Zinc in PDB 6ivr: Crystal Structure of A Membrane Protein W16A

The structure of Crystal Structure of A Membrane Protein W16A, PDB code: 6ivr was solved by A.Kittredge, F.Fukuda, Y.Zhang, T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.73 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	113.914, 159.568, 161.724, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.8

The structure of Crystal Structure of A Membrane Protein W16A also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Membrane Protein W16A (pdb code 6ivr). 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 Membrane Protein W16A, PDB code: 6ivr:
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 Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:65.0 occ:1.00 NE2 E:HIS194 2.0 49.7 1.0 OE2 A:GLU191 2.1 68.7 1.0 CL A:CL305 2.1 67.1 1.0 O E:HOH408 2.3 58.8 1.0 OE1 A:GLU191 2.7 62.9 1.0 CD A:GLU191 2.7 65.8 1.0 CD2 E:HIS194 2.9 45.9 1.0 CE1 E:HIS194 3.1 54.7 1.0 CE A:LYS188 3.7 75.5 1.0 CG E:HIS194 4.1 41.8 1.0 CG A:GLU191 4.1 54.2 1.0 ND1 E:HIS194 4.1 56.2 1.0 NZ A:LYS188 4.2 75.3 1.0 CD A:LYS188 4.2 73.6 1.0 CG2 A:ILE91 4.6 43.9 1.0 CB E:ASP190 4.7 54.7 1.0

Zinc binding site 2 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:72.0 occ:1.00 ND1 A:HIS111 2.0 72.3 1.0 CL A:CL307 2.1 80.1 1.0 ND1 A:HIS108 2.2 87.9 1.0 CL A:CL308 2.4 84.8 1.0 CE1 A:HIS111 3.0 72.1 1.0 CG A:HIS108 3.0 82.2 1.0 CG A:HIS111 3.1 73.7 1.0 CE1 A:HIS108 3.2 84.0 1.0 CB A:HIS108 3.2 71.9 1.0 CA A:HIS108 3.3 73.8 1.0 CB A:HIS111 3.4 66.0 1.0 NE2 A:HIS111 4.1 71.9 1.0 CD2 A:HIS108 4.1 76.7 1.0 N A:HIS108 4.2 77.4 1.0 CD2 A:HIS111 4.2 71.1 1.0 NE2 A:HIS108 4.2 88.3 1.0 CG2 A:THR287 4.4 69.0 1.0 C A:HIS108 4.4 76.0 1.0 O A:HIS108 4.4 76.9 1.0 C A:GLU107 4.8 74.6 1.0 O A:GLU107 4.8 76.8 1.0 CB A:THR287 4.9 83.1 1.0 CA A:HIS111 4.9 65.5 1.0

Zinc binding site 3 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:74.6 occ:1.00 OD2 A:ASP269 2.0 63.5 1.0 OD2 A:ASP261 2.3 74.6 1.0 OD1 A:ASP261 2.4 84.8 1.0 CG A:ASP261 2.6 75.8 1.0 CG A:ASP269 3.0 61.4 1.0 CL A:CL309 3.1 93.6 1.0 OD1 A:ASP269 3.3 74.7 1.0 CB A:ALA266 3.4 63.7 1.0 CA A:GLY264 3.8 55.8 1.0 N A:ALA266 3.8 71.1 1.0 N A:THR265 4.0 67.8 1.0 O A:ASP261 4.0 64.5 1.0 CB A:ASP261 4.1 70.2 1.0 C A:GLY264 4.2 58.7 1.0 CA A:ALA266 4.3 70.0 1.0 CB A:ASP269 4.3 67.2 1.0 N A:GLY264 4.5 58.4 1.0 C A:THR265 4.9 68.0 1.0 C A:ASP261 4.9 66.5 1.0 CA A:ASP261 5.0 76.2 1.0

Zinc binding site 4 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:74.4 occ:1.00 CL B:CL306 2.0 73.2 1.0 NE2 A:HIS194 2.2 46.4 1.0 OE1 B:GLU191 2.4 58.8 1.0 CL A:CL306 2.4 88.5 1.0 OE2 B:GLU191 2.4 69.3 1.0 CD B:GLU191 2.7 66.2 1.0 CE1 A:HIS194 3.2 51.5 1.0 CD2 A:HIS194 3.2 46.6 1.0 NZ B:LYS188 3.4 74.4 1.0 CG B:GLU191 4.2 60.0 1.0 ND1 A:HIS194 4.3 54.0 1.0 CG A:HIS194 4.4 49.7 1.0 CE B:LYS188 4.5 63.4 1.0 CD B:LYS188 4.6 56.2 1.0 CG2 B:ILE91 4.6 38.6 1.0 CB A:ASP190 4.9 57.6 1.0

Zinc binding site 5 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.2 occ:1.00 ND1 B:HIS235 2.3 0.4 1.0 O B:HOH402 3.0 0.4 1.0 CG B:HIS235 3.1 0.7 1.0 CB B:HIS235 3.2 0.1 1.0 CE1 B:HIS235 3.4 0.6 1.0 CD1 B:ILE39 3.4 0.0 1.0 CA B:HIS235 3.5 0.0 1.0 CD2 B:TYR42 3.8 0.9 1.0 CE2 B:TYR42 4.2 0.0 1.0 C B:HIS235 4.3 0.7 1.0 CD2 B:HIS235 4.3 0.8 1.0 NE2 B:HIS235 4.4 0.6 1.0 OE1 B:GLN43 4.6 0.5 1.0 CG2 B:VAL231 4.7 0.1 1.0 N B:HIS235 4.7 0.2 1.0 CG1 B:ILE39 4.7 0.3 1.0 O B:HIS235 4.8 0.1 1.0 N B:TYR236 4.8 0.9 1.0 CG B:TYR42 4.8 0.6 1.0

Zinc binding site 6 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:73.8 occ:1.00 CL D:CL304 2.0 77.2 1.0 NE2 B:HIS194 2.1 56.6 1.0 O B:HOH411 2.2 70.2 1.0 OE1 D:GLU191 2.4 69.4 1.0 OE2 D:GLU191 2.6 74.5 1.0 CD D:GLU191 2.8 69.7 1.0 CD2 B:HIS194 3.0 53.3 1.0 CE1 B:HIS194 3.1 53.5 1.0 NZ D:LYS188 3.8 79.5 1.0 CG B:HIS194 4.2 49.5 1.0 O B:HOH413 4.2 65.6 1.0 ND1 B:HIS194 4.2 56.5 1.0 CG D:GLU191 4.3 59.1 1.0 CG2 D:ILE91 4.6 49.6 1.0 O D:HOH407 4.6 55.5 1.0 CD D:LYS188 4.7 63.5 1.0 CB B:ASP190 4.7 64.8 1.0 CE D:LYS188 4.8 71.4 1.0

Zinc binding site 7 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:70.0 occ:1.00 ND1 B:HIS111 2.0 60.2 1.0 O B:ACY305 2.0 66.6 1.0 NE2 B:HIS290 2.1 76.0 1.0 ND1 B:HIS108 2.1 76.4 1.0 C B:ACY305 2.6 74.0 1.0 OXT B:ACY305 2.7 74.8 1.0 CE1 B:HIS111 2.9 66.3 1.0 CE1 B:HIS108 2.9 74.0 1.0 CE1 B:HIS290 2.9 77.1 1.0 CG B:HIS111 3.1 62.1 1.0 CD2 B:HIS290 3.1 75.8 1.0 CG B:HIS108 3.3 70.5 1.0 CB B:HIS111 3.5 58.4 1.0 CB B:HIS108 3.8 68.0 1.0 CA B:HIS108 3.8 66.0 1.0 NE2 B:HIS111 4.0 61.7 1.0 ND1 B:HIS290 4.1 78.0 1.0 NE2 B:HIS108 4.1 71.8 1.0 CD2 B:HIS111 4.2 63.0 1.0 CH3 B:ACY305 4.2 72.7 1.0 O B:GLY288 4.2 92.4 1.0 CG B:HIS290 4.2 80.0 1.0 CD2 B:HIS108 4.3 71.0 1.0 O B:PRO105 4.3 66.5 1.0 N B:HIS108 4.5 67.2 1.0 CG B:ARG101 4.6 57.2 1.0 NE B:ARG101 4.6 79.3 1.0 O B:HIS108 4.9 68.7 1.0 C B:HIS108 4.9 67.4 1.0

Zinc binding site 8 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:62.3 occ:1.00 NE2 D:HIS194 2.0 54.1 1.0 O C:HOH404 2.0 56.6 1.0 CL C:CL305 2.1 61.9 1.0 OE2 C:GLU191 2.2 61.4 1.0 OE1 C:GLU191 2.6 61.4 1.0 CD C:GLU191 2.7 66.5 1.0 CD2 D:HIS194 2.9 54.2 1.0 CE1 D:HIS194 3.0 53.5 1.0 NZ C:LYS188 3.6 68.6 1.0 CG D:HIS194 4.1 54.3 1.0 ND1 D:HIS194 4.1 54.7 1.0 CG C:GLU191 4.2 60.8 1.0 O D:HOH416 4.3 65.6 1.0 CG2 C:ILE91 4.5 47.6 1.0 CE C:LYS188 4.7 59.0 1.0 CD C:LYS188 4.8 55.6 1.0 CB D:ASP190 5.0 59.0 1.0 CB C:GLU191 5.0 52.2 1.0

Zinc binding site 9 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:75.2 occ:1.00 CL E:CL303 2.0 59.3 0.7 NE2 C:HIS194 2.1 54.0 1.0 OE2 E:GLU191 2.3 58.9 1.0 OE1 E:GLU191 2.5 72.1 1.0 O C:HOH409 2.5 72.0 1.0 CD E:GLU191 2.7 64.1 1.0 OD1 C:ASP190 2.9 72.5 1.0 CE1 C:HIS194 3.0 46.7 1.0 CD2 C:HIS194 3.1 49.5 1.0 CG C:ASP190 3.9 73.9 1.0 ND1 C:HIS194 4.1 45.0 1.0 CG E:GLU191 4.2 53.0 1.0 CG C:HIS194 4.2 49.9 1.0 NZ E:LYS188 4.4 74.1 1.0 O E:HOH403 4.4 69.1 1.0 OD2 C:ASP190 4.4 82.6 1.0 CE E:LYS188 4.6 64.6 1.0 CD E:LYS188 4.6 56.7 1.0 CG2 E:ILE91 4.8 42.9 1.0 CB C:ASP190 5.0 57.6 1.0

Zinc binding site 10 out of 15 in the Crystal Structure of A Membrane Protein W16A


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 Membrane Protein W16A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:67.2 occ:1.00 ND1 C:HIS108 2.0 66.3 1.0 ND1 C:HIS111 2.1 70.0 1.0 O C:HOH405 2.3 59.5 1.0 CE1 C:HIS108 2.8 70.3 1.0 CE1 C:HIS111 3.0 65.1 1.0 CG C:HIS111 3.1 66.2 1.0 CG C:HIS108 3.2 70.3 1.0 CB C:HIS111 3.4 63.0 1.0 CB C:HIS108 3.6 73.2 1.0 O C:HOH401 3.7 77.5 1.0 CA C:HIS108 3.8 72.6 1.0 NE2 C:HIS108 4.0 76.5 1.0 NE C:ARG101 4.1 80.4 1.0 NE2 C:HIS111 4.2 67.5 1.0 CD2 C:HIS108 4.2 73.9 1.0 CD2 C:HIS111 4.2 65.8 1.0 N C:HIS108 4.6 73.9 1.0 CD C:ARG101 4.6 71.6 1.0 CZ C:ARG101 4.7 79.3 1.0 O C:HIS108 4.7 67.3 1.0 C C:HIS108 4.8 69.8 1.0 NH1 C:ARG101 4.8 74.1 1.0 O C:PRO105 4.9 68.9 1.0 CA C:HIS111 5.0 59.7 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