Zinc in PDB 6fi9: Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr

The structure of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr, PDB code: 6fi9 was solved by P.F.Varela, P.Legrand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.15 / 2.80
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	128.520, 128.520, 88.140, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 25.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr (pdb code 6fi9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr, PDB code: 6fi9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:94.4 occ:1.00 NE2 A:HIS111 2.0 81.9 1.0 OE1 A:GLU23 2.0 76.3 1.0 NE2 A:HIS107 2.2 86.4 1.0 CD A:GLU23 2.8 92.5 1.0 ND1 A:HIS41 2.8 0.3 1.0 CD2 A:HIS111 2.8 82.9 1.0 CD2 A:HIS107 2.9 87.3 1.0 OE2 A:GLU23 2.9 88.9 1.0 CE1 A:HIS111 3.0 80.6 1.0 CE1 A:HIS107 3.3 87.1 1.0 CG A:HIS41 3.4 0.2 1.0 CB A:HIS41 3.6 0.5 1.0 CE1 A:HIS41 3.7 0.7 1.0 CG A:HIS111 4.0 80.4 1.0 CG A:HIS107 4.1 87.1 1.0 CD1 A:LEU25 4.1 84.7 1.0 ND1 A:HIS111 4.1 81.3 1.0 CG A:GLU23 4.2 84.8 1.0 ND1 A:HIS107 4.3 89.0 1.0 CA A:HIS41 4.4 0.5 1.0 CD2 A:HIS41 4.4 0.2 1.0 NE2 A:HIS41 4.6 0.9 1.0 CD2 A:LEU25 4.7 84.3 1.0 CG A:LEU25 4.7 83.3 1.0 SD A:MET44 4.8 0.1 1.0 O A:SER37 4.8 0.3 1.0 CB A:GLU23 5.0 81.1 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:0.1 occ:1.00 OE1 A:GLU106 2.0 0.1 1.0 OE1 A:GLU40 2.3 0.4 1.0 SG A:CYS29 2.8 0.6 1.0 CD A:GLU106 3.3 0.4 1.0 CD A:GLU40 3.5 0.0 1.0 ND1 A:HIS107 3.5 89.0 1.0 OG A:SER31 3.5 0.6 1.0 ND1 A:HIS110 3.9 77.9 1.0 CA A:HIS107 3.9 85.2 1.0 N A:HIS107 3.9 88.4 1.0 OE2 A:GLU106 4.0 99.0 1.0 OE2 A:GLU40 4.1 0.7 1.0 C A:GLU106 4.2 93.8 1.0 CB A:HIS107 4.2 85.5 1.0 CG A:GLU106 4.2 0.8 1.0 CB A:CYS29 4.2 0.1 1.0 CB A:SER31 4.3 1.0 1.0 CB A:GLU106 4.3 95.3 1.0 CG A:HIS107 4.3 87.1 1.0 CB A:HIS110 4.3 73.8 1.0 O A:GLU106 4.4 93.0 1.0 CG A:HIS110 4.5 76.1 1.0 CE1 A:HIS107 4.6 87.1 1.0 CA A:CYS29 4.6 0.7 1.0 CG A:GLU40 4.7 0.8 1.0 N A:SER31 4.8 0.3 1.0 N A:GLU30 4.8 0.0 1.0 CE1 A:HIS110 4.8 76.8 1.0 CB A:GLU40 4.9 0.4 1.0 CA A:GLU106 4.9 92.6 1.0 O A:VAL103 4.9 0.8 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:89.5 occ:1.00 OE1 B:GLU23 1.9 98.9 1.0 NE2 B:HIS111 2.0 72.3 1.0 NE2 B:HIS107 2.2 87.6 1.0 ND1 B:HIS41 2.2 97.5 1.0 CD B:GLU23 2.6 0.1 1.0 CE1 B:HIS111 2.7 70.6 1.0 OE2 B:GLU23 2.8 0.5 1.0 CD2 B:HIS107 3.0 89.0 1.0 CE1 B:HIS41 3.2 96.0 1.0 CD2 B:HIS111 3.2 73.5 1.0 CG B:HIS41 3.3 97.1 1.0 CE1 B:HIS107 3.3 88.0 1.0 CB B:HIS41 3.6 95.6 1.0 CD1 B:LEU25 3.7 80.7 1.0 ND1 B:HIS111 3.9 71.4 1.0 CG B:GLU23 4.0 99.6 1.0 CG B:HIS111 4.2 71.7 1.0 CG B:HIS107 4.2 88.6 1.0 NE2 B:HIS41 4.3 96.9 1.0 ND1 B:HIS107 4.4 90.1 1.0 CD2 B:HIS41 4.4 98.4 1.0 CA B:HIS41 4.4 97.7 1.0 CG B:LEU25 4.4 80.0 1.0 CD2 B:LEU25 4.5 82.1 1.0 O B:SER37 4.7 0.0 1.0 CB B:GLU23 4.8 89.8 1.0 SD B:MET44 4.9 0.8 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:0.9 occ:1.00 OE1 B:GLU106 1.9 96.8 1.0 OE1 B:GLU40 2.2 0.6 1.0 SG B:CYS29 2.9 0.8 1.0 ND1 B:HIS107 3.1 90.1 1.0 CD B:GLU106 3.1 0.9 1.0 CD B:GLU40 3.3 0.6 1.0 OG B:SER31 3.6 0.2 1.0 CA B:HIS107 3.6 86.2 1.0 N B:HIS107 3.8 90.6 1.0 CB B:HIS107 3.8 87.1 1.0 CG B:HIS107 3.9 88.6 1.0 OE2 B:GLU106 3.9 0.8 1.0 OE2 B:GLU40 3.9 0.7 1.0 CG B:GLU106 4.1 0.7 1.0 CE1 B:HIS107 4.2 88.0 1.0 CB B:CYS29 4.3 0.2 1.0 C B:GLU106 4.3 97.5 1.0 ND1 B:HIS110 4.3 83.1 1.0 CG B:GLU40 4.4 0.3 1.0 CB B:GLU106 4.4 99.8 1.0 CB B:GLU40 4.4 0.9 1.0 CB B:SER31 4.5 0.3 1.0 O B:GLU106 4.6 96.7 1.0 CB B:HIS110 4.6 79.3 1.0 CA B:CYS29 4.7 0.2 1.0 O B:VAL103 4.8 0.6 1.0 C B:HIS107 4.9 86.2 1.0 CG B:HIS110 5.0 81.4 1.0 N B:SER31 5.0 0.3 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:84.7 occ:1.00 NE2 C:HIS107 2.0 89.8 1.0 NE2 C:HIS111 2.0 72.9 1.0 OE1 C:GLU23 2.0 75.5 1.0 ND1 C:HIS41 2.7 82.5 1.0 CD C:GLU23 2.8 92.8 1.0 CD2 C:HIS111 2.8 74.8 1.0 CD2 C:HIS107 2.8 91.9 1.0 OE2 C:GLU23 2.9 93.1 1.0 CE1 C:HIS111 3.0 71.0 1.0 CE1 C:HIS107 3.0 90.3 1.0 CG C:HIS41 3.4 81.1 1.0 CE1 C:HIS41 3.5 80.6 1.0 CB C:HIS41 3.6 79.7 1.0 CD1 C:LEU25 3.9 70.9 1.0 CG C:HIS111 4.0 72.7 1.0 CG C:HIS107 4.0 91.8 1.0 ND1 C:HIS111 4.1 72.4 1.0 ND1 C:HIS107 4.1 92.9 1.0 CG C:GLU23 4.1 74.0 1.0 CD2 C:HIS41 4.4 81.2 1.0 CA C:HIS41 4.5 82.5 1.0 NE2 C:HIS41 4.5 80.3 1.0 CD2 C:LEU25 4.6 71.6 1.0 CG C:LEU25 4.6 69.9 1.0 O C:SER37 4.7 0.6 1.0 SD C:MET44 4.9 96.2 1.0 CB C:GLU23 5.0 65.5 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:0.2 occ:1.00 OE1 C:GLU106 1.9 0.7 1.0 OE1 C:GLU40 2.2 0.9 1.0 CD C:GLU106 3.1 0.9 1.0 OG C:SER31 3.4 0.7 1.0 CD C:GLU40 3.4 0.0 1.0 SG C:CYS29 3.4 0.3 1.0 ND1 C:HIS107 3.7 92.9 1.0 CB C:SER31 3.9 0.5 1.0 OE2 C:GLU106 3.9 0.1 1.0 CA C:HIS107 4.0 90.5 1.0 N C:HIS107 4.0 94.9 1.0 OE2 C:GLU40 4.1 0.9 1.0 CG C:GLU106 4.1 0.5 1.0 C C:GLU106 4.2 0.1 1.0 CB C:GLU106 4.3 0.0 1.0 ND1 C:HIS110 4.3 76.1 1.0 CB C:HIS107 4.3 91.1 1.0 N C:SER31 4.4 0.7 1.0 O C:GLU106 4.4 98.9 1.0 CG C:HIS107 4.5 91.8 1.0 CG C:GLU40 4.5 0.8 1.0 CB C:HIS110 4.6 74.1 1.0 CB C:CYS29 4.6 0.3 1.0 CA C:SER31 4.7 0.8 1.0 N C:GLU30 4.7 0.9 1.0 CE1 C:HIS107 4.7 90.3 1.0 CA C:CYS29 4.7 0.3 1.0 CB C:GLU40 4.8 93.4 1.0 CG C:HIS110 4.9 75.0 1.0 O C:VAL103 4.9 0.6 1.0 CA C:GLU106 4.9 0.3 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:73.5 occ:1.00 OE1 D:GLU23 1.9 85.8 1.0 ND1 D:HIS41 2.2 75.4 1.0 NE2 D:HIS107 2.2 84.3 1.0 NE2 D:HIS111 2.3 66.6 1.0 CD D:GLU23 2.6 97.2 1.0 OE2 D:GLU23 2.7 0.5 1.0 CG D:HIS41 3.0 74.1 1.0 CE1 D:HIS41 3.1 74.3 1.0 CD2 D:HIS107 3.1 85.4 1.0 CD2 D:HIS111 3.2 67.8 1.0 CE1 D:HIS107 3.2 84.3 1.0 CE1 D:HIS111 3.3 65.4 1.0 CB D:HIS41 3.3 71.7 1.0 CD1 D:LEU25 3.9 60.3 1.0 CD2 D:HIS41 4.0 75.7 1.0 NE2 D:HIS41 4.1 74.8 1.0 CG D:GLU23 4.1 76.2 1.0 CA D:HIS41 4.2 72.6 1.0 CG D:HIS107 4.3 84.2 1.0 CG D:HIS111 4.3 65.7 1.0 ND1 D:HIS107 4.3 85.8 1.0 ND1 D:HIS111 4.4 66.3 1.0 O D:SER37 4.5 93.1 1.0 SD D:MET44 4.8 86.3 1.0 N D:HIS41 4.8 73.8 1.0 CG D:LEU25 4.8 59.9 1.0 CB D:GLU23 4.9 68.8 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:0.6 occ:1.00 OE1 D:GLU106 1.9 0.3 1.0 SG D:CYS29 2.4 97.6 1.0 OE1 D:GLU40 2.6 60.3 1.0 CD D:GLU106 2.8 0.3 1.0 OE2 D:GLU106 3.0 0.5 1.0 CB D:CYS29 3.6 92.6 1.0 CD D:GLU40 3.6 91.5 1.0 ND1 D:HIS110 3.6 65.3 1.0 OG D:SER31 3.8 0.9 1.0 CA D:CYS29 3.8 92.7 1.0 ND1 D:HIS107 3.9 85.8 1.0 OE2 D:GLU40 3.9 86.4 1.0 CG D:GLU106 4.2 0.4 1.0 N D:GLU30 4.2 0.1 1.0 CA D:HIS107 4.3 81.1 1.0 CB D:HIS110 4.3 62.1 1.0 CG D:HIS110 4.3 64.1 1.0 CB D:SER31 4.4 0.2 1.0 C D:CYS29 4.4 0.2 1.0 N D:HIS107 4.4 83.6 1.0 N D:SER31 4.5 0.5 1.0 CE1 D:HIS110 4.5 64.2 1.0 CB D:HIS107 4.7 82.0 1.0 CG D:HIS107 4.7 84.2 1.0 C D:GLU106 4.7 88.3 1.0 CE1 D:HIS107 4.8 84.3 1.0 CB D:GLU106 4.8 89.0 1.0 O D:GLU106 4.8 87.1 1.0 CG D:GLU40 4.9 86.2 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:0.1 occ:1.00 OE2 E:GLU23 1.9 0.3 1.0 ND1 E:HIS41 1.9 0.2 1.0 OE1 E:GLU23 2.1 0.3 1.0 CD E:GLU23 2.3 0.4 1.0 CG E:HIS41 2.6 0.8 1.0 CE1 E:HIS41 2.7 0.7 1.0 NE2 E:HIS107 2.9 0.8 1.0 NE2 E:HIS111 2.9 0.1 1.0 CB E:HIS41 3.1 0.6 1.0 CD2 E:HIS41 3.6 0.6 1.0 NE2 E:HIS41 3.6 0.1 1.0 CE1 E:HIS111 3.7 0.9 1.0 CE1 E:HIS107 3.8 0.8 1.0 CG E:GLU23 3.8 0.1 1.0 CD2 E:HIS107 3.8 0.3 1.0 CD2 E:HIS111 3.9 0.3 1.0 CA E:HIS41 4.2 0.5 1.0 O E:SER37 4.3 0.8 1.0 CD1 E:LEU25 4.4 0.0 1.0 CB E:GLU23 4.7 1.0 1.0 N E:HIS41 4.8 0.6 1.0 ND1 E:HIS107 4.9 0.8 1.0 ND1 E:HIS111 5.0 0.0 1.0 CG E:HIS107 5.0 0.3 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of A Zinc-Responsive Marr Family Member, Lactococcus Lactis Zitr within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:0.4 occ:1.00 OE1 E:GLU106 2.3 0.9 1.0 OE1 E:GLU40 2.9 0.9 1.0 SG E:CYS29 3.0 0.9 1.0 ND1 E:HIS107 3.3 0.8 1.0 CD E:GLU106 3.5 0.5 1.0 CA E:HIS107 3.5 0.6 1.0 CD E:GLU40 3.6 0.7 1.0 N E:HIS107 3.8 0.5 1.0 OG E:SER31 3.8 0.0 1.0 CB E:HIS107 3.9 0.1 1.0 OE2 E:GLU40 3.9 0.4 1.0 CG E:HIS107 4.0 0.3 1.0 ND1 E:HIS110 4.1 0.6 1.0 C E:GLU106 4.2 0.1 1.0 OE2 E:GLU106 4.2 0.6 1.0 O E:GLU106 4.3 0.8 1.0 CB E:HIS110 4.4 0.7 1.0 CB E:CYS29 4.4 0.9 1.0 CE1 E:HIS107 4.4 0.8 1.0 CG E:GLU106 4.5 1.0 1.0 CB E:GLU106 4.5 0.7 1.0 CB E:SER31 4.6 0.9 1.0 CG E:HIS110 4.7 0.5 1.0 CB E:GLU40 4.7 0.9 1.0 CG E:GLU40 4.7 0.2 1.0 CA E:CYS29 4.8 0.2 1.0 C E:HIS107 4.8 0.4 1.0 O E:VAL103 4.9 0.4 1.0

P.F.Varela, C.Velours, M.Aumont-Nicaise, B.Pineau, P.Legrand, I.Poquet. Biophysical and Structural Characterization of A Zinc-Responsive Repressor of the Marr Superfamily. Plos One V. 14 10123 2019.
ISSN: ESSN 1932-6203
PubMed: 30753183
DOI: 10.1371/JOURNAL.PONE.0210123