Mercury in PDB 5nml: NB36 SER85CYS with Hg Bound

The structure of NB36 SER85CYS with Hg Bound, PDB code: 5nml was solved by S.B.Hansen, K.R.Andersen, N.S.Laursen, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.42 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.960, 99.110, 85.410, 90.00, 105.77, 90.00
R / Rfree (%)	23.8 / 26.5

The binding sites of Mercury atom in the NB36 SER85CYS with Hg Bound (pdb code 5nml). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 9 binding sites of Mercury where determined in the NB36 SER85CYS with Hg Bound, PDB code: 5nml:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Mercury binding site 1 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg201 b:0.2 occ:1.00 SG G:CYS85 2.3 77.3 1.0 SG A:CYS85 2.3 78.7 1.0 CB G:CYS85 3.2 73.5 1.0 CB A:CYS85 3.3 71.3 1.0 CA G:CYS85 3.8 68.6 1.0 O A:GLY66 3.8 54.7 1.0 CG A:ARG67 3.8 54.3 1.0 N G:CYS85 4.2 65.5 1.0 C A:GLY66 4.4 55.5 1.0 CA A:ARG67 4.5 53.2 1.0 CD A:ARG67 4.5 51.6 1.0 CB A:ARG67 4.6 51.0 1.0 CA A:CYS85 4.7 66.5 1.0 N A:ARG67 4.7 54.1 1.0

Mercury binding site 2 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg202 b:91.2 occ:1.00 SG B:CYS85 2.3 85.6 1.0 CB B:CYS85 3.3 79.1 1.0 CA B:CYS85 3.6 76.9 1.0 O B:GLY16 3.7 75.7 1.0 N B:CYS85 4.3 77.0 1.0 CA B:GLY16 4.4 81.4 1.0 C B:GLY16 4.5 77.5 1.0 C B:CYS85 4.9 74.2 1.0

Mercury binding site 3 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg203 b:0.1 occ:1.00 O B:LEU86 4.1 76.9 1.0 CA B:GLY16 4.5 81.4 1.0 N B:GLY16 4.5 83.7 1.0 O B:CYS85 4.6 75.0 1.0 CG B:LYS87 4.7 75.6 1.0 C B:CYS85 4.9 74.2 1.0

Mercury binding site 4 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg202 b:86.2 occ:1.00 O C:GLY66 3.1 69.5 1.0 SG C:CYS85 3.2 87.3 1.0 CB C:CYS85 3.8 78.8 1.0 C C:GLY66 4.0 68.9 1.0 CG C:ARG67 4.1 69.9 1.0 CA C:ARG67 4.2 65.3 1.0 N C:ARG67 4.5 66.9 1.0 CB C:ARG67 4.6 65.9 1.0

Mercury binding site 5 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg203 b:96.9 occ:1.00 SG C:CYS85 2.3 87.3 1.0 CB C:CYS85 3.3 78.8 1.0 CA C:CYS85 3.6 73.2 1.0 O C:GLY16 4.0 79.7 1.0 N C:CYS85 4.3 70.8 1.0 CA C:GLY16 4.4 81.8 1.0 C C:GLY16 4.7 79.3 1.0 C C:CYS85 4.8 72.0 1.0

Mercury binding site 6 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Hg201 b:0.3 occ:0.60 SG D:CYS85 2.3 79.5 0.6 CB D:CYS85 3.0 73.0 0.4 CB D:CYS85 3.0 73.1 0.6 SG D:CYS85 3.4 78.3 0.4 CG D:ARG67 4.2 62.7 1.0 O D:GLY66 4.4 68.6 1.0 CA D:CYS85 4.5 72.0 0.4 CA D:CYS85 4.5 72.1 0.6 CD D:ARG67 4.8 64.0 1.0 N D:CYS85 4.8 66.6 1.0 CA D:ARG67 4.8 61.5 1.0 CB D:ARG67 4.8 59.5 1.0

Mercury binding site 7 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Hg202 b:0.4 occ:0.40 SG D:CYS85 2.3 78.3 0.4 O D:CYS85 3.4 68.4 1.0 CB D:CYS85 3.6 73.1 0.6 CB D:CYS85 3.7 73.0 0.4 C D:CYS85 3.8 64.8 1.0 CA D:CYS85 3.9 72.1 0.6 CA D:CYS85 3.9 72.0 0.4 O D:LEU86 4.1 69.8 1.0 CG D:LYS87 4.4 74.9 1.0 CA D:GLY16 4.4 55.2 1.0 SG D:CYS85 4.5 79.5 0.6 CE D:LYS87 4.6 82.5 1.0 N D:LEU86 4.7 62.9 1.0 C D:LEU86 4.7 66.1 1.0 N D:GLY16 4.7 53.6 1.0

Mercury binding site 8 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Hg201 b:0.9 occ:1.00 SG F:CYS85 2.3 90.7 1.0 CB F:CYS85 3.3 82.0 1.0 O F:GLY66 3.8 72.8 1.0 CG F:ARG67 3.9 65.3 1.0 C F:GLY66 4.5 71.2 1.0 CA F:ARG67 4.5 65.2 1.0 CB F:ARG67 4.6 62.1 1.0 CD F:ARG67 4.6 64.2 1.0 CA F:CYS85 4.7 77.7 1.0 N F:ARG67 4.7 66.8 1.0

Mercury binding site 9 out of 9 in the NB36 SER85CYS with Hg Bound


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of NB36 SER85CYS with Hg Bound within 5.0Å range: probe atom residue distance (Å) B Occ H:Hg202 b:0.4 occ:1.00 SG H:CYS85 2.3 0.1 1.0 CB H:CYS85 3.1 97.9 1.0 O H:CYS85 3.4 94.4 1.0 C H:CYS85 3.8 89.9 1.0 CA H:CYS85 3.8 91.2 1.0 NZ H:LYS87 3.9 0.3 1.0 CE H:LYS87 4.5 0.2 1.0 CG H:LYS87 4.7 96.6 1.0 N H:LEU86 4.8 85.1 1.0 O H:LEU86 4.8 89.6 1.0 CD H:ARG67 4.9 81.3 1.0

S.B.Hansen, N.S.Laursen, G.R.Andersen, K.R.Andersen. Introducing Site-Specific Cysteines Into Nanobodies For Mercury Labelling Allows De Novo Phasing of Their Crystal Structures. Acta Crystallogr D Struct V. 73 804 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28994409
DOI: 10.1107/S2059798317013171