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Zinc in PDB 6ivw: Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A

Protein crystallography data

The structure of Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A, PDB code: 6ivw was solved by S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.19 / 3.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.966, 161.770, 162.371, 90.00, 90.00, 90.00
R / Rfree (%) 28.9 / 35.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A (pdb code 6ivw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A, PDB code: 6ivw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6ivw

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Zinc binding site 1 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:0.2
occ:1.00
NE2 E:HIS194 2.0 95.8 1.0
NZ A:LYS188 2.0 98.1 1.0
OE1 A:GLU191 2.1 0.6 1.0
OE2 A:GLU191 2.1 0.5 1.0
CD A:GLU191 2.3 0.5 1.0
CE1 E:HIS194 2.8 96.0 1.0
CD2 E:HIS194 3.0 93.5 1.0
CE A:LYS188 3.4 0.1 1.0
CD A:LYS188 3.8 0.4 1.0
CG A:GLU191 3.8 90.7 1.0
ND1 E:HIS194 3.9 88.4 1.0
CG E:HIS194 4.0 82.8 1.0
CB E:ASP190 4.6 0.0 1.0
CB A:GLU191 4.7 91.8 1.0

Zinc binding site 2 out of 9 in 6ivw

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Zinc binding site 2 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:96.8
occ:1.00
NE2 A:HIS194 2.1 89.4 1.0
OE2 B:GLU191 2.4 82.6 1.0
OE1 B:GLU191 2.6 83.1 1.0
CE1 A:HIS194 2.7 88.0 1.0
CD B:GLU191 2.8 76.5 1.0
CD2 A:HIS194 3.1 99.3 1.0
CE B:LYS188 3.6 0.9 1.0
ND1 A:HIS194 3.8 84.0 1.0
CD B:LYS188 4.0 88.8 1.0
CG A:HIS194 4.0 92.6 1.0
OG1 B:THR95 4.3 98.2 1.0
CG B:GLU191 4.4 69.9 1.0
CB A:ASP190 4.4 97.1 1.0
CG2 B:THR95 4.6 92.6 1.0
CG2 B:ILE91 4.6 93.6 1.0
NZ B:LYS188 4.8 0.5 1.0
O A:ASP190 4.9 84.8 1.0

Zinc binding site 3 out of 9 in 6ivw

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Zinc binding site 3 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:0.2
occ:1.00
CE1 A:HIS108 2.1 0.5 1.0
ND1 A:HIS108 2.2 0.9 1.0
ND1 A:HIS111 2.6 0.5 1.0
NE2 A:HIS108 3.1 0.4 1.0
CG A:HIS108 3.3 0.3 1.0
CG A:HIS111 3.5 0.2 1.0
CE1 A:HIS111 3.6 0.3 1.0
CB A:HIS111 3.6 0.3 1.0
CD2 A:HIS108 3.7 0.7 1.0
CG2 A:THR287 3.9 0.6 1.0
CA A:THR287 4.0 0.4 1.0
CB A:THR287 4.2 0.3 1.0
CB A:HIS108 4.3 0.2 1.0
O A:MET286 4.4 0.7 1.0
CZ A:ARG101 4.6 0.1 1.0
NE A:ARG101 4.6 0.6 1.0
C A:THR287 4.6 0.6 1.0
NH2 A:ARG101 4.6 0.6 1.0
CD2 A:HIS111 4.7 0.9 1.0
CD A:ARG101 4.7 0.2 1.0
NE2 A:HIS111 4.7 0.2 1.0
CA A:HIS108 4.8 0.8 1.0

Zinc binding site 4 out of 9 in 6ivw

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Zinc binding site 4 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:0.4
occ:1.00
CD2 B:HIS111 2.2 0.4 1.0
ND1 B:HIS108 2.5 0.7 1.0
CE1 B:HIS108 2.5 0.3 1.0
CG B:HIS108 2.5 0.2 1.0
NE2 B:HIS108 2.5 0.5 1.0
CD2 B:HIS108 2.6 0.2 1.0
CG B:HIS111 2.7 0.0 1.0
NE2 B:HIS111 3.0 0.9 1.0
CB B:HIS111 3.2 0.3 1.0
CB B:HIS108 3.5 0.6 1.0
ND1 B:HIS111 3.5 0.6 1.0
CE1 B:HIS111 3.6 0.6 1.0
CA B:HIS108 3.8 0.8 1.0
NH2 B:ARG101 4.1 0.5 1.0
CE B:MET286 4.3 0.1 1.0
SD B:MET286 4.3 0.7 1.0
O B:HIS108 4.7 0.6 1.0
CA B:HIS111 4.7 0.9 1.0
N B:HIS108 4.7 0.7 1.0
C B:HIS108 4.8 0.5 1.0

Zinc binding site 5 out of 9 in 6ivw

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Zinc binding site 5 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:0.1
occ:1.00
ND1 C:HIS108 2.0 0.7 1.0
CE1 C:HIS108 2.1 0.5 1.0
ND1 C:HIS111 2.2 0.9 1.0
CG C:HIS108 3.0 0.1 1.0
NE2 C:HIS108 3.0 0.2 1.0
CE1 C:HIS111 3.1 0.2 1.0
O C:THR287 3.2 0.5 1.0
CG C:HIS111 3.3 0.9 1.0
CD2 C:HIS108 3.4 0.1 1.0
CB C:HIS111 3.6 0.9 1.0
CB C:HIS108 3.9 0.5 1.0
C C:THR287 4.1 0.2 1.0
CA C:THR287 4.2 0.4 1.0
NE2 C:HIS111 4.3 100.0 1.0
CA C:HIS108 4.3 0.4 1.0
CD2 C:HIS111 4.4 0.5 1.0
O C:MET286 4.5 94.6 1.0
CG C:ARG101 4.7 0.6 1.0
CD C:ARG101 4.7 0.2 1.0
NE C:ARG101 4.9 0.7 1.0
CB C:THR287 4.9 0.8 1.0

Zinc binding site 6 out of 9 in 6ivw

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Zinc binding site 6 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:1.0
occ:1.00
OE1 D:GLU191 2.1 94.0 1.0
OE2 D:GLU191 2.2 0.3 1.0
NE2 B:HIS194 2.2 90.6 1.0
CD D:GLU191 2.4 95.5 1.0
CE D:LYS188 2.7 0.7 1.0
CE1 B:HIS194 3.2 91.5 1.0
CD2 B:HIS194 3.2 95.0 1.0
CD D:LYS188 3.4 95.5 1.0
NZ D:LYS188 3.6 99.8 1.0
CG D:GLU191 3.9 87.7 1.0
CB B:ASP190 3.9 85.9 1.0
CG B:ASP190 4.2 99.8 1.0
ND1 B:HIS194 4.3 91.6 1.0
CG B:HIS194 4.3 89.0 1.0
OD2 B:ASP190 4.3 0.1 1.0
CG2 D:ILE91 4.6 88.6 1.0
CB D:GLU191 4.6 88.3 1.0
OG1 D:THR95 4.6 90.7 1.0
OD1 B:ASP190 4.7 97.2 1.0
CG D:LYS188 4.8 90.1 1.0
CA B:ASP190 5.0 79.8 1.0
CA D:ALA92 5.0 79.9 1.0

Zinc binding site 7 out of 9 in 6ivw

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Zinc binding site 7 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:0.0
occ:1.00
ND1 D:HIS111 2.1 0.1 1.0
CG D:HIS108 2.2 0.1 1.0
CD2 D:HIS108 2.3 0.7 1.0
ND1 D:HIS108 2.4 0.3 1.0
NE2 D:HIS108 2.4 0.1 1.0
CE1 D:HIS108 2.5 0.8 1.0
CE1 D:HIS111 2.7 0.0 1.0
CB D:HIS108 3.1 0.8 1.0
CG D:HIS111 3.3 0.1 1.0
CA D:HIS108 3.5 0.0 1.0
NE2 D:HIS111 3.9 0.0 1.0
CB D:HIS111 3.9 0.9 1.0
CD2 D:HIS111 4.2 97.8 1.0
O D:PRO105 4.3 0.1 1.0
N D:HIS108 4.4 0.5 1.0
CG D:ARG101 4.5 0.8 1.0
CD D:ARG101 4.6 0.3 1.0
C D:HIS108 4.6 0.3 1.0
O D:HIS108 4.7 0.1 1.0
NE D:ARG101 4.8 0.8 1.0
O D:THR287 4.9 0.4 1.0

Zinc binding site 8 out of 9 in 6ivw

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Zinc binding site 8 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:0.2
occ:1.00
CE1 C:HIS194 2.1 92.8 1.0
NZ E:LYS188 2.3 0.8 1.0
OE1 E:GLU191 2.4 0.9 1.0
NE2 C:HIS194 2.5 90.8 1.0
OE2 E:GLU191 2.9 97.0 1.0
CD E:GLU191 3.0 0.7 1.0
ND1 C:HIS194 3.2 0.3 1.0
CE E:LYS188 3.5 0.8 1.0
CD E:LYS188 3.7 0.6 1.0
CD2 C:HIS194 3.7 90.6 1.0
OG1 E:THR95 3.8 91.7 1.0
CG2 E:ILE91 4.0 85.1 1.0
CG C:HIS194 4.0 92.3 1.0
CB C:ASP190 4.3 0.6 1.0
CG2 E:THR95 4.3 96.1 1.0
CG E:GLU191 4.4 0.1 1.0
CB E:THR95 4.5 97.1 1.0
CA E:ALA92 4.6 82.7 1.0
O E:ILE91 4.8 82.5 1.0
N E:ALA92 4.8 84.6 1.0
O C:ASP190 4.8 93.1 1.0
CG C:ASP190 4.9 0.5 1.0
C E:ILE91 4.9 86.1 1.0
OD2 C:ASP190 4.9 1.0 1.0
CB E:ILE91 5.0 84.0 1.0
CB E:GLU191 5.0 97.0 1.0

Zinc binding site 9 out of 9 in 6ivw

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Zinc binding site 9 out of 9 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae with A Mutation D269A


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 D269A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:0.9
occ:1.00
NE2 E:HIS108 2.1 0.8 1.0
ND1 E:HIS111 2.1 0.1 1.0
CE1 E:HIS108 2.3 0.2 1.0
CD2 E:HIS108 2.3 0.4 1.0
ND1 E:HIS108 2.6 0.6 1.0
CG E:HIS108 2.6 0.1 1.0
CE1 E:HIS111 3.1 0.8 1.0
CG E:HIS111 3.2 0.7 1.0
CB E:HIS111 3.5 0.1 1.0
CB E:HIS108 3.7 0.7 1.0
O E:THR287 3.8 1.0 1.0
CA E:HIS108 4.0 0.4 1.0
CB E:THR287 4.1 0.6 1.0
NE2 E:HIS111 4.2 0.4 1.0
CA E:THR287 4.2 0.7 1.0
CD2 E:HIS111 4.2 0.9 1.0
CG2 E:THR287 4.4 0.0 1.0
O E:HIS108 4.4 0.8 1.0
C E:THR287 4.5 0.8 1.0
CG E:ARG101 4.7 0.1 1.0
CD E:ARG101 4.7 0.1 1.0
C E:HIS108 4.7 0.3 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 12:02:16 2020

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