Zinc in PDB 3rym: Structure of Oxidized M98K Mutant of Amicyanin

The structure of Structure of Oxidized M98K Mutant of Amicyanin, PDB code: 3rym was solved by N.Sukumar, V.L.Davidson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.29 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.367, 51.668, 56.543, 105.97, 96.48, 108.35
R / Rfree (%)	19 / 21.5

The binding sites of Zinc atom in the Structure of Oxidized M98K Mutant of Amicyanin (pdb code 3rym). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Oxidized M98K Mutant of Amicyanin, PDB code: 3rym:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of Oxidized M98K Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Oxidized M98K Mutant of Amicyanin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:12.4 occ:1.00 ND1 A:HIS53 2.1 14.8 1.0 NZ A:LYS98 2.1 12.6 1.0 ND1 A:HIS95 2.1 15.8 1.0 SG A:CYS92 2.3 13.3 1.0 CE1 A:HIS53 2.9 15.1 1.0 CE A:LYS98 2.9 16.0 1.0 CG A:HIS95 3.1 19.0 1.0 CE1 A:HIS95 3.1 20.6 1.0 CG A:HIS53 3.2 13.9 1.0 CB A:CYS92 3.2 13.0 1.0 CB A:HIS95 3.4 18.4 1.0 CB A:HIS53 3.6 13.6 1.0 O A:HOH350 4.0 20.4 1.0 CA A:HIS53 4.1 9.8 1.0 NE2 A:HIS53 4.1 16.0 1.0 CD2 A:HIS53 4.2 14.9 1.0 NE2 A:HIS95 4.2 20.7 1.0 CD2 A:HIS95 4.2 17.9 1.0 CD A:LYS98 4.3 13.7 1.0 O A:PRO52 4.4 15.0 1.0 N A:HIS95 4.5 13.0 1.0 CA A:HIS95 4.5 15.1 1.0 CG A:PRO94 4.6 20.4 1.0 CA A:CYS92 4.7 12.0 1.0 O A:HIS95 4.7 14.0 1.0 CB A:LYS98 5.0 13.1 1.0 N A:ASN54 5.0 11.3 1.0

Zinc binding site 2 out of 6 in the Structure of Oxidized M98K Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Oxidized M98K Mutant of Amicyanin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:17.0 occ:1.00 OE2 C:GLU105 2.0 21.8 1.0 ND1 A:HIS36 2.1 15.3 1.0 OE2 A:GLU105 2.2 21.8 1.0 ND1 C:HIS36 2.3 16.6 1.0 CD C:GLU105 2.6 20.7 1.0 OE1 A:GLU105 2.6 23.9 1.0 OE1 C:GLU105 2.6 27.4 1.0 CD A:GLU105 2.7 21.9 1.0 CE1 A:HIS36 3.0 16.1 1.0 CG A:HIS36 3.1 12.8 1.0 CG C:HIS36 3.2 13.9 1.0 CE1 C:HIS36 3.3 14.3 1.0 CB C:HIS36 3.4 13.7 1.0 CB A:HIS36 3.4 13.4 1.0 CG C:GLU105 4.0 24.0 1.0 NE2 A:HIS36 4.1 15.3 1.0 CD2 A:HIS36 4.2 13.4 1.0 CG A:GLU105 4.2 24.4 1.0 CD2 C:HIS36 4.3 14.1 1.0 NE2 C:HIS36 4.4 16.7 1.0 O C:HOH129 4.7 28.4 1.0 O A:HOH142 4.7 27.5 1.0 CA C:HIS36 4.8 10.8 1.0 CA A:HIS36 4.9 11.3 1.0

Zinc binding site 3 out of 6 in the Structure of Oxidized M98K Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Oxidized M98K Mutant of Amicyanin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn106 b:13.5 occ:1.00 ND1 B:HIS95 2.1 14.4 1.0 ND1 B:HIS53 2.1 14.8 1.0 SG B:CYS92 2.2 12.0 1.0 NZ B:LYS98 2.3 16.7 1.0 CE1 B:HIS53 3.0 19.7 1.0 CG B:HIS95 3.0 18.4 1.0 CE1 B:HIS95 3.1 20.6 1.0 CB B:CYS92 3.1 9.7 1.0 CG B:HIS53 3.2 15.1 1.0 CE B:LYS98 3.2 13.2 1.0 CB B:HIS95 3.3 18.8 1.0 CB B:HIS53 3.6 12.8 1.0 CA B:HIS53 3.9 11.5 1.0 NE2 B:HIS53 4.1 16.7 1.0 O B:PRO52 4.2 16.1 1.0 CD2 B:HIS95 4.2 22.9 1.0 NE2 B:HIS95 4.2 21.7 1.0 CD2 B:HIS53 4.3 14.2 1.0 CG B:PRO94 4.4 19.9 1.0 CA B:HIS95 4.4 15.3 1.0 N B:HIS95 4.5 14.1 1.0 CD B:LYS98 4.6 14.6 1.0 CA B:CYS92 4.6 10.5 1.0 O B:HIS95 4.7 15.0 1.0 N B:ASN54 4.8 11.6 1.0 N B:HIS53 4.9 14.3 1.0 CD B:PRO94 4.9 16.1 1.0 C B:PRO52 4.9 19.0 1.0 C B:HIS53 4.9 13.2 1.0 C B:CYS92 5.0 13.9 1.0

Zinc binding site 4 out of 6 in the Structure of Oxidized M98K Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Oxidized M98K Mutant of Amicyanin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:14.4 occ:1.00 OE2 B:GLU105 1.9 21.9 1.0 ND1 B:HIS36 2.1 16.0 1.0 ND1 D:HIS36 2.1 14.9 1.0 OE2 D:GLU105 2.2 20.0 1.0 OE1 B:GLU105 2.5 21.9 1.0 CD B:GLU105 2.5 16.4 1.0 CD D:GLU105 2.8 19.2 1.0 OE1 D:GLU105 2.9 16.4 1.0 CG D:HIS36 3.1 13.7 1.0 CG B:HIS36 3.1 13.8 1.0 CE1 D:HIS36 3.1 15.0 1.0 CE1 B:HIS36 3.1 12.9 1.0 CB D:HIS36 3.4 12.8 1.0 CB B:HIS36 3.4 14.3 1.0 CG B:GLU105 3.9 22.4 1.0 O B:HOH183 4.0 25.2 1.0 NE2 D:HIS36 4.2 13.5 1.0 CD2 D:HIS36 4.2 12.7 1.0 NE2 B:HIS36 4.2 12.4 1.0 CD2 B:HIS36 4.2 14.5 1.0 CG D:GLU105 4.3 20.4 1.0 O D:HOH119 4.6 29.5 1.0 O B:HOH218 4.6 21.3 1.0 CA B:HIS36 4.8 10.5 1.0 CA D:HIS36 4.9 10.7 1.0 CB B:GLU105 5.0 23.1 1.0

Zinc binding site 5 out of 6 in the Structure of Oxidized M98K Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Oxidized M98K Mutant of Amicyanin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn106 b:17.4 occ:1.00 ND1 C:HIS53 2.1 15.4 1.0 ND1 C:HIS95 2.1 13.9 1.0 NZ C:LYS98 2.3 18.0 1.0 SG C:CYS92 2.3 16.0 1.0 CE1 C:HIS53 3.0 20.0 1.0 CE1 C:HIS95 3.0 22.9 1.0 CG C:HIS95 3.1 20.9 1.0 CG C:HIS53 3.1 15.4 1.0 CE C:LYS98 3.1 14.7 1.0 CB C:CYS92 3.2 14.5 1.0 CB C:HIS95 3.5 20.7 1.0 CB C:HIS53 3.5 15.6 1.0 CA C:HIS53 3.8 13.6 1.0 NE2 C:HIS53 4.1 17.9 1.0 NE2 C:HIS95 4.2 22.1 1.0 O C:PRO52 4.2 19.6 1.0 CD2 C:HIS53 4.2 16.1 1.0 CD2 C:HIS95 4.2 21.3 1.0 CG C:PRO94 4.4 21.8 1.0 N C:HIS95 4.5 18.3 1.0 CA C:HIS95 4.5 17.1 1.0 CD C:LYS98 4.6 19.0 1.0 CA C:CYS92 4.6 11.8 1.0 N C:ASN54 4.8 13.3 1.0 N C:HIS53 4.8 15.6 1.0 O C:HIS95 4.9 17.4 1.0 CD C:PRO94 4.9 18.2 1.0 C C:PRO52 4.9 16.6 1.0 C C:HIS53 4.9 12.4 1.0

Zinc binding site 6 out of 6 in the Structure of Oxidized M98K Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Oxidized M98K Mutant of Amicyanin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn106 b:17.9 occ:1.00 ND1 D:HIS95 2.1 19.5 1.0 ND1 D:HIS53 2.1 18.4 1.0 NZ D:LYS98 2.2 15.4 1.0 SG D:CYS92 2.3 15.5 1.0 CE1 D:HIS53 3.0 15.4 1.0 CE D:LYS98 3.0 15.9 1.0 CG D:HIS95 3.1 21.2 1.0 CE1 D:HIS95 3.1 23.0 1.0 CG D:HIS53 3.2 15.0 1.0 CB D:CYS92 3.2 14.0 1.0 CB D:HIS95 3.3 21.1 1.0 CB D:HIS53 3.6 16.0 1.0 CA D:HIS53 4.0 12.4 1.0 NE2 D:HIS53 4.1 18.7 1.0 NE2 D:HIS95 4.2 21.6 1.0 CD2 D:HIS95 4.2 22.2 1.0 CD2 D:HIS53 4.3 15.9 1.0 O D:PRO52 4.3 17.7 1.0 N D:HIS95 4.4 17.3 1.0 CD D:LYS98 4.4 15.2 1.0 CA D:HIS95 4.4 17.8 1.0 CG D:PRO94 4.5 24.3 1.0 CA D:CYS92 4.6 13.2 1.0 O D:HIS95 4.7 15.3 1.0 N D:ASN54 4.9 13.1 1.0 N D:HIS53 5.0 17.1 1.0 CB D:LYS98 5.0 15.9 1.0

N.Sukumar, M.Choi, V.L.Davidson. Replacement of the Axial Copper Ligand Methionine with Lysine in Amicyanin Converts It to A Zinc-Binding Protein That No Longer Binds Copper. J.Inorg.Biochem. V. 105 1638 2011.
ISSN: ISSN 0162-0134
PubMed: 22071089
DOI: 10.1016/J.JINORGBIO.2011.08.002