Zinc in PDB 6ivo: Crystal Structure of A Membrane Protein P208A

Protein crystallography data

The structure of Crystal Structure of A Membrane Protein P208A, PDB code: 6ivo 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) 48.76 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.009, 160.062, 161.843, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.8

Other elements in 6ivo:

The structure of Crystal Structure of A Membrane Protein P208A also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Membrane Protein P208A (pdb code 6ivo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of A Membrane Protein P208A, PDB code: 6ivo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 6ivo

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Zinc binding site 1 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:58.0
occ:1.00
NE2 E:HIS194 2.0 41.0 1.0
O A:HOH428 2.1 47.2 1.0
CL A:CL308 2.2 63.2 1.0
OE2 A:GLU191 2.3 69.1 1.0
OE1 A:GLU191 2.7 61.8 1.0
CD A:GLU191 2.8 65.3 1.0
CE1 E:HIS194 3.0 41.4 1.0
CD2 E:HIS194 3.1 32.3 1.0
OD2 E:ASP190 3.9 82.1 1.0
ND1 E:HIS194 4.1 41.2 1.0
CG E:HIS194 4.2 38.5 1.0
CG A:GLU191 4.3 54.2 1.0
CD A:LYS188 4.5 50.1 1.0
CE A:LYS188 4.5 61.9 1.0
NZ A:LYS188 4.5 80.6 1.0
CG2 A:ILE91 4.5 39.5 1.0
CG E:ASP190 4.7 62.4 1.0
CB E:ASP190 4.9 48.8 1.0

Zinc binding site 2 out of 18 in 6ivo

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Zinc binding site 2 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:59.4
occ:1.00
NE2 A:HIS194 2.1 41.0 1.0
CL B:CL308 2.2 75.2 1.0
OE1 B:GLU191 2.3 61.0 1.0
O A:HOH434 2.4 50.8 1.0
OE2 B:GLU191 2.6 75.0 1.0
CD B:GLU191 2.8 64.1 1.0
CE1 A:HIS194 3.0 40.1 1.0
CD2 A:HIS194 3.1 37.3 1.0
CE B:LYS188 4.1 62.3 1.0
ND1 A:HIS194 4.2 41.9 1.0
CG A:HIS194 4.2 37.6 1.0
CG B:GLU191 4.3 57.7 1.0
CG2 B:ILE91 4.5 35.0 1.0
CD B:LYS188 4.6 54.5 1.0
CB A:ASP190 4.7 56.1 1.0

Zinc binding site 3 out of 18 in 6ivo

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Zinc binding site 3 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:57.8
occ:1.00
ND1 A:HIS108 2.1 64.2 1.0
ND1 A:HIS111 2.1 46.0 1.0
CL A:CL310 2.1 68.3 1.0
CL A:CL309 2.1 64.0 1.0
CE1 A:HIS108 3.0 61.7 1.0
CE1 A:HIS111 3.0 48.7 1.0
CG A:HIS108 3.1 61.0 1.0
CG A:HIS111 3.1 49.2 1.0
CB A:HIS108 3.5 60.9 1.0
CB A:HIS111 3.5 47.3 1.0
CA A:HIS108 3.6 59.7 1.0
NE2 A:HIS108 4.1 66.7 1.0
NE2 A:HIS111 4.2 45.8 1.0
CD2 A:HIS108 4.2 62.5 1.0
CD2 A:HIS111 4.2 48.0 1.0
O A:HOH405 4.3 76.7 1.0
N A:HIS108 4.4 56.1 1.0
O A:HIS108 4.5 61.5 1.0
C A:HIS108 4.6 59.5 1.0
CG2 A:THR287 4.6 56.0 1.0
O A:PRO105 4.7 57.1 1.0
CB A:THR287 4.7 59.7 1.0
O A:GLU107 4.9 56.1 1.0
C A:GLU107 4.9 56.0 1.0
O A:THR287 5.0 65.6 1.0

Zinc binding site 4 out of 18 in 6ivo

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Zinc binding site 4 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:59.7
occ:1.00
OD2 A:ASP261 2.0 71.5 1.0
OD2 A:ASP269 2.1 51.4 1.0
CG A:ASP269 2.8 47.9 1.0
O A:HOH441 2.9 54.0 1.0
OD1 A:ASP269 3.0 49.7 1.0
CG A:ASP261 3.0 68.7 1.0
CB A:ASP261 3.4 59.4 1.0
CB A:ALA266 3.7 51.8 1.0
CA A:GLY264 3.8 39.1 1.0
O A:ASP261 3.9 40.2 1.0
N A:ALA266 4.1 49.4 1.0
N A:THR265 4.1 52.8 1.0
OD1 A:ASP261 4.2 72.5 1.0
C A:GLY264 4.2 47.5 1.0
CB A:ASP269 4.3 46.5 1.0
N A:GLY264 4.5 43.8 1.0
CA A:ALA266 4.5 55.0 1.0
CA A:ASP261 4.6 56.6 1.0
O A:HOH442 4.6 69.8 1.0
C A:ASP261 4.7 48.1 1.0

Zinc binding site 5 out of 18 in 6ivo

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Zinc binding site 5 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:0.9
occ:1.00
O A:HOH440 2.5 74.9 1.0
NE2 A:HIS51 2.6 0.9 1.0
CD2 A:HIS51 3.4 0.6 1.0
CE1 A:HIS51 3.7 0.9 1.0
CA A:GLU46 4.4 0.4 1.0
CA A:GLY49 4.6 0.5 1.0
CB A:GLU46 4.6 0.5 1.0
CG A:HIS51 4.6 0.6 1.0
ND1 A:HIS51 4.7 0.2 1.0
N A:GLY49 4.9 0.1 1.0

Zinc binding site 6 out of 18 in 6ivo

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Zinc binding site 6 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:0.7
occ:1.00
O B:HOH430 2.1 78.8 1.0
ND1 B:HIS235 2.2 0.4 1.0
CG B:HIS235 3.0 0.7 1.0
CE1 B:HIS235 3.2 0.9 1.0
CB B:HIS235 3.2 0.8 1.0
CA B:HIS235 3.8 99.2 1.0
CD2 B:TYR42 4.1 84.5 1.0
CD2 B:HIS235 4.2 0.7 1.0
NE2 B:HIS235 4.2 99.0 1.0
O B:HOH422 4.3 71.0 1.0
C B:HIS235 4.6 97.0 1.0
CG1 B:VAL231 4.7 76.1 1.0
CE2 B:TYR42 4.8 87.8 1.0
N B:TYR236 4.9 98.5 1.0
N B:HIS235 4.9 95.3 1.0
CG B:TYR42 5.0 80.3 1.0
CB B:TYR42 5.0 78.0 1.0

Zinc binding site 7 out of 18 in 6ivo

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Zinc binding site 7 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:61.3
occ:1.00
NE2 B:HIS194 2.0 43.1 1.0
OE1 D:GLU191 2.0 68.8 1.0
O B:HOH427 2.1 52.8 1.0
CL B:CL309 2.2 78.0 1.0
CD D:GLU191 2.8 68.5 1.0
OE2 D:GLU191 2.9 72.8 1.0
CD2 B:HIS194 3.0 35.6 1.0
CE1 B:HIS194 3.0 39.5 1.0
NZ D:LYS188 3.7 84.4 1.0
OD2 B:ASP190 3.9 85.5 1.0
ND1 B:HIS194 4.1 43.4 1.0
CG B:HIS194 4.1 39.5 1.0
CG D:GLU191 4.2 55.9 1.0
CE D:LYS188 4.5 62.4 1.0
CD D:LYS188 4.5 58.7 1.0
CG B:ASP190 4.6 77.7 1.0
CG2 D:ILE91 4.6 37.6 1.0
CB B:ASP190 4.9 62.4 1.0

Zinc binding site 8 out of 18 in 6ivo

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Zinc binding site 8 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:55.9
occ:1.00
NE2 B:HIS290 2.0 54.3 1.0
ND1 B:HIS111 2.1 48.8 1.0
ND1 B:HIS108 2.2 63.3 1.0
OXT B:ACY304 2.4 64.7 1.0
CE1 B:HIS290 2.9 69.8 1.0
CE1 B:HIS111 3.0 49.7 1.0
CE1 B:HIS108 3.1 62.1 1.0
CD2 B:HIS290 3.1 62.2 1.0
CG B:HIS111 3.2 48.7 1.0
CG B:HIS108 3.3 60.3 1.0
C B:ACY304 3.3 85.0 1.0
O B:ACY304 3.5 76.9 1.0
CB B:HIS111 3.5 46.3 1.0
CA B:HIS108 3.6 53.4 1.0
CB B:HIS108 3.7 52.7 1.0
ND1 B:HIS290 4.1 69.5 1.0
CG B:HIS290 4.2 71.2 1.0
NE2 B:HIS111 4.2 48.5 1.0
NE2 B:HIS108 4.3 67.9 1.0
CD2 B:HIS111 4.3 49.6 1.0
N B:HIS108 4.4 46.3 1.0
CD2 B:HIS108 4.4 64.3 1.0
O B:GLY288 4.5 62.1 1.0
O B:PRO105 4.5 55.9 1.0
O B:HIS108 4.7 58.8 1.0
C B:HIS108 4.7 52.6 1.0
CG B:ARG101 4.7 49.4 1.0
NE B:ARG101 4.7 65.0 1.0
CH3 B:ACY304 4.8 74.2 1.0
C B:GLU107 4.8 48.8 1.0
O B:GLU107 4.9 52.0 1.0

Zinc binding site 9 out of 18 in 6ivo

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Zinc binding site 9 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:0.4
occ:1.00
NE2 B:HIS235 2.1 99.0 1.0
CD2 B:HIS235 3.0 0.7 1.0
CE1 B:HIS235 3.1 0.9 1.0
O B:GLY232 3.4 97.1 1.0
O A:HOH440 4.0 74.9 1.0
ND1 B:HIS235 4.2 0.4 1.0
CG B:HIS235 4.2 0.7 1.0
C B:GLY232 4.5 81.9 1.0
CD2 A:HIS51 4.6 0.6 1.0
O B:ASP233 4.9 83.3 1.0

Zinc binding site 10 out of 18 in 6ivo

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Zinc binding site 10 out of 18 in the Crystal Structure of A Membrane Protein P208A


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 P208A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn306

b:82.0
occ:0.30
NE2 B:HIS51 2.4 0.7 1.0
CE1 B:HIS51 2.5 0.7 1.0
ND1 B:HIS51 3.8 0.6 1.0
CD2 B:HIS51 3.8 0.3 1.0
NE2 D:HIS235 4.4 99.6 1.0
CD2 D:HIS235 4.4 91.2 1.0
CG B:HIS51 4.5 1.0 1.0

Reference:

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
Page generated: Wed Dec 16 12:02:10 2020

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