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Mercury in PDB 2ypd: Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein

Protein crystallography data

The structure of Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein, PDB code: 2ypd was solved by M.Vollmar, C.Johansson, T.Krojer, G.Berridge, N.Burgess-Brown, C.Strain-Damerell, S.Froese, E.Williams, S.Goubin, D.Coutandin, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.82 / 2.10
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.718, 112.206, 165.173, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24

Other elements in 2ypd:

The structure of Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein (pdb code 2ypd). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 11 binding sites of Mercury where determined in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein, PDB code: 2ypd:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 11 in 2ypd

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Mercury binding site 1 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg3498

b:37.8
occ:0.63
HG A:EMT3498 0.0 37.8 0.6
C1 A:EMT3498 2.4 36.7 1.0
SG A:CYS2163 2.7 29.1 0.7
O A:CYS2163 3.1 27.5 1.0
C2 A:EMT3498 3.2 35.6 1.0
SG A:CYS2448 3.3 22.6 0.5
CB A:CYS2163 3.3 29.5 1.0
O A:THR2447 3.3 22.9 1.0
C A:CYS2163 3.5 30.2 1.0
CA A:CYS2448 3.6 22.6 1.0
CA A:CYS2163 3.9 30.9 1.0
C A:THR2447 3.9 23.2 1.0
N A:CYS2448 3.9 22.5 1.0
CB A:CYS2448 4.0 22.3 1.0
OE2 A:GLU2164 4.0 42.7 1.0
CB A:GLU2164 4.1 37.3 1.0
CG A:GLU2164 4.1 40.3 1.0
N A:GLU2164 4.2 32.4 1.0
CD A:GLU2164 4.2 43.2 1.0
HG A:EMT3499 4.5 42.4 0.6
O A:HOH2009 4.5 27.4 1.0
CB A:HIS2166 4.7 35.4 1.0
CA A:GLU2164 4.8 35.5 1.0
C A:CYS2448 4.8 23.4 1.0
N A:THR2449 4.9 22.8 1.0

Mercury binding site 2 out of 11 in 2ypd

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Mercury binding site 2 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg3499

b:42.4
occ:0.59
HG A:EMT3499 0.0 42.4 0.6
SG A:CYS2448 2.2 22.6 0.5
C1 A:EMT3499 2.4 43.4 1.0
CB A:CYS2448 3.2 22.3 1.0
C2 A:EMT3499 3.3 40.7 1.0
N A:CYS2448 3.5 22.5 1.0
ND1 A:HIS2166 3.5 43.0 1.0
O A:ILE2393 3.6 21.1 1.0
CE1 A:HIS2166 3.8 44.3 1.0
C2 A:EMT3498 3.8 35.6 1.0
C1 A:EMT3498 3.8 36.7 1.0
CA A:CYS2448 3.8 22.6 1.0
CG A:HIS2166 4.1 41.5 1.0
C A:THR2447 4.3 23.2 1.0
NE2 A:HIS2166 4.4 47.0 1.0
HG A:EMT3498 4.5 37.8 0.6
C A:ILE2393 4.5 21.0 1.0
O A:ARG2446 4.6 23.7 1.0
O A:HOH2096 4.6 28.0 1.0
CD2 A:HIS2166 4.7 43.9 1.0
CB A:HIS2166 4.7 35.4 1.0
CA A:TYR2394 4.8 23.2 1.0
N A:ALA2395 4.9 25.9 1.0
N A:TYR2394 5.0 21.9 1.0

Mercury binding site 3 out of 11 in 2ypd

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Mercury binding site 3 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg3500

b:48.5
occ:0.54
HG A:EMT3500 0.0 48.5 0.5
C1 A:EMT3500 2.4 52.2 1.0
SG A:CYS2185 2.8 45.5 0.7
C2 A:EMT3500 3.3 48.3 1.0
CA A:CYS2185 3.4 41.3 1.0
CB A:CYS2185 3.4 45.1 1.0
NE2 A:GLN2190 3.7 47.3 1.0
OE1 A:GLN2188 3.8 71.2 1.0
N A:CYS2185 3.9 40.6 1.0
CZ2 A:TRP2161 4.0 31.4 1.0
NE1 A:TRP2161 4.2 28.7 1.0
C A:GLU2184 4.2 38.9 1.0
O A:GLU2184 4.3 38.9 1.0
CE2 A:TRP2161 4.4 29.6 1.0
CD A:GLN2190 4.6 47.5 1.0
OE1 A:GLN2190 4.7 52.1 1.0
CD A:GLN2188 4.8 65.8 1.0
C A:CYS2185 4.8 38.8 1.0
CB A:GLU2184 5.0 40.6 1.0

Mercury binding site 4 out of 11 in 2ypd

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Mercury binding site 4 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg3501

b:60.0
occ:0.27
HG A:EMT3501 0.0 60.0 0.3
C1 A:EMT3501 2.4 48.6 1.0
SG A:CYS2225 2.4 20.1 0.9
CB A:CYS2225 3.1 21.1 1.0
O A:THR2332 3.2 18.3 1.0
C2 A:EMT3501 3.2 49.9 1.0
CD A:LYS2260 3.3 29.7 1.0
CA A:CYS2225 3.3 22.1 1.0
CB A:LYS2260 3.8 25.2 1.0
C A:THR2332 3.9 18.4 1.0
O A:GLY2331 4.0 18.1 1.0
N A:CYS2225 4.1 22.6 1.0
CA A:THR2332 4.1 18.6 1.0
CG A:LYS2260 4.2 27.2 1.0
NZ A:LYS2260 4.2 36.9 1.0
CE A:LYS2260 4.3 33.9 1.0
C A:CYS2225 4.5 23.7 1.0
O A:CYS2225 4.5 24.1 1.0
CB A:LEU2223 4.7 25.6 1.0
C A:ASN2224 4.8 22.9 1.0
C A:GLY2331 4.9 18.3 1.0
N A:THR2333 5.0 18.6 1.0
O A:LEU2223 5.0 21.6 1.0

Mercury binding site 5 out of 11 in 2ypd

Go back to Mercury Binding Sites List in 2ypd
Mercury binding site 5 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 the Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg3502

b:62.6
occ:0.41
HG A:EMT3502 0.0 62.6 0.4
C1 A:EMT3502 2.4 50.9 1.0
SG A:CYS2317 2.5 18.9 0.3
O A:HOH2071 2.9 27.8 1.0
OD1 A:ASP2263 3.0 45.5 1.0
CB A:CYS2317 3.2 19.8 0.5
C2 A:EMT3502 3.3 53.8 1.0
CB A:CYS2317 3.3 19.1 0.5
HG A:EMT3503 4.1 58.7 0.4
SG A:CYS2317 4.1 20.1 0.4
CG A:ASP2263 4.2 47.0 1.0
CA A:CYS2317 4.4 19.9 0.5
CA A:CYS2317 4.4 19.5 0.5
C2 A:EMT3503 4.4 67.3 1.0
CB A:ARG2315 4.5 31.6 1.0
N A:CYS2317 4.5 20.4 0.5
N A:CYS2317 4.6 20.2 0.5
NE A:ARG2315 4.7 40.1 1.0
OG1 A:THR2478 4.7 25.9 1.0
N A:ASP2263 4.7 36.5 1.0
O A:LEU2316 4.7 23.7 1.0
C A:LEU2316 4.7 21.7 1.0
CG A:LYS2262 4.7 37.6 1.0
OD2 A:ASP2263 4.8 53.1 1.0
CD A:ARG2315 4.9 37.8 1.0
O A:ARG2315 5.0 29.8 1.0

Mercury binding site 6 out of 11 in 2ypd

Go back to Mercury Binding Sites List in 2ypd
Mercury binding site 6 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 the Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg3503

b:58.7
occ:0.43
HG A:EMT3503 0.0 58.7 0.4
C1 A:EMT3503 2.4 65.7 1.0
SG A:CYS2317 2.6 20.1 0.4
OE1 A:GLN2476 3.2 29.7 0.5
C1 A:EMT3502 3.3 50.9 1.0
C2 A:EMT3503 3.3 67.3 1.0
CB A:CYS2317 3.3 19.1 0.5
CB A:CYS2317 3.3 19.8 0.5
OG1 A:THR2333 3.4 21.1 1.0
O A:HOH2080 3.6 24.3 1.0
SG A:CYS2317 3.7 18.9 0.3
O A:HOH2072 3.9 13.5 1.0
C2 A:EMT3502 4.0 53.8 1.0
CD A:GLN2476 4.1 28.1 0.5
HG A:EMT3502 4.1 62.6 0.4
CE A:LYS2260 4.2 33.9 1.0
CG A:GLN2476 4.4 22.8 0.5
CB A:GLN2476 4.4 21.8 0.5
CB A:GLN2476 4.5 23.8 0.5
O A:HOH2071 4.6 27.8 1.0
NZ A:LYS2260 4.6 36.9 1.0
CA A:CYS2317 4.7 19.9 0.5
CA A:CYS2317 4.7 19.5 0.5
CB A:THR2333 4.8 19.8 1.0
NE2 A:GLN2476 4.8 28.1 0.5
CG A:GLN2476 4.9 25.9 0.5
C A:CYS2317 4.9 19.6 0.5
O A:CYS2317 4.9 20.1 0.5
O A:CYS2317 4.9 19.9 0.5
C A:CYS2317 4.9 19.4 0.5

Mercury binding site 7 out of 11 in 2ypd

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Mercury binding site 7 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 the Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg3498

b:54.0
occ:0.62
HG B:EMT3498 0.0 54.0 0.6
SG B:CYS2448 2.3 38.7 0.6
C1 B:EMT3498 2.4 55.4 1.0
CB B:CYS2448 3.2 35.6 1.0
C2 B:EMT3498 3.2 54.9 1.0
C1 B:EMT3499 3.4 48.3 1.0
ND1 B:HIS2166 3.5 48.6 1.0
N B:CYS2448 3.6 36.6 1.0
O B:ILE2393 3.6 35.3 1.0
CE1 B:HIS2166 3.8 48.4 1.0
O B:HOH2004 3.8 42.7 1.0
CA B:CYS2448 3.9 35.2 1.0
CG B:HIS2166 4.1 46.8 1.0
C2 B:EMT3499 4.2 47.7 1.0
HG B:EMT3499 4.4 49.6 0.7
C B:THR2447 4.4 40.5 1.0
C B:ILE2393 4.4 33.2 1.0
NE2 B:HIS2166 4.4 51.7 1.0
O B:ARG2446 4.6 42.0 1.0
CD2 B:HIS2166 4.7 49.9 1.0
CA B:TYR2394 4.7 36.4 1.0
CB B:HIS2166 4.8 44.0 1.0
N B:ALA2395 4.8 42.0 1.0
O B:HOH2094 4.9 38.9 1.0
N B:TYR2394 4.9 36.0 1.0

Mercury binding site 8 out of 11 in 2ypd

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Mercury binding site 8 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 the Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg3499

b:49.6
occ:0.65
HG B:EMT3499 0.0 49.6 0.7
C1 B:EMT3499 2.4 48.3 1.0
SG B:CYS2163 2.6 33.0 0.6
O B:CYS2163 3.1 35.5 1.0
SG B:CYS2448 3.1 38.7 0.6
C2 B:EMT3499 3.2 47.7 1.0
CB B:CYS2163 3.3 34.5 1.0
O B:THR2447 3.4 40.8 1.0
C B:CYS2163 3.5 37.5 1.0
CA B:CYS2448 3.6 35.2 1.0
CB B:CYS2448 3.9 35.6 1.0
CA B:CYS2163 3.9 35.5 1.0
N B:CYS2448 3.9 36.6 1.0
C B:THR2447 3.9 40.5 1.0
OE2 B:GLU2164 4.1 49.3 1.0
CB B:GLU2164 4.1 43.6 1.0
CG B:GLU2164 4.2 46.7 1.0
N B:GLU2164 4.3 39.6 1.0
CD B:GLU2164 4.3 50.6 1.0
HG B:EMT3498 4.4 54.0 0.6
CB B:HIS2166 4.6 44.0 1.0
CA B:GLU2164 4.8 42.6 1.0
C B:CYS2448 4.8 34.2 1.0
N B:THR2449 4.9 33.5 1.0

Mercury binding site 9 out of 11 in 2ypd

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Mercury binding site 9 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 the Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg3500

b:57.3
occ:0.52
HG B:EMT3500 0.0 57.3 0.5
C1 B:EMT3500 2.4 57.8 1.0
SG B:CYS2185 2.9 48.8 0.5
C2 B:EMT3500 3.2 55.4 1.0
CB B:CYS2185 3.5 47.1 1.0
CA B:CYS2185 3.5 45.7 1.0
NE2 B:GLN2190 3.6 67.4 1.0
OE1 B:GLN2188 3.8 65.8 1.0
CZ2 B:TRP2161 4.0 40.0 1.0
N B:CYS2185 4.0 47.3 1.0
NE1 B:TRP2161 4.1 36.6 1.0
CE2 B:TRP2161 4.3 37.6 1.0
C B:GLU2184 4.4 47.7 1.0
O B:GLU2184 4.4 51.3 1.0
CD B:GLN2190 4.5 62.9 1.0
OE1 B:GLN2190 4.6 70.5 1.0
CD B:GLN2188 4.8 64.0 1.0
C B:CYS2185 4.8 43.1 1.0

Mercury binding site 10 out of 11 in 2ypd

Go back to Mercury Binding Sites List in 2ypd
Mercury binding site 10 out of 11 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


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 the Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg3501

b:79.0
occ:0.44
HG B:EMT3501 0.0 79.0 0.4
C1 B:EMT3501 2.3 67.0 1.0
OD1 B:ASP2263 3.0 53.1 1.0
CB B:CYS2317 3.1 21.6 0.5
CB B:CYS2317 3.1 21.7 0.5
SG B:CYS2317 3.2 22.2 0.3
C2 B:EMT3501 3.2 62.3 1.0
HG B:EMT3502 3.7 66.3 0.4
C1 B:EMT3502 3.8 72.4 1.0
SG B:CYS2317 3.9 21.9 0.2
CG B:ASP2263 4.2 51.0 1.0
CA B:CYS2317 4.3 22.0 0.5
CA B:CYS2317 4.3 22.0 0.5
CG B:LYS2262 4.4 45.5 1.0
C2 B:EMT3502 4.4 72.9 1.0
N B:ASP2263 4.6 41.0 1.0
N B:CYS2317 4.6 22.5 1.0
CD B:LYS2262 4.7 51.2 1.0
OD2 B:ASP2263 4.8 54.6 1.0
O B:LEU2316 4.9 23.7 1.0
CB B:ARG2315 4.9 33.1 1.0
C B:LEU2316 4.9 24.2 1.0
NE B:ARG2315 5.0 39.6 1.0

Reference:

M.Vollmar, C.Johansson, T.Krojer, C.Strain-Damerell, S.Froese, E.Williams, D.Coutandin, F.Von Delft, J.Weigelt, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann. Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein To Be Published.
Page generated: Sun Dec 13 19:08:41 2020

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