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Mercury in PDB 5nm0: NB36 SER85CYS with Hg, Crystal Form 1

Protein crystallography data

The structure of NB36 SER85CYS with Hg, Crystal Form 1, PDB code: 5nm0 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) 71.26 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.610, 93.070, 142.510, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.1

Mercury Binding Sites:

The binding sites of Mercury atom in the NB36 SER85CYS with Hg, Crystal Form 1 (pdb code 5nm0). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the NB36 SER85CYS with Hg, Crystal Form 1, PDB code: 5nm0:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 5nm0

Go back to Mercury Binding Sites List in 5nm0
Mercury binding site 1 out of 2 in the NB36 SER85CYS with Hg, Crystal Form 1


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, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg201

b:39.1
occ:1.00
SG A:CYS85 2.3 27.8 1.0
SG C:CYS85 2.3 22.7 1.0
O C:HOH281 3.0 27.3 1.0
HG2 A:ARG67 3.0 21.5 1.0
HA C:CYS85 3.1 20.1 1.0
O C:HOH217 3.3 24.2 1.0
HB2 A:CYS85 3.3 27.6 1.0
CB C:CYS85 3.3 17.8 1.0
CB A:CYS85 3.3 23.0 1.0
HB3 C:CYS85 3.4 21.3 1.0
HB3 A:CYS85 3.5 27.6 1.0
HA A:ARG67 3.5 23.1 1.0
CA C:CYS85 3.6 16.8 1.0
H C:CYS85 3.8 20.1 1.0
O A:GLY66 4.0 26.3 1.0
CG A:ARG67 4.0 17.9 1.0
O C:GLY16 4.0 25.5 1.0
N C:CYS85 4.0 16.7 1.0
HB2 C:CYS85 4.2 21.3 1.0
O C:HOH282 4.3 47.5 1.0
CA A:ARG67 4.3 19.2 1.0
HB3 A:ARG67 4.3 24.4 1.0
CB A:ARG67 4.4 20.3 1.0
HA2 C:GLY16 4.4 30.5 1.0
O A:HOH360 4.5 37.7 1.0
HD2 A:ARG67 4.5 26.8 1.0
C A:GLY66 4.6 23.8 1.0
HD3 A:ARG67 4.6 26.8 1.0
HG3 A:ARG67 4.6 21.5 1.0
HB3 C:ASN84 4.6 21.0 1.0
CD A:ARG67 4.6 22.3 1.0
HB2 A:ASN84 4.7 28.1 1.0
O A:HOH345 4.7 39.4 1.0
N A:ARG67 4.7 20.9 1.0
CA A:CYS85 4.8 24.4 1.0
HB3 A:ASN84 4.9 28.1 1.0
C C:GLY16 4.9 23.7 1.0
C C:CYS85 5.0 20.3 1.0

Mercury binding site 2 out of 2 in 5nm0

Go back to Mercury Binding Sites List in 5nm0
Mercury binding site 2 out of 2 in the NB36 SER85CYS with Hg, Crystal Form 1


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, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg201

b:37.9
occ:1.00
SG B:CYS85 2.3 26.6 1.0
SG D:CYS85 2.3 26.0 1.0
O D:HOH266 2.9 34.3 1.0
HG D:CYS85 3.0 31.2 1.0
HA D:CYS85 3.1 27.3 1.0
HG2 B:ARG67 3.1 24.3 1.0
HB2 B:CYS85 3.3 34.0 1.0
CB B:CYS85 3.3 28.4 1.0
CB D:CYS85 3.4 21.2 1.0
O D:HOH219 3.4 24.8 1.0
HB3 D:CYS85 3.5 25.4 1.0
HB3 B:CYS85 3.5 34.0 1.0
HA B:ARG67 3.6 24.4 1.0
CA D:CYS85 3.6 22.8 1.0
H D:CYS85 3.8 26.0 1.0
O B:GLY66 3.9 26.3 1.0
N D:CYS85 4.0 21.7 1.0
CG B:ARG67 4.1 20.2 1.0
O D:GLY16 4.1 33.5 1.0
HB2 D:CYS85 4.2 25.4 1.0
CA B:ARG67 4.4 20.3 1.0
HB3 B:ARG67 4.4 27.1 1.0
HA2 D:GLY16 4.5 37.2 1.0
CB B:ARG67 4.5 22.6 1.0
HD2 B:ARG67 4.5 25.7 1.0
C B:GLY66 4.6 21.9 1.0
O B:HOH348 4.6 41.0 1.0
HD3 B:ARG67 4.6 25.7 1.0
HB3 D:ASN84 4.6 23.7 1.0
HG3 B:ARG67 4.7 24.3 1.0
CD B:ARG67 4.7 21.4 1.0
CA B:CYS85 4.7 23.4 1.0
N B:ARG67 4.8 20.5 1.0
O B:HOH368 4.8 37.0 1.0
HB2 B:ASN84 4.8 27.1 1.0

Reference:

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
Page generated: Sun Dec 13 19:13:03 2020

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