Zinc in PDB 5x87: Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T

The structure of Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T, PDB code: 5x87 was solved by Y.Zhang, S.Chen, T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.73 / 3.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.485, 160.573, 162.657, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T (pdb code 5x87). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T, PDB code: 5x87:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:74.3 occ:1.00 O A:HOH403 2.1 87.7 1.0 NE2 E:HIS194 2.2 78.6 1.0 OE2 A:GLU191 2.3 84.9 1.0 O A:HOH402 2.4 52.5 1.0 OE1 A:GLU191 2.8 88.4 1.0 CD A:GLU191 2.8 84.6 1.0 CD2 E:HIS194 3.1 56.2 1.0 CE1 E:HIS194 3.1 60.5 1.0 ND1 E:HIS194 4.2 52.1 1.0 CG E:HIS194 4.2 48.4 1.0 CG A:GLU191 4.2 70.1 1.0 CD A:LYS188 4.5 67.4 1.0 CG2 A:ILE91 4.5 46.9 1.0 CE A:LYS188 4.5 85.7 1.0 CB E:ASP190 4.7 83.1 1.0 OD2 E:ASP190 4.8 0.5 1.0 CG E:ASP190 4.8 0.3 1.0 O E:ASP190 5.0 62.4 1.0 OG1 A:THR95 5.0 72.9 1.0

Zinc binding site 2 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:77.9 occ:1.00 NE2 A:HIS194 2.3 63.6 1.0 O B:HOH401 2.3 51.9 1.0 O A:HOH406 2.4 59.1 1.0 OE1 B:GLU191 2.5 93.3 1.0 OE2 B:GLU191 2.8 89.3 1.0 CD B:GLU191 3.0 86.9 1.0 CD2 A:HIS194 3.1 59.6 1.0 CE1 A:HIS194 3.4 67.4 1.0 CG A:HIS194 4.3 51.6 1.0 ND1 A:HIS194 4.4 59.5 1.0 CG B:GLU191 4.5 66.8 1.0 CE B:LYS188 4.5 95.3 1.0 CG2 B:ILE91 4.7 46.0 1.0 CD B:LYS188 4.9 75.4 1.0 CB A:ASP190 5.0 83.3 1.0

Zinc binding site 3 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:83.6 occ:1.00 O A:HOH404 2.1 83.8 1.0 O A:HOH405 2.1 69.6 1.0 ND1 A:HIS111 2.3 82.9 1.0 ND1 A:HIS108 2.7 0.2 1.0 CE1 A:HIS111 3.1 86.7 1.0 CG A:HIS111 3.4 83.2 1.0 CG A:HIS108 3.5 0.5 1.0 CA A:HIS108 3.6 0.4 1.0 CE1 A:HIS108 3.7 0.4 1.0 CB A:HIS108 3.7 0.3 1.0 CB A:HIS111 3.7 88.8 1.0 O A:HIS108 4.3 79.5 1.0 NE2 A:HIS111 4.3 84.7 1.0 CD2 A:HIS111 4.4 83.6 1.0 C A:HIS108 4.5 0.8 1.0 N A:HIS108 4.6 0.9 1.0 CD2 A:HIS108 4.7 0.4 1.0 NE2 A:HIS108 4.7 0.6 1.0 O A:GLU107 4.8 99.8 1.0 O A:PRO105 5.0 90.2 1.0

Zinc binding site 4 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:91.9 occ:1.00 OD2 A:ASP261 2.0 0.8 1.0 OD2 A:ASP269 2.3 86.1 1.0 CG A:ASP261 3.0 0.8 1.0 CG A:ASP269 3.1 94.6 1.0 OD1 A:ASP269 3.2 96.2 1.0 CB A:ASP261 3.4 0.8 1.0 CB A:ALA266 3.5 0.8 1.0 O A:ASP261 3.9 89.4 1.0 N A:ALA266 4.0 76.1 1.0 CA A:GLY264 4.1 68.5 1.0 OD1 A:ASP261 4.2 0.1 1.0 N A:THR265 4.3 69.0 1.0 CA A:ALA266 4.4 95.5 1.0 CB A:ASP269 4.5 94.1 1.0 CA A:ASP261 4.6 96.6 1.0 C A:GLY264 4.6 66.8 1.0 C A:ASP261 4.7 92.4 1.0 N A:GLY264 4.7 53.6 1.0

Zinc binding site 5 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.3 occ:1.00 CB B:HIS235 2.7 0.5 1.0 CD2 B:HIS235 3.0 0.1 1.0 CG B:HIS235 3.1 0.9 1.0 O B:HOH402 3.1 91.4 1.0 CA B:HIS235 3.5 0.6 1.0 CD2 B:TYR42 4.0 0.1 1.0 C B:HIS235 4.1 0.7 1.0 O B:HIS235 4.1 0.4 1.0 NE2 B:HIS235 4.4 0.4 1.0 ND1 B:HIS235 4.5 0.5 1.0 CE2 B:TYR42 4.5 0.4 1.0 N B:HIS235 4.8 0.3 1.0 CG B:TYR42 4.9 99.2 1.0 O B:VAL231 4.9 0.5 1.0

Zinc binding site 6 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:84.9 occ:1.00 NE2 B:HIS194 2.1 71.3 1.0 O D:HOH405 2.2 59.3 1.0 O D:HOH407 2.4 81.2 1.0 OE1 D:GLU191 2.5 99.0 1.0 OE2 D:GLU191 2.7 0.1 1.0 CD D:GLU191 2.9 98.4 1.0 CD2 B:HIS194 3.0 55.5 1.0 CE1 B:HIS194 3.2 70.7 1.0 NZ D:LYS188 3.9 0.5 1.0 CG B:HIS194 4.2 52.3 1.0 ND1 B:HIS194 4.3 66.1 1.0 CG D:GLU191 4.4 84.5 1.0 CG2 D:ILE91 4.6 56.3 1.0 CD D:LYS188 4.8 60.8 1.0 CB B:ASP190 4.8 78.2 1.0 CE D:LYS188 4.9 87.2 1.0

Zinc binding site 7 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:74.3 occ:1.00 ND1 B:HIS108 2.1 0.5 1.0 ND1 B:HIS111 2.3 75.9 1.0 CE1 B:HIS108 2.8 0.2 1.0 CG B:HIS111 3.2 75.9 1.0 CG B:HIS108 3.3 0.2 1.0 CE1 B:HIS111 3.3 75.9 1.0 CB B:HIS111 3.4 67.6 1.0 CA B:HIS108 3.8 85.7 1.0 CB B:HIS108 3.8 85.2 1.0 NE2 B:HIS108 4.0 0.4 1.0 NH2 B:ARG101 4.1 0.1 1.0 CD2 B:HIS108 4.3 0.5 1.0 CA B:GLY288 4.3 0.1 1.0 CD2 B:HIS111 4.4 75.3 1.0 NE2 B:HIS111 4.4 73.0 1.0 CD B:ARG101 4.5 98.6 1.0 N B:HIS108 4.6 94.6 1.0 O B:HIS108 4.6 0.1 1.0 C B:HIS108 4.7 91.5 1.0 CZ B:ARG101 4.9 0.6 1.0 CA B:HIS111 4.9 76.4 1.0 N B:GLY288 5.0 1.0 1.0 O B:PRO105 5.0 0.8 1.0

Zinc binding site 8 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:61.2 occ:1.00 NE2 D:HIS194 2.1 67.4 1.0 OE1 C:GLU191 2.4 91.7 1.0 O C:HOH403 2.6 52.6 1.0 OE2 C:GLU191 2.7 91.0 1.0 CD C:GLU191 2.9 82.8 1.0 CD2 D:HIS194 3.0 65.8 1.0 NZ C:LYS188 3.2 98.0 1.0 CE1 D:HIS194 3.2 72.9 1.0 CG D:HIS194 4.2 55.5 1.0 ND1 D:HIS194 4.2 67.4 1.0 CG C:GLU191 4.4 60.9 1.0 CE C:LYS188 4.5 84.2 1.0 CG2 C:ILE91 4.6 60.0 1.0 CD C:LYS188 4.7 70.3 1.0 CB D:ASP190 4.8 87.9 1.0 O D:ASP190 4.9 68.2 1.0 O D:HOH409 4.9 77.7 1.0

Zinc binding site 9 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:79.9 occ:1.00 NE2 C:HIS194 2.4 61.2 1.0 O C:HOH402 2.6 73.2 1.0 OE1 E:GLU191 2.6 79.5 1.0 OE2 E:GLU191 2.7 74.0 1.0 OD2 C:ASP190 2.8 0.9 1.0 CD E:GLU191 3.0 70.5 1.0 CD2 C:HIS194 3.2 58.4 1.0 CE1 C:HIS194 3.4 63.5 1.0 CG C:ASP190 3.6 0.8 1.0 OD1 C:ASP190 3.8 0.8 1.0 CD E:LYS188 4.2 83.7 1.0 CE E:LYS188 4.2 0.9 1.0 CG C:HIS194 4.3 58.7 1.0 ND1 C:HIS194 4.4 65.7 1.0 CG E:GLU191 4.5 68.5 1.0 CG2 E:ILE91 4.5 64.4 1.0 OG1 E:THR95 4.6 90.9 1.0 O C:ASP190 4.8 50.6 1.0 NZ E:LYS188 4.9 0.9 1.0 CB C:ASP190 5.0 61.9 1.0

Zinc binding site 10 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T


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 Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation L177T within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:71.5 occ:1.00 ND1 C:HIS111 2.0 91.2 1.0 ND1 C:HIS108 2.0 92.3 1.0 O C:HOH405 2.2 54.8 1.0 O C:HOH404 2.8 66.9 1.0 CE1 C:HIS108 2.9 86.3 1.0 CE1 C:HIS111 3.0 80.8 1.0 CG C:HIS111 3.1 84.5 1.0 CG C:HIS108 3.1 90.8 1.0 CB C:HIS111 3.4 83.8 1.0 CB C:HIS108 3.6 91.5 1.0 CA C:HIS108 3.7 84.2 1.0 NE2 C:HIS108 4.0 89.6 1.0 NE2 C:HIS111 4.1 82.7 1.0 CD2 C:HIS111 4.2 77.4 1.0 CD2 C:HIS108 4.2 93.6 1.0 NE C:ARG101 4.2 79.8 1.0 NH1 C:ARG101 4.4 0.1 1.0 N C:HIS108 4.6 92.1 1.0 CZ C:ARG101 4.6 98.7 1.0 O C:HIS108 4.7 93.0 1.0 C C:HIS108 4.7 90.1 1.0 CA C:HIS111 5.0 73.1 1.0

Y.Li, Y.Zhang, Y.Xu, A.Kittredge, N.Ward, S.Chen, S.H.Tsang, T.Yang. Patient-Specific Mutations Impair BESTROPHIN1'S Essential Role in Mediating CA2+-Dependent Cl-Currents in Human Rpe. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 29063836
DOI: 10.7554/ELIFE.29914