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Mercury in PDB 6b7q: Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910

Protein crystallography data

The structure of Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910, PDB code: 6b7q was solved by Y.Mao, A.Akturk, J.Wasilko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.51 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.806, 80.616, 85.612, 90.00, 109.87, 90.00
R / Rfree (%) 19.5 / 24.1

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 (pdb code 6b7q). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 10 binding sites of Mercury where determined in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910, PDB code: 6b7q:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 10 in 6b7q

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Mercury binding site 1 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


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 Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1001

b:58.8
occ:0.41
NE2 A:HIS276 2.6 42.4 1.0
OE2 A:GLU261 3.3 70.8 1.0
OE1 A:GLN275 3.4 38.0 1.0
CD2 A:HIS276 3.4 40.2 1.0
CE1 A:HIS276 3.6 43.1 1.0
CG A:GLU261 3.7 73.3 1.0
CD A:GLU261 3.7 79.2 1.0
CD A:GLN275 4.1 38.4 1.0
O A:GLU261 4.3 53.4 1.0
CG A:GLN275 4.6 36.5 1.0
CG A:HIS276 4.6 41.0 1.0
ND1 A:HIS276 4.7 43.0 1.0
OE1 A:GLU261 4.7 78.5 1.0
NE2 A:GLN275 5.0 38.0 1.0
CB A:GLU261 5.0 65.7 1.0

Mercury binding site 2 out of 10 in 6b7q

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Mercury binding site 2 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


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 Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1002

b:60.6
occ:0.78
NE2 A:HIS407 2.4 33.5 1.0
CD2 A:HIS407 3.3 34.8 1.0
O A:HOH1244 3.3 39.4 1.0
CE A:MET408 3.4 46.6 1.0
CE1 A:HIS407 3.4 34.9 1.0
SD A:MET408 4.3 44.9 0.7
CE1 A:TYR347 4.3 47.6 1.0
CG A:HIS407 4.5 35.8 1.0
ND1 A:HIS407 4.5 39.8 1.0
OH A:TYR347 4.8 42.8 1.0
CE1 A:HIS277 4.9 39.2 1.0
O A:HOH1159 4.9 39.6 1.0

Mercury binding site 3 out of 10 in 6b7q

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Mercury binding site 3 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


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 Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1003

b:72.0
occ:0.29
ND1 A:HIS535 2.4 52.4 1.0
O A:HOH1206 2.9 50.9 1.0
OD1 A:ASP460 3.1 43.6 1.0
CG A:ASP460 3.1 43.8 1.0
CE1 A:HIS535 3.3 53.3 1.0
OD2 A:ASP460 3.3 51.0 1.0
CG A:HIS535 3.3 49.5 1.0
CB A:HIS535 3.6 45.9 1.0
CB A:ASP460 3.8 42.1 1.0
CA A:ASP460 4.1 39.9 1.0
NE2 A:HIS535 4.4 54.8 1.0
O A:PHE459 4.4 38.1 1.0
CD2 A:HIS535 4.4 50.7 1.0
CA A:HIS535 4.5 45.2 1.0

Mercury binding site 4 out of 10 in 6b7q

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Mercury binding site 4 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


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 Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1004

b:76.0
occ:0.66
NE2 A:HIS535 2.4 54.8 1.0
CE1 A:HIS535 3.1 53.3 1.0
OG A:SER461 3.2 39.3 1.0
CD2 A:HIS535 3.4 50.7 1.0
O A:GLY533 3.5 43.8 1.0
OD1 A:ASP462 3.7 47.9 1.0
OD2 A:ASP462 3.8 47.5 1.0
C A:GLY533 3.9 41.4 1.0
CG A:ASP462 4.0 46.2 1.0
ND1 A:HIS535 4.3 52.4 1.0
CA A:GLY533 4.3 41.0 1.0
CG A:HIS535 4.5 49.5 1.0
CB A:SER461 4.6 38.3 1.0
N A:LYS534 4.7 42.1 1.0
O A:LYS534 4.9 40.7 1.0

Mercury binding site 5 out of 10 in 6b7q

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Mercury binding site 5 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1005

b:60.5
occ:0.90
SG A:CYS643 2.0 41.3 0.9
O A:HOH1267 2.5 18.6 1.0
O A:HOH1235 2.8 47.3 1.0
CB A:CYS643 3.1 40.0 1.0
N A:CYS643 3.4 42.1 1.0
CD2 A:LEU639 3.5 42.8 1.0
CA A:CYS643 3.6 41.1 1.0
CA A:LEU639 3.9 43.1 1.0
O A:LEU639 4.0 45.5 1.0
C A:LYS642 4.0 44.9 1.0
CB A:ASP601 4.1 46.4 1.0
CB A:LYS642 4.1 50.8 1.0
O A:ASP638 4.3 40.5 1.0
C A:LEU639 4.4 41.2 1.0
O A:ASP601 4.4 42.4 1.0
O A:LYS642 4.5 49.5 1.0
CA A:LYS642 4.6 46.8 1.0
CB A:LEU639 4.7 43.4 1.0
C A:ASP601 4.7 40.9 1.0
CG A:LEU639 4.7 43.9 1.0
CB A:ALA605 4.7 35.5 1.0
N A:LEU639 4.8 41.8 1.0
CG A:ASP601 4.9 49.4 1.0
C A:ASP638 4.9 42.9 1.0
CA A:ASP601 5.0 44.5 1.0

Mercury binding site 6 out of 10 in 6b7q

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Mercury binding site 6 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1006

b:52.6
occ:0.65
O A:LEU625 2.5 51.7 1.0
SG A:CYS618 2.7 48.3 0.8
CB A:CYS618 3.2 42.7 1.0
C A:LEU625 3.7 51.5 1.0
CA A:CYS618 3.7 43.8 1.0
CA A:ILE626 3.9 57.0 1.0
O A:ILE626 4.2 72.0 1.0
N A:ILE626 4.3 51.3 1.0
N A:CYS618 4.4 43.2 1.0
C A:ILE626 4.6 59.9 1.0
CG1 A:ILE626 4.7 60.4 1.0
CB A:ILE626 4.8 59.0 1.0
CB A:LEU625 4.8 50.4 1.0
CA A:LEU625 4.8 51.8 1.0
C A:CYS618 4.9 44.4 1.0
HG A:HG1007 5.0 71.1 0.5

Mercury binding site 7 out of 10 in 6b7q

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Mercury binding site 7 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1007

b:71.1
occ:0.52
NE2 A:HIS620 2.3 53.9 1.0
CE1 A:HIS620 2.8 52.9 1.0
O A:ASP617 2.9 40.8 1.0
CD2 A:HIS620 3.5 51.8 1.0
C A:ASP617 4.0 43.7 1.0
ND1 A:HIS620 4.0 53.5 1.0
CA A:CYS618 4.3 43.8 1.0
CG A:HIS620 4.4 46.9 1.0
N A:CYS618 4.6 43.2 1.0
C A:CYS618 4.7 44.4 1.0
O A:CYS618 4.8 43.9 1.0
HG A:HG1006 5.0 52.6 0.7
CB A:ASP617 5.0 46.0 1.0

Mercury binding site 8 out of 10 in 6b7q

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Mercury binding site 8 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1008

b:43.3
occ:0.78
NE2 A:HIS666 2.7 37.4 1.0
OD1 A:ASP617 2.7 43.9 1.0
CD2 A:HIS666 3.1 38.0 1.0
CG A:ASP617 3.6 46.8 1.0
CA A:ASP617 3.6 45.1 1.0
CB A:ASP617 3.7 46.0 1.0
CE1 A:HIS666 3.9 40.6 1.0
O A:ASP617 4.3 40.8 1.0
CG A:HIS666 4.4 40.2 1.0
C A:ASP617 4.5 43.7 1.0
N A:ASP617 4.6 45.4 1.0
OD2 A:ASP617 4.8 42.7 1.0
ND1 A:HIS666 4.8 41.6 1.0
O A:PRO616 4.8 46.5 1.0
O A:ILE619 4.9 41.2 1.0

Mercury binding site 9 out of 10 in 6b7q

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Mercury binding site 9 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1009

b:64.9
occ:0.43
ND1 A:HIS706 2.4 53.8 1.0
CE1 A:HIS706 3.3 56.1 1.0
CG A:HIS706 3.3 50.6 1.0
CB A:HIS706 3.6 48.9 1.0
CA A:HIS706 3.7 48.7 1.0
O A:HIS706 4.0 51.7 1.0
C A:HIS706 4.3 47.8 1.0
NE2 A:HIS706 4.5 56.2 1.0
CD1 A:ILE709 4.5 46.0 1.0
CD2 A:HIS706 4.5 52.0 1.0
CG2 A:ILE709 4.5 49.9 1.0
CB A:ILE709 4.6 46.3 1.0
N A:HIS706 5.0 47.2 1.0

Mercury binding site 10 out of 10 in 6b7q

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Mercury binding site 10 out of 10 in the Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of Legionella Effector Protein Sdea (LPG2157) Aa. 211-910 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1010

b:55.8
occ:0.26
O A:ALA679 2.7 56.1 1.0
O A:PRO677 2.9 65.3 1.0
NE2 A:HIS673 3.0 87.7 1.0
CD A:PRO681 3.6 61.9 1.0
CE1 A:HIS673 3.7 88.7 1.0
CD2 A:HIS673 3.7 82.5 1.0
C A:ALA679 3.9 58.7 1.0
CG A:PRO681 4.0 58.6 1.0
C A:PRO677 4.1 62.2 1.0
C A:GLU678 4.5 64.9 1.0
N A:ALA679 4.5 62.4 1.0
N A:PRO681 4.6 61.2 1.0
ND1 A:HIS673 4.6 81.8 1.0
CG A:HIS673 4.6 75.4 1.0
CA A:GLU678 4.7 68.3 1.0
O A:GLU678 4.8 68.0 1.0
CA A:ALA679 4.8 60.8 1.0
N A:VAL680 4.8 58.0 1.0
N A:GLU678 4.9 64.2 1.0
CA A:VAL680 4.9 61.2 1.0
C A:VAL680 4.9 63.3 1.0
O A:ASN676 5.0 53.2 1.0
CA A:PRO677 5.0 63.4 1.0

Reference:

A.Akturk, D.J.Wasilko, X.Wu, Y.Liu, Y.Zhang, J.Qiu, Z.Q.Luo, K.H.Reiter, P.S.Brzovic, R.E.Klevit, Y.Mao. Mechanism of Phosphoribosyl-Ubiquitination Mediated By A Single Legionella Effector. Nature V. 557 729 2018.
ISSN: ESSN 1476-4687
PubMed: 29795346
DOI: 10.1038/S41586-018-0147-6
Page generated: Sun Dec 13 19:13:28 2020

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