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Mercury in PDB 4q84: Apo Ycao

Protein crystallography data

The structure of Apo Ycao, PDB code: 4q84 was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.946, 140.386, 163.345, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.8

Mercury Binding Sites:

The binding sites of Mercury atom in the Apo Ycao (pdb code 4q84). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Apo Ycao, PDB code: 4q84:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 4q84

Go back to Mercury Binding Sites List in 4q84
Mercury binding site 1 out of 4 in the Apo Ycao


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Apo Ycao within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg601

b:86.1
occ:1.00
O A:HOH909 2.4 46.7 1.0
O A:HOH717 2.9 26.2 1.0
OG A:SER568 3.2 57.2 1.0
CB A:SER568 3.7 47.1 1.0
O A:HOH753 3.8 25.8 1.0
O A:HOH723 3.9 38.3 1.0
O A:HOH923 4.2 48.5 1.0
N A:LEU55 4.2 73.1 1.0
CD1 A:LEU55 4.3 84.9 1.0
CB A:LEU55 4.5 78.8 1.0
O A:ALA565 4.6 38.5 1.0
N A:ALA54 4.6 67.0 1.0
CB A:ALA54 4.8 73.3 1.0
CA A:ALA565 4.9 46.3 1.0

Mercury binding site 2 out of 4 in 4q84

Go back to Mercury Binding Sites List in 4q84
Mercury binding site 2 out of 4 in the Apo Ycao


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Apo Ycao within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg602

b:88.0
occ:1.00
SG A:CYS56 2.6 76.8 1.0
O A:HOH717 3.3 26.2 1.0
N A:CYS56 3.3 71.0 1.0
O A:HOH808 3.4 26.7 1.0
CA A:CYS56 3.5 66.8 1.0
CB A:CYS56 3.5 73.5 1.0
C A:LEU55 3.6 68.1 1.0
O A:LEU55 3.7 54.7 1.0
CD1 A:LEU569 4.0 42.6 1.0
CB A:LEU55 4.3 78.8 1.0
CA A:LEU55 4.4 71.3 1.0
N A:LEU55 4.7 73.1 1.0
CA A:LEU569 4.9 39.2 1.0

Mercury binding site 3 out of 4 in 4q84

Go back to Mercury Binding Sites List in 4q84
Mercury binding site 3 out of 4 in the Apo Ycao


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Apo Ycao within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg601

b:86.4
occ:1.00
SG B:CYS53 3.0 76.9 1.0
OG B:SER568 3.3 46.5 1.0
CA B:CYS53 3.7 63.8 1.0
CB B:SER568 3.8 42.2 1.0
CB B:CYS53 3.8 69.4 1.0
CD2 B:LEU55 4.0 64.4 1.0
N B:ALA54 4.2 66.9 1.0
O B:GLU52 4.2 62.2 1.0
C B:CYS53 4.3 65.2 1.0
O B:ALA565 4.5 36.4 1.0
N B:LEU55 4.7 59.5 1.0
N B:CYS53 4.8 61.5 1.0
CA B:ALA565 4.8 42.2 1.0
C B:GLU52 4.9 68.2 1.0

Mercury binding site 4 out of 4 in 4q84

Go back to Mercury Binding Sites List in 4q84
Mercury binding site 4 out of 4 in the Apo Ycao


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Apo Ycao within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg602

b:95.8
occ:1.00
SG B:CYS56 2.5 49.6 1.0
CG B:LEU55 3.1 73.8 1.0
SG B:CYS53 3.1 76.9 1.0
CD2 B:LEU55 3.2 64.4 1.0
N B:CYS56 3.3 54.0 1.0
CB B:CYS56 3.3 59.3 1.0
CA B:CYS56 3.4 53.0 1.0
C B:LEU55 3.5 54.5 1.0
O B:LEU55 3.8 50.0 1.0
CB B:LEU55 3.9 74.1 1.0
CD1 B:LEU569 4.0 43.7 1.0
CA B:LEU55 4.1 60.1 1.0
CD1 B:LEU55 4.2 69.9 1.0
CB B:CYS53 4.5 69.4 1.0
O B:HOH704 4.5 37.6 1.0
N B:LEU55 4.6 59.5 1.0
O B:HOH761 4.8 36.6 1.0
C B:CYS56 5.0 51.9 1.0
O B:CYS53 5.0 62.2 1.0

Reference:

K.L.Dunbar, J.R.Chekan, C.L.Cox, B.J.Burkhart, S.K.Nair, D.A.Mitchell. Discovery of A New Atp-Binding Motif Involved in Peptidic Azoline Biosynthesis. Nat.Chem.Biol. V. 10 823 2014.
ISSN: ISSN 1552-4450
PubMed: 25129028
DOI: 10.1038/NCHEMBIO.1608
Page generated: Sun Dec 13 19:11:48 2020

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