Zinc in PDB 6twm: Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi

The structure of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi, PDB code: 6twm was solved by C.-N.Mais, F.Altegoer, G.Bange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.64 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.667, 145.949, 164.116, 90.00, 92.30, 90.00
R / Rfree (%)	20.9 / 26.2

The binding sites of Zinc atom in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi (pdb code 6twm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi, PDB code: 6twm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.9 occ:1.00 OXT A:DAB402 2.0 0.5 1.0 OE2 A:GLU61 2.5 39.7 1.0 ND1 A:HIS58 2.7 30.7 1.0 OE1 A:GLU61 2.8 35.7 1.0 ND1 A:HIS144 2.8 35.1 1.0 CD A:GLU61 3.0 36.2 1.0 C A:DAB402 3.2 0.9 1.0 O A:HOH508 3.3 37.6 1.0 CE1 A:HIS58 3.4 30.1 1.0 O A:SER145 3.4 37.7 1.0 CG A:HIS144 3.6 34.4 1.0 CB A:HIS144 3.6 31.8 1.0 CG A:HIS58 3.8 30.4 1.0 NH1 A:ARG100 3.8 37.8 1.0 CE1 A:HIS144 3.8 35.1 1.0 O A:DAB402 3.8 0.2 1.0 OE2 A:GLU209 4.0 47.4 1.0 CB A:HIS58 4.2 29.5 1.0 N A:SER145 4.3 32.0 1.0 CA A:HIS144 4.4 31.1 1.0 CA A:DAB402 4.4 0.4 1.0 CG A:GLU61 4.5 32.0 1.0 NE2 A:HIS58 4.5 30.3 1.0 OE1 A:GLU209 4.6 47.2 1.0 C A:SER145 4.6 36.4 1.0 O A:HOH523 4.6 24.8 1.0 N A:DAB402 4.6 0.4 1.0 CD A:GLU209 4.7 45.8 1.0 CD2 A:HIS58 4.8 30.6 1.0 CZ A:ARG100 4.8 37.3 1.0 CD2 A:HIS144 4.8 35.3 1.0 C A:HIS144 4.8 29.8 1.0 NE2 A:HIS144 4.9 35.3 1.0 NH2 A:ARG100 4.9 37.8 1.0 CB A:DAB402 4.9 0.4 1.0

Zinc binding site 2 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:84.6 occ:1.00 OXT B:DAB402 1.9 81.6 1.0 ND1 B:HIS144 2.6 41.6 1.0 OE2 B:GLU61 2.7 31.5 1.0 ND1 B:HIS58 2.7 35.3 1.0 OE1 B:GLU61 2.8 30.2 1.0 C B:DAB402 3.0 78.6 1.0 CD B:GLU61 3.1 31.2 1.0 CE1 B:HIS58 3.3 35.9 1.0 CG B:HIS144 3.3 41.2 1.0 CB B:HIS144 3.4 38.8 1.0 O B:DAB402 3.5 78.6 1.0 O B:SER145 3.5 40.4 1.0 CE1 B:HIS144 3.6 41.7 1.0 CG B:HIS58 3.8 34.8 1.0 N B:SER145 4.1 37.8 1.0 CA B:HIS144 4.2 36.1 1.0 OE2 B:GLU209 4.2 57.1 1.0 O B:HOH512 4.2 21.5 1.0 CB B:HIS58 4.3 35.1 1.0 CA B:DAB402 4.3 76.1 1.0 NH2 B:ARG100 4.4 45.1 1.0 NE2 B:HIS58 4.4 35.9 1.0 CD2 B:HIS144 4.5 42.2 1.0 OE1 B:GLU209 4.6 56.6 1.0 CG B:GLU61 4.6 31.2 1.0 C B:SER145 4.6 38.0 1.0 C B:HIS144 4.6 35.9 1.0 NE2 B:HIS144 4.7 41.7 1.0 CD2 B:HIS58 4.7 34.8 1.0 CD B:GLU209 4.8 55.1 1.0

Zinc binding site 3 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:0.6 occ:1.00 O C:ACT402 2.2 0.9 1.0 OE2 C:GLU61 2.5 41.5 1.0 ND1 C:HIS58 2.5 41.2 1.0 ND1 C:HIS144 2.7 26.9 1.0 C C:ACT402 2.9 0.8 1.0 OE1 C:GLU61 3.0 39.2 1.0 CD C:GLU61 3.1 39.6 1.0 CE1 C:HIS58 3.2 41.5 1.0 OXT C:ACT402 3.2 0.6 1.0 CG C:HIS144 3.5 24.6 1.0 CG C:HIS58 3.6 40.0 1.0 CE1 C:HIS144 3.6 25.7 1.0 O C:SER145 3.7 31.8 1.0 CB C:HIS144 3.7 25.8 1.0 NH1 C:ARG100 3.8 31.4 1.0 O C:HOH524 3.9 54.4 1.0 CB C:HIS58 4.0 36.8 1.0 NE2 C:HIS58 4.3 41.4 1.0 OE2 C:GLU209 4.3 47.7 1.0 CH3 C:ACT402 4.4 0.1 1.0 N C:SER145 4.4 28.3 1.0 CA C:HIS144 4.5 26.4 1.0 O C:HOH515 4.5 15.1 1.0 CD2 C:HIS58 4.5 40.9 1.0 O C:HOH548 4.5 35.2 1.0 NH2 C:ARG100 4.5 38.4 1.0 CG C:GLU61 4.6 38.7 1.0 CZ C:ARG100 4.6 36.1 1.0 OE1 C:GLU209 4.7 45.7 1.0 CD2 C:HIS144 4.7 26.6 1.0 NE2 C:HIS144 4.7 26.7 1.0 C C:SER145 4.8 32.6 1.0 C C:HIS144 4.9 29.9 1.0 CD C:GLU209 5.0 46.3 1.0

Zinc binding site 4 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:0.9 occ:1.00 ND1 D:HIS144 2.5 32.7 1.0 OXT D:DAB402 2.6 85.2 1.0 O D:DAB402 2.6 84.8 1.0 C D:DAB402 2.8 85.1 1.0 OE2 D:GLU61 2.9 44.7 1.0 OE1 D:GLU61 3.0 43.4 1.0 ND1 D:HIS58 3.1 36.1 1.0 CG D:HIS144 3.2 31.6 1.0 CD D:GLU61 3.3 42.6 1.0 CB D:HIS144 3.3 29.8 1.0 CE1 D:HIS144 3.5 33.2 1.0 O D:HOH582 3.5 36.2 1.0 O D:SER145 3.5 35.6 1.0 CE1 D:HIS58 3.7 36.7 1.0 OE2 D:GLU209 3.9 52.0 1.0 NH1 D:ARG100 4.0 29.4 1.0 CG D:HIS58 4.1 35.6 1.0 CA D:DAB402 4.2 85.6 1.0 CA D:HIS144 4.2 29.2 1.0 N D:SER145 4.2 30.8 1.0 OE1 D:GLU209 4.3 50.8 1.0 CD2 D:HIS144 4.4 33.0 1.0 NE2 D:HIS144 4.5 33.2 1.0 CB D:HIS58 4.5 35.3 1.0 CB D:DAB402 4.5 86.5 1.0 CD D:GLU209 4.5 51.2 1.0 C D:SER145 4.6 35.1 1.0 C D:HIS144 4.7 29.9 1.0 CG D:GLU61 4.8 39.5 1.0 N D:DAB402 4.8 85.6 1.0 NE2 D:HIS58 4.9 37.3 1.0 CZ D:ARG100 4.9 31.3 1.0 O D:HOH553 5.0 36.7 1.0 NH2 D:ARG100 5.0 30.3 1.0

Zinc binding site 5 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:0.7 occ:1.00 OXT E:DAB402 2.2 95.5 1.0 OE2 E:GLU61 2.6 43.7 1.0 ND1 E:HIS144 2.8 33.0 1.0 ND1 E:HIS58 2.8 35.5 1.0 OE1 E:GLU61 3.0 43.0 1.0 C E:DAB402 3.1 88.0 1.0 CD E:GLU61 3.1 42.2 1.0 O E:HOH546 3.2 34.4 1.0 O E:DAB402 3.5 89.6 1.0 O E:SER145 3.5 31.5 1.0 CE1 E:HIS58 3.5 35.5 1.0 CG E:HIS144 3.6 32.2 1.0 CB E:HIS144 3.7 30.9 1.0 NH1 E:ARG100 3.7 33.2 1.0 CE1 E:HIS144 3.8 34.4 1.0 CG E:HIS58 3.9 33.9 1.0 OE2 E:GLU209 4.2 54.5 1.0 CB E:HIS58 4.3 31.2 1.0 CA E:DAB402 4.3 77.8 1.0 N E:SER145 4.4 33.3 1.0 OE1 E:GLU209 4.4 53.3 1.0 CA E:HIS144 4.5 33.3 1.0 CG E:GLU61 4.6 39.2 1.0 O E:HOH523 4.6 32.0 1.0 C E:SER145 4.6 31.9 1.0 CZ E:ARG100 4.6 35.4 1.0 NE2 E:HIS58 4.7 35.5 1.0 NH2 E:ARG100 4.7 36.0 1.0 CD2 E:HIS144 4.7 33.6 1.0 NE2 E:HIS144 4.8 34.0 1.0 CD E:GLU209 4.8 52.9 1.0 O E:HOH557 4.8 29.6 1.0 CD2 E:HIS58 4.9 35.0 1.0 C E:HIS144 4.9 33.6 1.0

Zinc binding site 6 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn401 b:83.3 occ:1.00 OE2 G:GLU61 2.1 99.1 1.0 OE1 G:GLU61 2.4 93.7 1.0 CD G:GLU61 2.5 89.0 1.0 ND1 G:HIS58 2.6 42.7 1.0 ND1 G:HIS144 2.7 36.6 1.0 O G:ACT402 2.8 83.3 1.0 O G:SER145 3.4 42.9 1.0 CE1 G:HIS58 3.5 43.5 1.0 CG G:HIS144 3.5 37.5 1.0 CG G:HIS58 3.6 41.2 1.0 CB G:HIS144 3.6 36.9 1.0 CE1 G:HIS144 3.7 35.5 1.0 CB G:HIS58 3.8 38.3 1.0 C G:ACT402 3.9 83.5 1.0 NH1 G:ARG100 3.9 33.6 1.0 CG G:GLU61 4.0 75.2 1.0 N G:SER145 4.0 39.8 1.0 O G:HOH526 4.1 38.3 1.0 CA G:HIS144 4.2 38.2 1.0 CH3 G:ACT402 4.3 82.8 1.0 C G:SER145 4.5 41.1 1.0 OE1 G:GLU209 4.5 52.7 1.0 OE2 G:GLU209 4.6 53.1 1.0 NE2 G:HIS58 4.6 43.2 1.0 C G:HIS144 4.6 39.4 1.0 CD2 G:HIS58 4.6 42.5 1.0 O G:HOH541 4.7 25.2 1.0 CD2 G:HIS144 4.8 37.9 1.0 NE2 G:HIS144 4.8 37.3 1.0 N G:HIS58 4.8 42.4 1.0 CZ G:ARG100 4.9 44.1 1.0 CB G:GLU61 4.9 62.2 1.0 CA G:SER145 4.9 39.9 1.0 CA G:HIS58 5.0 39.7 1.0

Zinc binding site 7 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn401 b:0.6 occ:1.00 OXT H:ACT402 2.5 76.4 1.0 OE2 H:GLU61 2.6 47.5 1.0 ND1 H:HIS144 3.0 48.5 1.0 O H:SER145 3.0 45.2 1.0 OE1 H:GLU61 3.1 47.3 1.0 C H:ACT402 3.1 75.8 1.0 CD H:GLU61 3.2 46.8 1.0 ND1 H:HIS58 3.3 33.0 1.0 CH3 H:ACT402 3.5 75.2 1.0 CB H:HIS144 3.7 47.0 1.0 CG H:HIS144 3.7 48.7 1.0 OE2 H:GLU209 3.8 55.0 1.0 CE1 H:HIS58 3.9 33.6 1.0 NH1 H:ARG100 3.9 31.1 1.0 CE1 H:HIS144 4.0 48.6 1.0 O H:ACT402 4.1 76.0 1.0 OE1 H:GLU209 4.1 53.5 1.0 N H:SER145 4.2 43.8 1.0 C H:SER145 4.2 44.1 1.0 CG H:HIS58 4.4 31.0 1.0 CD H:GLU209 4.4 54.4 1.0 CA H:HIS144 4.4 45.8 1.0 CG H:GLU61 4.6 43.7 1.0 O H:HOH533 4.7 31.7 1.0 C H:HIS144 4.7 45.4 1.0 CB H:HIS58 4.8 31.9 1.0 CZ H:ARG100 4.8 36.7 1.0 NH2 H:ARG100 4.8 38.6 1.0 CA H:SER145 4.9 43.5 1.0 CD2 H:HIS144 4.9 50.0 1.0

Zinc binding site 8 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn401 b:95.2 occ:1.00 OE2 I:GLU61 2.6 41.8 1.0 ND1 I:HIS144 2.6 48.3 1.0 ND1 I:HIS58 2.6 33.7 1.0 O I:HOH533 2.7 49.0 1.0 OE1 I:GLU61 2.8 43.3 1.0 CD I:GLU61 3.0 40.6 1.0 CE1 I:HIS58 3.3 34.5 1.0 CG I:HIS144 3.4 47.9 1.0 CG I:HIS58 3.5 32.4 1.0 CB I:HIS144 3.5 43.1 1.0 O I:SER145 3.6 39.5 1.0 CE1 I:HIS144 3.6 49.2 1.0 O I:HOH596 3.7 31.0 1.0 CB I:HIS58 3.9 30.7 1.0 O I:HOH528 4.1 45.7 1.0 N I:SER145 4.3 36.3 1.0 CA I:HIS144 4.3 38.1 1.0 NH1 I:ARG100 4.3 41.6 1.0 NE2 I:HIS58 4.4 34.6 1.0 OE2 I:GLU209 4.5 60.5 1.0 O I:HOH534 4.5 23.6 1.0 CD2 I:HIS58 4.5 33.0 1.0 CG I:GLU61 4.5 35.5 1.0 CD2 I:HIS144 4.6 49.9 1.0 NE2 I:HIS144 4.7 50.7 1.0 C I:SER145 4.7 38.0 1.0 C I:HIS144 4.8 37.2 1.0 OE1 I:GLU209 4.9 58.2 1.0

Zinc binding site 9 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn401 b:72.2 occ:1.00 OE2 J:GLU61 2.2 83.4 1.0 OE1 J:GLU61 2.3 79.9 1.0 OXT J:DAB402 2.5 90.2 1.0 ND1 J:HIS144 2.5 34.6 1.0 CD J:GLU61 2.5 76.3 1.0 ND1 J:HIS58 2.8 31.1 1.0 C J:DAB402 3.1 89.6 1.0 O J:DAB402 3.2 89.6 1.0 CG J:HIS144 3.4 35.0 1.0 O J:SER145 3.4 39.9 1.0 CE1 J:HIS144 3.5 34.7 1.0 CB J:HIS144 3.5 34.4 1.0 CG J:HIS58 3.7 31.3 1.0 O J:HOH513 3.7 25.4 1.0 CE1 J:HIS58 3.8 32.1 1.0 CB J:HIS58 3.8 31.2 1.0 N J:SER145 4.0 35.6 1.0 CG J:GLU61 4.0 66.5 1.0 CA J:HIS144 4.0 34.9 1.0 CG J:DAB402 4.1 86.7 1.0 ND J:DAB402 4.3 85.9 1.0 NH1 J:ARG100 4.4 39.4 1.0 CA J:DAB402 4.5 88.0 1.0 C J:SER145 4.5 38.6 1.0 C J:HIS144 4.5 35.3 1.0 CD2 J:HIS144 4.6 35.6 1.0 NE2 J:HIS144 4.6 36.1 1.0 CB J:DAB402 4.6 87.4 1.0 OE2 J:GLU209 4.7 50.8 1.0 N J:HIS58 4.8 33.6 1.0 OE1 J:GLU209 4.8 48.5 1.0 CD2 J:HIS58 4.8 32.0 1.0 CB J:GLU61 4.8 57.2 1.0 NE2 J:HIS58 4.8 32.3 1.0 CA J:HIS58 4.9 32.4 1.0 CA J:SER145 4.9 37.0 1.0

Zinc binding site 10 out of 10 in the Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Product Bound Structure of the Ectoine Utilization Protein Eute (Doeb) From Ruegeria Pomeroyi within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn401 b:0.1 occ:1.00 CE1 L:HIS58 3.3 49.4 1.0 ND1 L:HIS58 3.4 48.8 1.0 OE2 L:GLU61 3.5 48.2 1.0 OE2 L:GLU209 3.6 56.7 1.0 O L:SER145 3.6 36.6 1.0 ND1 L:HIS144 3.7 44.5 1.0 OE1 L:GLU209 3.7 58.5 1.0 NH1 L:ARG100 4.0 43.2 1.0 CD L:GLU209 4.0 56.9 1.0 CB L:HIS144 4.0 38.7 1.0 OE1 L:GLU61 4.1 47.8 1.0 CD L:GLU61 4.1 46.8 1.0 CG L:HIS144 4.2 39.4 1.0 NH2 L:ARG100 4.3 50.3 1.0 NE2 L:HIS58 4.6 48.2 1.0 CZ L:ARG100 4.6 48.5 1.0 CE1 L:HIS144 4.6 39.7 1.0 C L:SER145 4.7 34.9 1.0 CG L:HIS58 4.7 45.8 1.0 N L:SER145 4.8 36.6 1.0

C.-N.Mais, L.Hermann, F.Altegoer, A.Seubert, A.A.Richter, I.Wernersbach, L.Czech, E.Bremer, G.Bange. Degradation of the Microbial Stress Protectants and Chemical Chaperones Ectoine and Hydroxyectoine By A Bacterial Hydrolase-Deacetylase Complex J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X