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Mercury in PDB 1fmj: Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap

Protein crystallography data

The structure of Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap, PDB code: 1fmj was solved by S.Pakhomova, M.Kobayashi, J.Buck, M.E.Newcomer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.429, 66.183, 83.336, 90.00, 108.89, 90.00
R / Rfree (%) 23.1 / 26.4

Other elements in 1fmj:

The structure of Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap (pdb code 1fmj). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 8 binding sites of Mercury where determined in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap, PDB code: 1fmj:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Mercury binding site 1 out of 8 in 1fmj

Go back to Mercury Binding Sites List in 1fmj
Mercury binding site 1 out of 8 in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap


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 Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg451

b:39.8
occ:0.60
HG A:HG451 0.0 39.8 0.6
SG A:CYS258 2.4 30.2 1.0
HG A:HG451 2.6 57.6 0.4
O A:ASP254 2.8 32.1 1.0
N A:CYS258 3.1 29.5 1.0
CB A:CYS258 3.4 28.5 1.0
CA A:CYS258 3.4 28.6 1.0
O A:ASP250 3.6 25.6 1.0
C A:GLY257 3.7 30.1 1.0
C A:ASP254 3.8 31.6 1.0
CB A:ASP250 4.0 26.8 1.0
CB A:ASP254 4.0 31.4 1.0
CA A:GLY257 4.2 30.2 1.0
C A:ASP250 4.2 26.0 1.0
O A:GLY257 4.4 30.0 1.0
CA A:ASP254 4.4 31.7 1.0
CA A:ASP250 4.6 25.6 1.0
N A:GLY257 4.7 31.5 1.0
N A:ASP254 4.7 32.0 1.0
CG A:ASP254 4.8 30.4 1.0
N A:LEU255 4.8 31.6 1.0
CG A:ASP250 4.9 28.9 1.0
C A:CYS258 4.9 28.0 1.0

Mercury binding site 2 out of 8 in 1fmj

Go back to Mercury Binding Sites List in 1fmj
Mercury binding site 2 out of 8 in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap


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 Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg451

b:57.6
occ:0.40
HG A:HG451 0.0 57.6 0.4
SG A:CYS258 2.5 30.2 1.0
HG A:HG451 2.6 39.8 0.6
CD A:ARG261 3.5 33.5 1.0
NH1 A:ARG261 3.6 35.8 1.0
CB A:CYS258 3.6 28.5 1.0
CA A:CYS258 3.7 28.6 1.0
O A:HOH482 3.7 28.7 1.0
CB A:ASP250 3.8 26.8 1.0
CD2 A:LEU246 4.2 22.0 1.0
N A:CYS258 4.2 29.5 1.0
NE A:ARG261 4.4 35.0 1.0
CZ A:ARG261 4.4 35.8 1.0
CG A:ARG261 4.4 32.0 1.0
CG A:ASP250 4.5 28.9 1.0
OD2 A:ASP250 4.5 29.3 1.0
C A:GLY257 4.8 30.1 1.0
O A:GLY257 4.9 30.0 1.0
CB A:ARG261 4.9 30.1 1.0
C A:CYS258 5.0 28.0 1.0

Mercury binding site 3 out of 8 in 1fmj

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Mercury binding site 3 out of 8 in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap


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 Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg452

b:83.2
occ:1.00
SG A:CYS279 2.5 36.4 1.0
CB A:CYS279 2.9 33.6 1.0
C A:CYS279 3.4 32.6 1.0
N A:GLU280 3.5 32.9 1.0
O A:CYS279 3.7 32.9 1.0
CA A:CYS279 3.8 32.8 1.0
CA A:GLU280 4.0 32.2 1.0
O A:HOH548 4.0 27.5 1.0
O A:GLN276 4.4 33.4 1.0
CB A:GLU280 4.6 34.6 1.0
N A:CYS279 4.9 32.1 1.0

Mercury binding site 4 out of 8 in 1fmj

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Mercury binding site 4 out of 8 in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap


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 Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg453

b:0.1
occ:0.50
SG A:CYS318 2.7 32.0 1.0
OD2 A:ASP321 3.3 33.2 1.0
CB A:CYS318 3.5 24.4 1.0
CA A:CYS318 3.7 24.2 1.0
N A:CYS318 4.4 23.9 1.0
CG A:ASP321 4.5 32.8 1.0
C A:CYS318 4.9 22.9 1.0
CB A:LYS315 4.9 22.4 1.0
C A:GLY317 5.0 24.6 1.0
O A:CYS318 5.0 22.0 1.0

Mercury binding site 5 out of 8 in 1fmj

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Mercury binding site 5 out of 8 in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap


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 Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg551

b:36.9
occ:0.60
HG B:HG551 0.0 36.9 0.6
HG B:HG551 1.9 58.4 0.4
SG B:CYS258 2.4 22.1 1.0
O B:ASP254 2.9 24.0 1.0
N B:CYS258 3.0 22.4 1.0
CB B:CYS258 3.5 21.2 1.0
CA B:CYS258 3.5 20.8 1.0
C B:GLY257 3.8 23.9 1.0
O B:ASP250 3.8 26.4 1.0
C B:ASP254 3.8 25.7 1.0
CB B:ASP254 3.9 27.1 1.0
CB B:ASP250 4.0 24.9 1.0
CA B:GLY257 4.1 24.3 1.0
C B:ASP250 4.3 25.0 1.0
CA B:ASP254 4.3 26.7 1.0
CG B:ASP254 4.5 30.0 1.0
O B:GLY257 4.6 23.1 1.0
N B:ASP254 4.6 27.0 1.0
CA B:ASP250 4.6 24.8 1.0
N B:GLY257 4.7 24.9 1.0
CG B:ASP250 4.8 24.8 1.0
N B:LEU255 4.9 26.6 1.0
OD2 B:ASP254 4.9 29.6 1.0
N B:TYR251 5.0 24.5 1.0

Mercury binding site 6 out of 8 in 1fmj

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Mercury binding site 6 out of 8 in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap


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 Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg551

b:58.4
occ:0.40
HG B:HG551 0.0 58.4 0.4
HG B:HG551 1.9 36.9 0.6
SG B:CYS258 2.4 22.1 1.0
CB B:CYS258 3.6 21.2 1.0
CA B:CYS258 3.6 20.8 1.0
CB B:ASP250 3.7 24.9 1.0
O B:HOH589 3.7 17.5 1.0
N B:CYS258 3.8 22.4 1.0
NH1 B:ARG261 4.3 27.4 1.0
CD B:ARG261 4.3 24.3 1.0
CG B:ASP250 4.3 24.8 1.0
OD2 B:ASP250 4.5 24.9 1.0
C B:GLY257 4.5 23.9 1.0
CD2 B:LEU246 4.7 16.6 1.0
O B:ASP254 4.7 24.0 1.0
C B:ASP250 4.8 25.0 1.0
CA B:ASP250 4.8 24.8 1.0
O B:ASP250 4.9 26.4 1.0
O B:GLY257 5.0 23.1 1.0

Mercury binding site 7 out of 8 in 1fmj

Go back to Mercury Binding Sites List in 1fmj
Mercury binding site 7 out of 8 in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap


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 Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg552

b:87.4
occ:1.00
SG B:CYS279 2.5 34.1 1.0
CB B:CYS279 3.1 29.5 1.0
C B:CYS279 3.7 29.0 1.0
N B:GLU280 3.8 28.7 1.0
CA B:CYS279 4.0 29.1 1.0
O B:CYS279 4.1 29.1 1.0
NE2 B:GLN276 4.2 39.3 1.0
CA B:GLU280 4.3 28.3 1.0
O B:GLN276 4.7 29.9 1.0
CB B:GLU280 4.9 31.0 1.0

Mercury binding site 8 out of 8 in 1fmj

Go back to Mercury Binding Sites List in 1fmj
Mercury binding site 8 out of 8 in the Crystal Structure of Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap


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 Mercury Derivative of Retinol Dehydratase in A Complex with Retinol and Pap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg553

b:0.6
occ:0.50
SG B:CYS318 2.5 32.6 1.0
CB B:CYS318 3.2 27.6 1.0
CA B:CYS318 3.3 25.6 1.0
OD2 B:ASP321 3.5 34.4 1.0
O B:HOH665 3.6 35.2 1.0
N B:CYS318 4.0 25.2 1.0
C B:CYS318 4.5 25.0 1.0
CG B:ASP321 4.5 32.4 1.0
O B:GLY317 4.6 25.4 1.0
C B:GLY317 4.6 24.6 1.0
O B:CYS318 4.6 24.5 1.0

Reference:

S.Pakhomova, M.Kobayashi, J.Buck, M.E.Newcomer. A Helical Lid Converts A Sulfotransferase to A Dehydratase. Nat.Struct.Biol. V. 8 447 2001.
ISSN: ISSN 1072-8368
PubMed: 11323722
DOI: 10.1038/87617
Page generated: Wed Oct 28 18:39:16 2020

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