Zinc in PDB 6jlf: Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr

The structure of Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr, PDB code: 6jlf was solved by S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.20 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	113.970, 159.468, 161.901, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.6

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr (pdb code 6jlf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr, PDB code: 6jlf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:71.7 occ:1.00 OE2 A:GLU191 2.0 77.6 1.0 O E:HOH418 2.1 68.3 1.0 NE2 E:HIS194 2.2 50.6 1.0 O A:HOH407 2.3 47.4 1.0 OE1 A:GLU191 2.5 73.9 1.0 CD A:GLU191 2.6 69.0 1.0 CE1 E:HIS194 3.2 54.0 1.0 CD2 E:HIS194 3.2 47.0 1.0 CG A:GLU191 4.0 58.8 1.0 CG2 A:ILE91 4.2 51.4 1.0 ND1 E:HIS194 4.3 56.7 1.0 CG E:HIS194 4.3 51.6 1.0 CE A:LYS188 4.5 78.9 1.0 CD A:LYS188 4.6 71.3 1.0 CB A:ALA92 4.9 51.2 1.0 NZ A:LYS188 5.0 86.3 1.0

Zinc binding site 2 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:78.3 occ:1.00 NE2 A:HIS194 2.0 75.0 1.0 O B:HOH405 2.0 62.9 1.0 OE2 B:GLU191 2.0 93.7 1.0 O B:HOH403 2.4 72.5 1.0 OE1 B:GLU191 2.7 79.0 1.0 CD B:GLU191 2.7 81.3 1.0 CE1 A:HIS194 2.9 58.1 1.0 CD2 A:HIS194 3.1 63.3 1.0 ND1 A:HIS194 4.0 62.4 1.0 CG A:HIS194 4.2 59.1 1.0 CG B:GLU191 4.2 73.0 1.0 CD B:LYS188 4.6 76.6 1.0 CE B:LYS188 4.7 87.8 1.0 CG2 B:ILE91 4.7 57.8 1.0 CB A:ASP190 5.0 66.9 1.0

Zinc binding site 3 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:98.7 occ:1.00 ND1 A:HIS111 1.9 80.3 1.0 O A:HOH408 2.0 74.0 1.0 ND1 A:HIS108 2.6 93.4 1.0 CE1 A:HIS111 2.8 82.7 1.0 CG A:HIS111 3.0 80.5 1.0 CB A:HIS111 3.4 81.3 1.0 CG A:HIS108 3.4 86.6 1.0 CE1 A:HIS108 3.4 94.8 1.0 CA A:HIS108 3.6 85.2 1.0 CB A:HIS108 3.7 77.3 1.0 NH2 A:ARG101 3.7 99.3 1.0 O A:THR287 3.9 0.2 1.0 NE2 A:HIS111 4.0 77.7 1.0 CD2 A:HIS111 4.1 77.6 1.0 NE2 A:HIS108 4.4 92.8 1.0 CD2 A:HIS108 4.4 89.2 1.0 N A:HIS108 4.5 86.0 1.0 CG2 A:THR287 4.5 84.6 1.0 C A:HIS108 4.7 85.2 1.0 O A:HIS108 4.7 87.7 1.0 O A:PRO105 4.7 87.9 1.0 CA A:THR287 4.7 98.3 1.0 CB A:THR287 4.7 96.8 1.0 CG A:ARG101 4.8 79.9 1.0 C A:THR287 4.8 92.2 1.0 CA A:HIS111 4.9 79.6 1.0

Zinc binding site 4 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:73.2 occ:1.00 NE2 B:HIS194 2.0 69.8 1.0 O B:HOH404 2.0 63.7 1.0 O D:HOH410 2.1 55.9 1.0 OE2 D:GLU191 2.1 74.0 1.0 OE1 D:GLU191 2.5 77.5 1.0 CD D:GLU191 2.6 74.2 1.0 CD2 B:HIS194 3.0 68.7 1.0 CE1 B:HIS194 3.0 67.0 1.0 ND1 B:HIS194 4.1 67.7 1.0 CG B:HIS194 4.1 67.4 1.0 CE D:LYS188 4.1 80.5 1.0 CG D:GLU191 4.2 67.0 1.0 CD D:LYS188 4.5 77.3 1.0 CG2 D:ILE91 4.6 61.1 1.0 CB B:ASP190 4.8 73.1 1.0

Zinc binding site 5 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.1 occ:1.00 ND1 B:HIS108 2.0 0.4 1.0 CD2 B:HIS111 2.3 91.6 1.0 CE1 B:HIS108 3.0 0.3 1.0 CG B:HIS108 3.1 95.4 1.0 CG B:HIS111 3.2 89.3 1.0 NE2 B:HIS111 3.3 92.9 1.0 CB B:HIS108 3.5 96.8 1.0 CB B:HIS111 3.7 82.5 1.0 CA B:HIS108 3.8 95.1 1.0 NE2 B:HIS108 4.1 0.0 1.0 CD2 B:HIS108 4.2 94.7 1.0 CG2 B:THR287 4.2 84.5 1.0 CB B:THR287 4.3 92.7 1.0 ND1 B:HIS111 4.4 89.2 1.0 CE1 B:HIS111 4.4 88.0 1.0 N B:HIS108 4.5 96.8 1.0 O B:THR287 4.6 0.3 1.0 CA B:THR287 4.7 96.7 1.0 O B:PRO105 4.8 98.5 1.0 C B:HIS108 4.9 92.4 1.0 O B:HIS108 4.9 96.1 1.0

Zinc binding site 6 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:77.8 occ:1.00 ND1 C:HIS111 2.1 70.8 1.0 ND1 C:HIS108 2.5 80.4 1.0 CE1 C:HIS111 3.0 70.5 1.0 CG C:HIS111 3.1 63.7 1.0 CE1 C:HIS108 3.3 75.2 1.0 CB C:HIS111 3.5 63.5 1.0 CG C:HIS108 3.5 76.4 1.0 CB C:HIS108 3.9 68.6 1.0 CA C:HIS108 3.9 72.3 1.0 NE2 C:HIS111 4.2 73.6 1.0 O C:THR287 4.2 73.8 1.0 CB C:THR287 4.2 72.8 1.0 CD2 C:HIS111 4.2 67.1 1.0 CG2 C:THR287 4.5 66.4 1.0 NE2 C:HIS108 4.5 83.1 1.0 CA C:THR287 4.6 72.3 1.0 CD2 C:HIS108 4.6 77.2 1.0 O C:HIS108 4.7 69.7 1.0 N C:HIS108 4.8 73.2 1.0 C C:THR287 4.8 73.0 1.0 C C:HIS108 4.8 70.4 1.0 NE C:ARG101 4.9 93.7 1.0 O C:PRO105 5.0 76.7 1.0 CA C:HIS111 5.0 62.5 1.0

Zinc binding site 7 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:76.0 occ:1.00 NE2 D:HIS194 2.1 57.2 1.0 OE1 C:GLU191 2.1 71.7 1.0 CD C:GLU191 2.8 72.8 1.0 OE2 C:GLU191 2.8 80.4 1.0 CE1 D:HIS194 2.9 50.3 1.0 CD2 D:HIS194 3.2 51.4 1.0 ND1 D:HIS194 4.1 48.5 1.0 CG C:GLU191 4.2 60.5 1.0 CG D:HIS194 4.3 50.1 1.0 CE C:LYS188 4.4 83.5 1.0 CG2 C:ILE91 4.6 49.8 1.0 CB D:ASP190 4.9 59.5 1.0 NZ C:LYS188 4.9 74.9 1.0

Zinc binding site 8 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.2 occ:1.00 CD2 D:HIS235 2.6 0.7 1.0 NE2 D:HIS235 3.2 0.9 1.0 CG D:HIS235 3.6 1.0 1.0 CB D:HIS235 4.3 0.9 1.0 CE1 D:HIS235 4.3 1.0 1.0 ND1 D:HIS235 4.5 0.6 1.0 CB B:HIS51 4.8 0.8 1.0

Zinc binding site 9 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:85.2 occ:1.00 ND1 D:HIS108 2.1 74.5 1.0 ND1 D:HIS111 2.3 81.2 1.0 CG D:HIS108 2.9 78.5 1.0 CB D:HIS108 3.1 85.9 1.0 CG D:HIS111 3.2 79.5 1.0 CE1 D:HIS111 3.2 82.0 1.0 CE1 D:HIS108 3.2 83.8 1.0 CA D:HIS108 3.3 86.5 1.0 CB D:HIS111 3.5 77.1 1.0 CD D:ARG101 4.1 88.1 1.0 CD2 D:HIS108 4.2 86.1 1.0 N D:HIS108 4.2 86.6 1.0 NE2 D:HIS108 4.3 87.9 1.0 C D:HIS108 4.3 84.1 1.0 NE2 D:HIS111 4.4 83.5 1.0 O D:HIS108 4.4 85.0 1.0 CD2 D:HIS111 4.4 81.0 1.0 NH2 D:ARG101 4.7 93.0 1.0 O D:PRO105 4.9 87.6 1.0 C D:GLU107 4.9 84.8 1.0

Zinc binding site 10 out of 11 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae D179A Mutation - Hr


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 D179A Mutation - Hr within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:70.2 occ:1.00 O E:HOH417 1.8 67.0 1.0 CE1 C:HIS194 2.1 62.0 1.0 O E:HOH413 2.1 54.2 1.0 OE2 E:GLU191 2.4 72.3 1.0 OE1 E:GLU191 2.4 75.7 1.0 CD E:GLU191 2.7 73.3 1.0 NE2 C:HIS194 2.8 55.2 1.0 ND1 C:HIS194 3.2 59.0 1.0 CD2 C:HIS194 4.0 51.3 1.0 CG E:GLU191 4.2 63.5 1.0 CG C:HIS194 4.2 59.1 1.0 CD E:LYS188 4.6 75.7 1.0 CG2 E:ILE91 4.7 50.0 1.0 OG1 E:THR95 4.9 78.0 1.0 CB C:ASP190 4.9 62.8 1.0 CB E:ALA92 5.0 54.7 1.0 CE E:LYS188 5.0 86.7 1.0

C.Ji, A.Kittredge, A.Hopiavuori, N.Ward, S.Chen, Y.Fukuda, Y.Zhang, T.Yang. Dual CA2+-Dependent Gates in Human BESTROPHIN1 Underlie Disease-Causing Mechanisms of Gain-of-Function Mutations. Commun Biol V. 2 240 2019.
ISSN: ESSN 2399-3642
PubMed: 31263784
DOI: 10.1038/S42003-019-0433-3