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Mercury in PDB 3ebq: Crystal Structure of Human PPPDE1

Protein crystallography data

The structure of Crystal Structure of Human PPPDE1, PDB code: 3ebq was solved by J.R.Walker, M.Akutsu, L.Qiu, Y.Li, Y.Slessarev, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Botchkarev, S.Dhe-Paganon, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.04 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 41.625, 41.625, 184.239, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 27.3

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Human PPPDE1 (pdb code 3ebq). 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 Human PPPDE1, PDB code: 3ebq:
Jump to Mercury binding site number: 1; 2; 3;

Mercury binding site 1 out of 3 in 3ebq

Go back to Mercury Binding Sites List in 3ebq
Mercury binding site 1 out of 3 in the Crystal Structure of Human PPPDE1


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 Human PPPDE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg201

b:79.3
occ:1.00
SG A:CYS58 2.5 52.3 1.0
O A:GLY62 3.1 63.4 1.0
CB A:CYS58 3.1 49.7 1.0
CA A:THR63 4.0 59.3 1.0
C A:GLY62 4.0 61.1 1.0
CA A:CYS58 4.2 49.1 1.0
N A:THR63 4.3 59.2 1.0
C A:THR63 4.8 61.4 1.0
CB A:THR63 4.9 56.7 1.0
CD A:PRO59 4.9 52.2 1.0

Mercury binding site 2 out of 3 in 3ebq

Go back to Mercury Binding Sites List in 3ebq
Mercury binding site 2 out of 3 in the Crystal Structure of Human PPPDE1


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 Human PPPDE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg202

b:57.9
occ:0.50
HG A:HG202 0.0 57.9 0.5
SG A:CYS108 2.4 38.9 0.5
CB A:CYS108 3.5 34.6 0.5
CB A:CYS108 3.5 33.0 0.5
N A:CYS108 3.7 31.9 0.5
N A:CYS108 3.7 32.6 0.5
ND2 A:ASN109 3.9 31.8 1.0
HG A:HG202 3.9 36.1 0.5
ND1 A:HIS38 4.0 40.2 1.0
CB A:ASN107 4.0 33.1 1.0
CA A:CYS108 4.1 31.6 0.5
CG A:ASN107 4.1 32.7 1.0
CA A:CYS108 4.1 33.0 0.5
OH A:TYR101 4.1 41.5 1.0
N A:ASN109 4.2 29.6 1.0
CA A:HIS38 4.2 37.6 1.0
O A:TRP37 4.2 42.0 1.0
CB A:HIS38 4.2 37.9 1.0
CG A:ASN109 4.3 31.2 1.0
OD1 A:ASN107 4.3 28.9 1.0
ND2 A:ASN107 4.4 33.5 1.0
OD1 A:ASN109 4.5 30.5 1.0
SG A:CYS108 4.5 32.2 0.5
C A:CYS108 4.6 30.6 0.5
CG A:HIS38 4.6 38.3 1.0
C A:CYS108 4.6 31.3 0.5
C A:ASN107 4.7 32.4 1.0
CA A:ASN107 4.9 33.5 1.0
N A:HIS38 5.0 39.2 1.0

Mercury binding site 3 out of 3 in 3ebq

Go back to Mercury Binding Sites List in 3ebq
Mercury binding site 3 out of 3 in the Crystal Structure of Human PPPDE1


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 Human PPPDE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg202

b:36.1
occ:0.50
HG A:HG202 0.0 36.1 0.5
SG A:CYS108 2.3 32.2 0.5
CB A:CYS108 3.1 33.0 0.5
CB A:CYS108 3.2 34.6 0.5
ND1 A:HIS38 3.4 40.2 1.0
CE1 A:HIS38 3.7 39.5 1.0
SG A:CYS108 3.7 38.9 0.5
HG A:HG202 3.9 57.9 0.5
O A:PHE50 3.9 40.7 1.0
CE1 A:TYR101 3.9 40.0 1.0
OH A:TYR101 4.0 41.5 1.0
CA A:CYS108 4.3 33.0 0.5
CA A:CYS108 4.3 31.6 0.5
N A:CYS108 4.3 32.6 0.5
N A:CYS108 4.3 31.9 0.5
CZ A:TYR101 4.3 41.8 1.0
C A:PHE50 4.6 38.7 1.0
CG A:HIS38 4.7 38.3 1.0
CA A:GLY51 4.7 41.5 1.0
NE2 A:HIS38 4.9 34.8 1.0
CD1 A:TYR101 5.0 39.2 1.0

Reference:

J.R.Walker, M.Akutsu, L.Qiu, Y.Li, Y.Slessarev, J.Weigelt, C.Bountra, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon. Structure of Human PPPDE1 To Be Published.
Page generated: Wed Oct 28 18:42:27 2020

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