Zinc in PDB 8f1b: Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae

The structure of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae, PDB code: 8f1b was solved by D.W.Valencia, E.T.Yukl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.67 / 2.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.991, 66.914, 88.242, 90, 99.92, 90
R / Rfree (%)	21.8 / 26.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Zinc atom in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae (pdb code 8f1b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 21 binding sites of Zinc where determined in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae, PDB code: 8f1b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:32.9 occ:1.00 NE2 A:HIS35 2.0 33.5 1.0 NE2 A:HIS37 2.0 37.5 1.0 OE1 A:GLU66 2.1 34.2 1.0 O A:HOH421 2.1 29.1 1.0 OE2 A:GLU66 2.1 31.1 1.0 CD A:GLU66 2.4 31.4 1.0 CD2 A:HIS35 3.0 36.8 1.0 CD2 A:HIS37 3.0 35.2 1.0 CE1 A:HIS35 3.0 35.1 1.0 CE1 A:HIS37 3.0 39.5 1.0 CG A:GLU66 3.9 32.8 1.0 CG A:HIS35 4.1 38.9 1.0 ND1 A:HIS35 4.1 38.3 1.0 ND1 A:HIS37 4.1 38.9 1.0 CG A:HIS37 4.1 34.4 1.0 CA A:GLY123 4.5 61.3 1.0 O A:GLY185 4.6 33.7 1.0 CB A:GLU66 4.6 33.2 1.0 N A:GLY185 4.7 54.0 1.0

Zinc binding site 2 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:34.6 occ:1.00 ND1 D:HIS118 2.0 36.5 1.0 OE2 A:GLU196 2.0 28.9 1.0 ND1 A:HIS49 2.1 34.9 1.0 NE2 A:HIS194 2.1 32.1 1.0 OE1 A:GLU196 2.1 35.5 1.0 CD A:GLU196 2.3 30.3 1.0 CE1 D:HIS118 2.9 37.8 1.0 CE1 A:HIS49 3.0 36.6 1.0 CE1 A:HIS194 3.0 29.7 1.0 CD2 A:HIS194 3.0 29.5 1.0 CG A:HIS49 3.1 36.9 1.0 CG D:HIS118 3.1 34.3 1.0 CB A:HIS49 3.4 34.0 1.0 CB D:HIS118 3.5 33.3 1.0 CA D:HIS118 3.6 34.8 1.0 CG A:GLU196 3.8 32.0 1.0 NE2 D:HIS118 4.1 35.3 1.0 NE2 A:HIS49 4.1 36.2 1.0 ND1 A:HIS194 4.1 29.3 1.0 CD2 A:HIS49 4.1 37.5 1.0 CA A:GLU196 4.1 34.6 1.0 CG A:HIS194 4.1 30.6 1.0 CD2 D:HIS118 4.1 35.5 1.0 N D:SER119 4.2 30.9 1.0 CB A:GLU196 4.4 33.5 1.0 C D:HIS118 4.5 33.3 1.0 O A:CYS195 4.7 30.2 1.0 N D:HIS118 4.7 37.7 1.0 N A:GLU196 4.8 30.6 1.0 O D:GLN117 4.8 39.7 1.0 CA A:HIS49 4.9 32.8 1.0 C A:CYS195 5.0 29.1 1.0

Zinc binding site 3 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:33.4 occ:1.00 NE2 A:HIS87 2.0 28.8 1.0 NE2 A:HIS86 2.0 27.7 1.0 OE2 A:GLU83 2.0 30.1 1.0 OE2 D:GLU79 2.1 37.3 1.0 OE1 D:GLU79 2.1 37.0 1.0 CD D:GLU79 2.4 36.8 1.0 CE1 A:HIS87 2.9 28.7 1.0 CE1 A:HIS86 3.0 26.4 1.0 CD2 A:HIS87 3.0 27.9 1.0 CD A:GLU83 3.0 32.2 1.0 CD2 A:HIS86 3.0 28.9 1.0 CG A:GLU83 3.5 32.3 1.0 O A:GLU83 3.7 30.5 1.0 CG D:GLU79 3.9 35.6 1.0 ND1 A:HIS87 4.0 28.5 1.0 OE1 A:GLU83 4.1 34.9 1.0 CG A:HIS87 4.1 25.5 1.0 ND1 A:HIS86 4.1 25.6 1.0 CG A:HIS86 4.1 26.9 1.0 C A:GLU83 4.6 27.8 1.0 CB D:GLU79 4.8 36.5 1.0 CB A:GLU83 4.8 29.5 1.0 CA A:GLU83 4.9 27.2 1.0

Zinc binding site 4 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:40.4 occ:1.00 NE2 B:HIS37 1.9 37.5 1.0 NE2 B:HIS35 2.1 38.4 1.0 OE1 B:GLU66 2.1 42.3 1.0 O B:HOH421 2.1 38.9 1.0 OE2 B:GLU66 2.1 35.3 1.0 CD B:GLU66 2.4 35.7 1.0 CE1 B:HIS35 2.9 40.8 1.0 CE1 B:HIS37 2.9 38.7 1.0 CD2 B:HIS37 2.9 37.2 1.0 CD2 B:HIS35 3.1 38.7 1.0 CG B:GLU66 3.9 37.6 1.0 ND1 B:HIS37 4.0 38.2 1.0 ND1 B:HIS35 4.1 42.5 1.0 CG B:HIS37 4.1 37.5 1.0 CG B:HIS35 4.2 42.6 1.0 CB B:GLU66 4.7 39.1 1.0 O B:GLY123 4.7 78.0 1.0 O B:GLY185 4.7 37.8 1.0 CB B:PRO58 4.9 27.5 1.0

Zinc binding site 5 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:62.1 occ:0.86 NE2 B:HIS67 2.1 46.9 1.0 CE1 B:HIS67 3.0 47.9 1.0 CD2 B:HIS67 3.2 44.9 1.0 CB B:PHE65 4.1 34.5 1.0 ND1 B:HIS67 4.1 46.6 1.0 CG B:HIS67 4.2 46.3 1.0 OE1 B:GLN74 4.7 47.2 1.0 NE2 B:GLN74 4.8 54.0 1.0 CG B:PHE65 5.0 34.8 1.0

Zinc binding site 6 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:40.0 occ:1.00 NE2 B:HIS87 1.9 40.3 1.0 NE2 B:HIS86 1.9 40.3 1.0 OE2 B:GLU83 2.0 35.5 1.0 CE1 B:HIS86 2.8 40.8 1.0 CE1 B:HIS87 2.9 36.7 1.0 CD2 B:HIS87 2.9 36.6 1.0 CD2 B:HIS86 2.9 36.3 1.0 CD B:GLU83 3.2 36.3 1.0 ND1 B:HIS86 3.9 37.9 1.0 ND1 B:HIS87 4.0 34.9 1.0 OE1 B:GLU83 4.0 42.4 1.0 CG B:HIS87 4.0 32.8 1.0 CG B:HIS86 4.0 35.6 1.0 O B:GLU83 4.0 35.0 1.0 CG B:GLU83 4.1 37.4 1.0 C B:GLU83 4.9 33.1 1.0

Zinc binding site 7 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:51.4 occ:0.72 ND1 B:HIS49 2.0 53.5 1.0 OE2 B:GLU196 2.1 44.6 1.0 NE2 B:HIS194 2.3 46.8 1.0 CD B:GLU196 2.8 44.8 1.0 OE1 B:GLU196 2.9 44.8 1.0 CE1 B:HIS49 2.9 51.0 1.0 CG B:HIS49 3.1 50.8 1.0 CE1 B:HIS194 3.3 46.1 1.0 CD2 B:HIS194 3.3 41.8 1.0 CB B:HIS49 3.5 47.5 1.0 NE2 B:HIS49 4.1 50.0 1.0 CD2 B:HIS49 4.2 51.0 1.0 CG B:GLU196 4.3 48.0 1.0 O1 B:PGE301 4.3 61.4 1.0 ND1 B:HIS194 4.4 41.5 1.0 CG B:HIS194 4.4 40.3 1.0 C1 B:PGE301 4.5 66.8 1.0 CA B:GLU196 4.8 49.8 1.0 CA B:HIS49 5.0 42.0 1.0

Zinc binding site 8 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:31.5 occ:1.00 NE2 C:HIS35 1.9 31.5 1.0 OE2 C:GLU66 2.0 23.9 1.0 NE2 C:HIS37 2.0 36.0 1.0 O C:HOH418 2.1 30.3 1.0 CD C:GLU66 2.8 23.8 1.0 CD2 C:HIS35 2.9 34.0 1.0 CE1 C:HIS35 2.9 31.1 1.0 OE1 C:GLU66 3.0 22.2 1.0 CD2 C:HIS37 3.0 35.7 1.0 CE1 C:HIS37 3.0 37.0 1.0 CG C:HIS35 4.0 35.9 1.0 ND1 C:HIS35 4.0 32.9 1.0 ND1 C:HIS37 4.1 37.6 1.0 CG C:HIS37 4.1 35.9 1.0 CG C:GLU66 4.2 25.8 1.0 O C:GLY185 4.3 36.7 1.0 CA C:GLY123 4.5 61.4 1.0 N C:GLY185 4.6 48.3 1.0 CB C:GLU66 4.6 26.4 1.0 C C:GLY123 4.7 55.2 1.0 CB C:PRO58 4.9 28.9 1.0 CE2 C:TYR122 5.0 85.2 1.0

Zinc binding site 9 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:38.6 occ:1.00 NE2 C:HIS87 1.9 34.2 1.0 NE2 C:HIS86 2.0 31.9 1.0 OE1 C:GLU83 2.0 45.8 1.0 OE1 E:GLU79 2.1 42.9 1.0 OE2 E:GLU79 2.1 41.8 1.0 CD E:GLU79 2.4 36.9 1.0 CE1 C:HIS87 2.8 34.4 1.0 CD2 C:HIS87 2.8 33.5 1.0 CD2 C:HIS86 2.9 33.5 1.0 CE1 C:HIS86 3.0 34.0 1.0 CD C:GLU83 3.1 43.6 1.0 CG E:GLU79 3.9 38.3 1.0 OE2 C:GLU83 3.9 50.4 1.0 ND1 C:HIS87 3.9 30.8 1.0 CG C:HIS87 3.9 31.3 1.0 O C:GLU83 4.0 31.9 1.0 CG C:HIS86 4.1 30.9 1.0 ND1 C:HIS86 4.1 32.3 1.0 CG C:GLU83 4.1 38.2 1.0 O E:HOH404 4.3 22.0 1.0 CB E:GLU79 4.8 36.0 1.0 C C:GLU83 4.8 29.6 1.0 CA C:GLU83 4.9 31.9 1.0

Zinc binding site 10 out of 21 in the Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Zinc-Bound Zrga Deletion 124-184 From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:54.0 occ:0.35 NE2 C:HIS194 2.0 54.2 1.0 OE2 C:GLU196 2.1 53.2 1.0 OE1 C:GLU196 2.1 62.0 1.0 ND1 C:HIS49 2.2 66.3 1.0 CD C:GLU196 2.3 60.3 1.0 CE1 C:HIS194 2.9 53.0 1.0 CD2 C:HIS194 3.1 48.5 1.0 CE1 C:HIS49 3.1 67.7 1.0 CG C:HIS49 3.2 67.7 1.0 CB C:HIS49 3.6 63.0 1.0 CG C:GLU196 3.8 64.2 1.0 ND1 C:HIS194 4.0 49.3 1.0 CG C:HIS194 4.1 50.0 1.0 NE2 C:HIS49 4.2 72.0 1.0 CD2 C:HIS49 4.3 72.0 1.0 CA C:GLU196 4.4 62.1 1.0 O C:CYS195 4.5 54.2 1.0 CB C:GLU196 4.6 63.6 1.0 N C:GLU196 4.9 56.4 1.0 C C:CYS195 4.9 51.9 1.0

D.W.Valencia, A.B.Melendez, I.A.Melendrez, E.T.Yukl. Structure and Function of the Zinc Binding Protein Zrga From Vibrio Cholerae. Int J Mol Sci V. 24 2022.
ISSN: ESSN 1422-0067
PubMed: 36613986
DOI: 10.3390/IJMS24010548