binding site 2 out of 4 in the Crystal Structure of the Apc Core Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of the Apc Core Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg702

b:0.3
occ:0.37
O A:HOH805 2.3 92.1 1.0
SG A:CYS82 2.4 66.3 1.0
O A:CYS82 3.0 96.5 1.0
CD1 A:ILE331 3.8 87.7 1.0
N A:CYS82 3.9 74.1 1.0
C A:CYS82 3.9 83.0 1.0
CB A:CYS82 4.0 64.3 1.0
CA A:CYS82 4.2 74.1 1.0
CE1 A:TYR85 4.4 81.0 1.0
OH A:TYR85 4.6 0.4 1.0
CZ A:TYR85 4.7 91.6 1.0
O A:GLY80 4.8 78.4 1.0
C A:SER81 4.9 77.3 1.0
CA A:SER81 4.9 74.5 1.0
O B:HOH903 4.9 72.7 1.0
CE2 A:PHE443 5.0 91.3 1.0

Mercury binding site 3 out of 4 in 5l9w

Go back to Mercury Binding Sites List in 5l9w
Mercury binding site 3 out of 4 in the Crystal Structure of the Apc Core Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of the Apc Core Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg801

b:0.6
occ:0.29
O B:LYS36 2.3 0.6 1.0
SG B:CYS37 2.3 0.7 1.0
C B:LYS36 3.3 1.0 1.0
CB B:CYS37 3.4 0.5 1.0
CA B:CYS37 3.4 0.9 1.0
N B:CYS37 3.8 0.7 1.0
CB B:ALA54 4.3 0.5 1.0
CD B:PRO38 4.5 0.9 1.0
CA B:LYS36 4.6 0.6 1.0
N B:LYS36 4.7 0.9 1.0
C B:CYS37 4.8 0.5 1.0

Mercury binding site 4 out of 4 in 5l9w

Go back to Mercury Binding Sites List in 5l9w
Mercury binding site 4 out of 4 in the Crystal Structure of the Apc Core Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of the Apc Core Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg201

b:0.8
occ:0.22
SG C:CYS78 2.2 0.3 1.0
SG C:CYS22 2.2 0.6 1.0
SG C:CYS75 2.3 1.0 1.0
SG C:CYS25 2.3 0.3 1.0
CB C:CYS75 2.9 0.8 1.0
CB C:CYS22 3.5 0.8 1.0
CB C:ARG80 3.7 0.7 1.0
CB C:CYS78 4.0 0.8 1.0
CB C:CYS25 4.0 0.4 1.0
CA C:CYS75 4.2 0.5 1.0
N C:ARG80 4.3 0.5 1.0
N C:CYS25 4.4 0.3 1.0
CG C:ARG80 4.5 0.2 1.0
C C:CYS75 4.6 0.9 1.0
O C:CYS75 4.6 0.9 1.0
CA C:ARG80 4.6 0.6 1.0
CB C:ASP24 4.7 0.6 1.0
CA C:CYS22 4.8 0.2 1.0
N C:CYS78 4.8 0.6 1.0
CA C:CYS78 4.8 0.7 1.0
CA C:CYS25 4.9 0.6 1.0
N C:CYS75 4.9 0.6 1.0
N C:THR79 5.0 0.3 1.0

Reference:

S.Weidenweber, K.Schuhle, U.Demmer, E.Warkentin, U.Ermler, J.Heider. Structure of the Acetophenone Carboxylase Core Complex: Prototype of A New Class of Atp-Dependent Carboxylases/Hydrolases. Sci Rep V. 7 39674 2017.
ISSN: ESSN 2045-2322
PubMed: 28054554
DOI: 10.1038/SREP39674
Page generated: Sun Dec 13 19:12:52 2020

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