Mercury in PDB 4ri3: Crystal Structure of Dccd-Modified Psbs From Spinach

The structure of Crystal Structure of Dccd-Modified Psbs From Spinach, PDB code: 4ri3 was solved by M.Fan, M.Li, W.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.06 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.704, 77.697, 93.159, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 28.4

The binding sites of Mercury atom in the Crystal Structure of Dccd-Modified Psbs From Spinach (pdb code 4ri3). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 7 binding sites of Mercury where determined in the Crystal Structure of Dccd-Modified Psbs From Spinach, PDB code: 4ri3:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7;

Mercury binding site 1 out of 7 in the Crystal Structure of Dccd-Modified Psbs From Spinach


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 Dccd-Modified Psbs From Spinach within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg303 b:56.3 occ:0.50 O A:ALA6 2.5 57.6 1.0 CA A:ALA6 2.7 50.3 1.0 C A:ALA6 2.9 51.2 1.0 CB A:ALA6 3.1 54.7 1.0 N A:ALA6 4.0 49.5 1.0 N A:LYS7 4.2 48.0 1.0

Mercury binding site 2 out of 7 in the Crystal Structure of Dccd-Modified Psbs From Spinach


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 Dccd-Modified Psbs From Spinach within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg304 b:77.0 occ:0.68 CE2 A:TYR75 2.6 55.6 1.0 O B:ILE172 2.7 63.5 1.0 OH A:TYR75 3.0 60.6 1.0 CZ A:TYR75 3.2 61.5 1.0 C B:ILE172 3.5 59.8 1.0 CA B:GLY175 3.6 69.1 1.0 CD2 A:TYR75 3.7 58.2 1.0 CA B:ILE172 3.8 56.4 1.0 N B:GLY175 3.8 62.2 1.0 CB A:PRO73 3.8 53.9 1.0 O B:ASN171 4.1 59.3 1.0 CG2 B:ILE172 4.3 64.8 1.0 CG A:PRO73 4.4 53.9 1.0 CE1 A:TYR75 4.6 65.5 1.0 CB B:ILE172 4.6 58.9 1.0 C B:THR174 4.7 58.7 1.0 N B:GLU173 4.7 52.4 1.0 N B:ILE172 4.8 56.1 1.0 C B:ASN171 4.9 55.4 1.0 C B:GLY175 5.0 67.5 1.0 C B:GLU173 5.0 58.5 1.0 N B:THR174 5.0 61.8 1.0 CG A:TYR75 5.0 56.3 1.0

Mercury binding site 3 out of 7 in the Crystal Structure of Dccd-Modified Psbs From Spinach


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 Dccd-Modified Psbs From Spinach within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg305 b:98.3 occ:0.57 NH2 B:ARG101 2.4 64.7 1.0 C A:THR206 2.7 62.5 1.0 O A:THR206 3.0 67.8 1.0 CA A:THR206 3.2 53.9 1.0 CZ B:ARG101 3.7 69.8 1.0 O A:ILE205 4.1 58.2 1.0 CB A:THR206 4.2 57.1 1.0 N A:THR206 4.3 68.2 1.0 CA A:GLY100 4.4 41.3 1.0 NH1 B:ARG101 4.5 56.3 1.0 NE B:ARG101 4.5 63.0 1.0 CG2 A:VAL19 4.6 46.6 1.0 C A:ILE205 4.6 61.9 1.0 CG2 A:THR206 4.6 60.8 1.0 N A:GLY100 4.8 52.7 1.0

Mercury binding site 4 out of 7 in the Crystal Structure of Dccd-Modified Psbs From Spinach


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 Dccd-Modified Psbs From Spinach within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg306 b:0.0 occ:0.88 CE1 A:TYR75 2.5 65.5 1.0 OE1 A:GLU76 3.0 76.8 1.0 OH A:TYR75 3.2 60.6 1.0 CZ A:TYR75 3.2 61.5 1.0 CG A:GLU76 3.5 63.3 1.0 CD1 A:TYR75 3.5 62.7 1.0 CD A:GLU76 3.7 74.5 1.0 CE2 A:TYR75 4.5 55.6 1.0 CG A:TYR75 4.7 56.3 1.0 OE2 A:GLU76 4.9 69.6 1.0 CB A:GLU76 5.0 62.3 1.0

Mercury binding site 5 out of 7 in the Crystal Structure of Dccd-Modified Psbs From Spinach


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 Dccd-Modified Psbs From Spinach within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg305 b:61.6 occ:0.40 CE2 B:TYR75 2.6 45.0 1.0 O A:ILE172 2.6 48.2 1.0 OH B:TYR75 3.2 46.8 1.0 CZ B:TYR75 3.3 52.0 1.0 CD2 B:TYR75 3.6 48.9 1.0 C A:ILE172 3.6 41.5 1.0 CB B:PRO73 3.7 47.4 1.0 CA A:GLY175 3.8 49.3 1.0 CG B:PRO73 3.9 48.5 1.0 N A:GLY175 4.0 47.5 1.0 CA A:ILE172 4.0 41.1 1.0 CG2 A:ILE172 4.4 39.4 1.0 O A:ASN171 4.4 43.0 1.0 CE1 B:TYR75 4.7 55.7 1.0 N A:GLU173 4.8 37.5 1.0 CB A:ILE172 4.9 41.8 1.0 C A:THR174 4.9 47.5 1.0 CG B:TYR75 4.9 47.4 1.0 O A:GLU173 4.9 50.1 1.0 C A:GLU173 5.0 47.4 1.0

Mercury binding site 6 out of 7 in the Crystal Structure of Dccd-Modified Psbs From Spinach


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 Dccd-Modified Psbs From Spinach within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg306 b:83.2 occ:0.69 OE1 B:GLU76 2.3 75.3 1.0 CE1 B:TYR75 2.5 55.7 1.0 OH B:TYR75 2.5 46.8 1.0 CZ B:TYR75 2.8 52.0 1.0 CD B:GLU76 3.1 67.2 1.0 CG B:GLU76 3.3 58.2 1.0 CD1 B:TYR75 3.7 56.1 1.0 CE2 B:TYR75 4.1 45.0 1.0 OE2 B:GLU76 4.2 62.6 1.0 CG B:TYR75 4.8 47.4 1.0 CB B:GLU76 4.8 53.3 1.0 CD2 B:TYR75 4.9 48.9 1.0

Mercury binding site 7 out of 7 in the Crystal Structure of Dccd-Modified Psbs From Spinach


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 Dccd-Modified Psbs From Spinach within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg307 b:77.5 occ:0.40 NH2 A:ARG101 2.4 58.5 1.0 O B:THR206 2.4 64.2 1.0 C B:THR206 2.9 49.7 1.0 CZ A:ARG101 3.7 63.2 1.0 CA B:THR206 4.0 59.0 1.0 CA B:GLY100 4.1 34.5 1.0 CG2 B:VAL19 4.4 50.6 1.0 O B:ILE205 4.4 62.5 1.0 NE A:ARG101 4.5 62.1 1.0 N B:GLY100 4.5 40.5 1.0 NH1 A:ARG101 4.5 49.8 1.0 OD2 B:ASP21 4.8 47.9 1.0 C B:GLY100 4.9 45.3 1.0 CB B:THR206 4.9 65.9 1.0 N B:THR206 5.0 59.9 1.0 CG2 B:THR206 5.0 58.1 1.0

M.Fan, M.Li, Z.Liu, P.Cao, X.Pan, H.Zhang, X.Zhao, J.Zhang, W.Chang. Crystal Structures of the Psbs Protein Essential For Photoprotection in Plants. Nat.Struct.Mol.Biol. V. 22 729 2015.
ISSN: ISSN 1545-9993
PubMed: 26258636
DOI: 10.1038/NSMB.3068