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Mercury in PDB 5yc8: Crystal Structure of Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative)

Protein crystallography data

The structure of Crystal Structure of Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative), PDB code: 5yc8 was solved by R.Suno, S.Maeda, S.Yasuda, K.Yamashita, K.Hirata, S.Horita, M.S.Tawaramoto, H.Tsujimoto, T.Murata, M.Kinoshita, M.Yamamoto, B.K.Kobilka, S.Iwata, T.Kobayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.03 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.520, 59.000, 89.220, 90.00, 98.89, 90.00
R / Rfree (%) 23.7 / 27

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative) (pdb code 5yc8). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 3 binding sites of Mercury where determined in the Crystal Structure of Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative), PDB code: 5yc8:
Jump to Mercury binding site number: 1; 2; 3;

Mercury binding site 1 out of 3 in 5yc8

Go back to Mercury Binding Sites List in 5yc8
Mercury binding site 1 out of 3 in the Crystal Structure of Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative)


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 Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg502

b:71.5
occ:0.49
SG A:CYS67 2.6 43.9 1.0
O A:CYS67 3.4 38.7 1.0
O A:HOH622 3.5 39.5 1.0
CB A:CYS67 3.8 44.6 1.0
CA A:CYS67 3.9 41.9 1.0
CG1 A:ILE71 4.0 38.0 1.0
C A:CYS67 4.0 40.8 1.0
CD1 A:ILE71 4.1 40.5 1.0
HG A:HG503 4.2 89.5 0.3
CE A:MET45 4.3 35.9 1.0
CD2 A:LEU70 4.5 37.3 1.0
CB A:LEU70 4.7 36.3 1.0
SD A:MET45 4.9 34.0 0.7
CG A:LEU70 5.0 35.5 1.0

Mercury binding site 2 out of 3 in 5yc8

Go back to Mercury Binding Sites List in 5yc8
Mercury binding site 2 out of 3 in the Crystal Structure of Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative)


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 Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg503

b:89.5
occ:0.28
SG A:CYS67 2.7 43.9 1.0
CH2 A:TRP148 2.7 40.3 1.0
CZ2 A:TRP148 2.8 41.8 1.0
CZ3 A:TRP148 3.4 38.8 1.0
CD1 A:ILE71 3.5 40.5 1.0
CE2 A:TRP148 3.5 42.1 1.0
CB A:CYS67 3.9 44.6 1.0
CE3 A:TRP148 4.0 39.0 1.0
CD2 A:TRP148 4.1 40.7 1.0
C A:CYS67 4.1 40.8 1.0
O A:CYS67 4.2 38.7 1.0
HG A:HG502 4.2 71.5 0.5
N A:ALA68 4.3 33.8 1.0
NE1 A:TRP148 4.4 43.4 1.0
CA A:ALA68 4.5 33.1 1.0
CG1 A:ILE71 4.6 38.0 1.0
CA A:CYS67 4.7 41.9 1.0
O A:HOH622 5.0 39.5 1.0

Mercury binding site 3 out of 3 in 5yc8

Go back to Mercury Binding Sites List in 5yc8
Mercury binding site 3 out of 3 in the Crystal Structure of Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative)


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 Rationally Thermostabilized M2 Muscarinic Acetylcholine Receptor Bound with Nms (Hg-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg504

b:57.7
occ:0.69
SG A:CYS439 2.6 58.0 1.0
O A:ILE435 3.0 38.7 1.0
N A:CYS439 3.5 61.5 1.0
CA A:CYS439 3.6 61.9 1.0
CB A:CYS439 3.7 60.5 1.0
C A:ALA438 3.8 38.5 1.0
C A:ILE435 4.1 37.4 1.0
O A:ALA438 4.1 39.8 1.0
CB A:ALA438 4.1 38.4 1.0
CB A:ILE435 4.2 36.0 1.0
CG1 A:ILE435 4.4 34.0 1.0
CA A:ALA438 4.5 38.9 1.0
CA A:ILE435 4.7 36.9 1.0
CD1 A:ILE435 4.7 33.5 1.0
CB A:ALA395 4.8 26.1 1.0
N A:ALA438 5.0 37.8 1.0

Reference:

R.Suno, S.Lee, S.Maeda, S.Yasuda, K.Yamashita, K.Hirata, S.Horita, M.S.Tawaramoto, H.Tsujimoto, T.Murata, M.Kinoshita, M.Yamamoto, B.K.Kobilka, N.Vaidehi, S.Iwata, T.Kobayashi. Structural Insights Into the Subtype-Selective Antagonist Binding to the M2MUSCARINIC Receptor Nat. Chem. Biol. V. 14 1150 2018.
ISSN: ESSN 1552-4469
PubMed: 30420692
DOI: 10.1038/S41589-018-0152-Y
Page generated: Sun Dec 13 19:13:24 2020

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