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Zinc in PDB 4wd7: Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing

Protein crystallography data

The structure of Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing, PDB code: 4wd7 was solved by T.Yang, Q.Liu, W.A.Hendrickson, New York Consortium On Membrane Proteinstructure (Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.19 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.124, 160.587, 161.745, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 25.3

Zinc Binding Sites:

Pages:

>>> 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 By Zn-Sad Phasing (pdb code 4wd7). 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 By Zn-Sad Phasing, PDB code: 4wd7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 4wd7

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Zinc binding site 1 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:84.3
occ:1.00
OE2 A:GLU191 2.0 76.9 1.0
NE2 E:HIS194 2.1 61.8 1.0
OE1 A:GLU191 2.1 76.1 1.0
CD A:GLU191 2.4 76.0 1.0
NZ A:LYS188 2.8 73.6 1.0
CE1 E:HIS194 3.0 62.6 1.0
CD2 E:HIS194 3.1 60.0 1.0
CE A:LYS188 3.9 73.4 1.0
CG A:GLU191 3.9 75.2 1.0
CD A:LYS188 4.1 72.2 1.0
ND1 E:HIS194 4.1 61.5 1.0
CG E:HIS194 4.2 59.8 1.0
CG2 A:ILE91 4.5 54.6 1.0
CB A:GLU191 4.8 74.5 1.0

Zinc binding site 2 out of 15 in 4wd7

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Zinc binding site 2 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:96.1
occ:1.00
OE2 B:GLU191 2.1 69.0 1.0
NE2 A:HIS194 2.1 54.3 1.0
OE1 B:GLU191 2.1 69.7 1.0
CD B:GLU191 2.4 69.2 1.0
CE1 A:HIS194 3.0 54.7 1.0
CD2 A:HIS194 3.2 53.3 1.0
CG B:GLU191 4.0 69.1 1.0
ND1 A:HIS194 4.2 53.9 1.0
CG A:HIS194 4.3 53.1 1.0
CE B:LYS188 4.3 66.9 1.0
CD B:LYS188 4.3 66.5 1.0
CG2 B:ILE91 4.5 53.8 1.0
CB B:GLU191 4.8 69.8 1.0
NZ B:LYS188 4.9 67.7 1.0
CA B:ALA92 5.0 50.3 1.0
CB B:ALA92 5.0 49.9 1.0

Zinc binding site 3 out of 15 in 4wd7

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Zinc binding site 3 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:0.6
occ:1.00
ND1 A:HIS108 2.0 0.1 1.0
ND1 A:HIS111 2.1 84.0 1.0
CE1 A:HIS108 2.9 0.4 1.0
CG A:HIS108 2.9 0.8 1.0
CE1 A:HIS111 3.0 84.2 1.0
CG A:HIS111 3.1 81.8 1.0
CB A:HIS108 3.4 0.5 1.0
CB A:HIS111 3.4 81.4 1.0
CA A:HIS108 3.7 1.0 1.0
NE2 A:HIS108 3.9 0.2 1.0
CD2 A:HIS108 4.0 0.8 1.0
NE2 A:HIS111 4.2 82.1 1.0
CD2 A:HIS111 4.2 80.6 1.0
N A:HIS108 4.6 0.9 1.0
CG2 A:THR287 4.7 99.0 1.0
O A:HIS108 4.7 0.9 1.0
CB A:THR287 4.7 1.0 1.0
CG A:ARG101 4.7 90.3 1.0
C A:HIS108 4.7 0.5 1.0
CA A:THR287 4.9 0.1 1.0
O A:THR287 4.9 0.8 1.0
O A:PRO105 4.9 97.4 1.0
CA A:HIS111 4.9 79.7 1.0

Zinc binding site 4 out of 15 in 4wd7

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Zinc binding site 4 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:0.8
occ:1.00
OD2 A:ASP269 2.0 98.4 1.0
OD2 A:ASP261 2.0 0.7 1.0
CG A:ASP261 3.0 0.6 1.0
CG A:ASP269 3.0 97.5 1.0
OD1 A:ASP269 3.3 97.8 1.0
CB A:ASP261 3.3 0.6 1.0
O A:ASP261 3.7 0.8 1.0
CA A:GLY264 3.7 80.8 1.0
CB A:ALA266 3.9 87.3 1.0
OD1 A:ASP261 4.0 0.1 1.0
N A:ALA266 4.2 83.0 1.0
C A:GLY264 4.3 82.5 1.0
N A:THR265 4.3 0.9 1.0
CB A:ASP269 4.4 96.3 1.0
N A:GLY264 4.4 78.3 1.0
C A:ASP261 4.6 0.7 1.0
CA A:ASP261 4.6 0.0 1.0
CA A:ALA266 4.7 86.6 1.0

Zinc binding site 5 out of 15 in 4wd7

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Zinc binding site 5 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:0.6
occ:1.00
ND1 B:HIS235 2.1 0.3 1.0
CG B:HIS235 3.0 0.1 1.0
CE1 B:HIS235 3.1 0.6 1.0
CB B:HIS235 3.3 0.2 1.0
CA B:HIS235 3.8 0.3 1.0
CD2 B:TYR42 3.8 0.6 1.0
CD2 B:HIS235 4.1 0.1 1.0
NE2 B:HIS235 4.1 0.1 1.0
CE2 B:TYR42 4.3 0.0 1.0
O B:VAL231 4.5 0.7 1.0
C B:HIS235 4.7 0.8 1.0
CG B:TYR42 4.7 0.5 1.0
N B:HIS235 4.8 0.2 1.0
CG2 B:VAL231 4.9 0.2 1.0

Zinc binding site 6 out of 15 in 4wd7

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Zinc binding site 6 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:92.8
occ:1.00
OE2 D:GLU191 2.1 68.0 1.0
NE2 B:HIS194 2.1 55.6 1.0
OE1 D:GLU191 2.1 67.5 1.0
CD D:GLU191 2.4 67.4 1.0
OD2 B:ASP190 2.8 90.4 1.0
CE1 B:HIS194 3.0 55.6 1.0
CD2 B:HIS194 3.2 54.7 1.0
OD1 B:ASP190 3.3 90.1 1.0
CG B:ASP190 3.4 90.0 1.0
NZ D:LYS188 3.8 67.6 1.0
CG D:GLU191 4.0 66.8 1.0
ND1 B:HIS194 4.1 54.8 1.0
CG B:HIS194 4.3 54.2 1.0
CD D:LYS188 4.5 66.7 1.0
CG2 D:ILE91 4.6 58.8 1.0
CE D:LYS188 4.7 67.9 1.0
CB D:GLU191 4.8 66.3 1.0
CB B:ASP190 4.9 89.8 1.0

Zinc binding site 7 out of 15 in 4wd7

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Zinc binding site 7 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:0.5
occ:1.00
ND1 B:HIS108 2.0 0.8 1.0
NE2 B:HIS290 2.1 0.6 1.0
ND1 B:HIS111 2.1 78.3 1.0
CD2 B:HIS290 2.6 0.6 1.0
CE1 B:HIS108 2.8 0.6 1.0
CE1 B:HIS111 3.0 78.0 1.0
CG B:HIS108 3.1 0.3 1.0
CG B:HIS111 3.1 76.8 1.0
CE1 B:HIS290 3.3 0.6 1.0
CB B:HIS111 3.5 77.1 1.0
CB B:HIS108 3.6 0.7 1.0
CA B:HIS108 3.9 0.7 1.0
CG B:HIS290 3.9 0.6 1.0
NE2 B:HIS108 3.9 1.0 1.0
O B:GLY288 3.9 0.6 1.0
CD2 B:HIS108 4.0 0.4 1.0
NE2 B:HIS111 4.1 76.3 1.0
ND1 B:HIS290 4.2 0.6 1.0
CD2 B:HIS111 4.2 75.6 1.0
NE B:ARG101 4.5 80.0 1.0
CG B:ARG101 4.6 79.8 1.0
N B:HIS108 4.7 0.8 1.0
O B:PRO105 4.8 82.9 1.0
O B:HIS108 4.8 0.8 1.0
C B:HIS108 4.9 0.5 1.0

Zinc binding site 8 out of 15 in 4wd7

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Zinc binding site 8 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:88.2
occ:1.00
OE2 C:GLU191 2.1 69.0 1.0
NE2 D:HIS194 2.1 57.4 1.0
OE1 C:GLU191 2.1 69.0 1.0
CD C:GLU191 2.4 68.6 1.0
CE1 D:HIS194 3.0 57.8 1.0
CD2 D:HIS194 3.2 56.3 1.0
NZ C:LYS188 3.7 71.7 1.0
CG C:GLU191 4.0 67.7 1.0
ND1 D:HIS194 4.2 56.9 1.0
CG D:HIS194 4.3 56.0 1.0
CG2 C:ILE91 4.6 57.3 1.0
CD C:LYS188 4.7 70.8 1.0
CE C:LYS188 4.8 71.9 1.0
CB C:GLU191 4.8 67.5 1.0
CB D:ASP190 5.0 82.2 1.0

Zinc binding site 9 out of 15 in 4wd7

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Zinc binding site 9 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:0.9
occ:1.00
NE2 C:HIS194 1.9 52.5 1.0
OE2 E:GLU191 1.9 71.7 1.0
OE1 E:GLU191 2.1 70.0 1.0
OD1 C:ASP190 2.2 87.8 1.0
CD E:GLU191 2.4 70.3 1.0
CE1 C:HIS194 2.8 52.8 1.0
CD2 C:HIS194 3.0 51.9 1.0
CG C:ASP190 3.3 88.0 1.0
CE E:LYS188 3.8 72.5 1.0
OD2 C:ASP190 3.9 88.5 1.0
ND1 C:HIS194 3.9 52.3 1.0
CG E:GLU191 4.0 69.6 1.0
CD E:LYS188 4.0 70.8 1.0
CG C:HIS194 4.1 51.8 1.0
NZ E:LYS188 4.3 74.1 1.0
CG2 E:ILE91 4.4 52.9 1.0
CB C:ASP190 4.4 87.6 1.0
OG1 E:THR95 4.5 66.0 1.0
O C:ASP190 4.7 86.5 1.0
CG2 E:THR95 4.9 68.0 1.0
CB E:GLU191 4.9 68.3 1.0
CA C:ASP190 5.0 87.2 1.0
CA E:ALA92 5.0 47.9 1.0

Zinc binding site 10 out of 15 in 4wd7

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Zinc binding site 10 out of 15 in the Crystal Structure of A Bacterial Bestrophin Homolog From Klebsiella Pneumoniae By Zn-Sad Phasing


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 By Zn-Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:97.0
occ:1.00
ND1 C:HIS111 2.1 88.8 1.0
ND1 C:HIS108 2.1 86.7 1.0
CE1 C:HIS111 2.9 88.6 1.0
CE1 C:HIS108 3.0 87.5 1.0
CG C:HIS108 3.1 89.3 1.0
CG C:HIS111 3.2 86.2 1.0
CB C:HIS108 3.4 89.5 1.0
CA C:HIS108 3.5 85.8 1.0
CB C:HIS111 3.6 86.1 1.0
NE2 C:HIS111 4.1 85.9 1.0
NE2 C:HIS108 4.1 90.6 1.0
CD2 C:HIS108 4.2 91.8 1.0
CD2 C:HIS111 4.2 84.4 1.0
N C:HIS108 4.3 86.0 1.0
O C:PRO105 4.5 90.0 1.0
O C:HIS108 4.6 83.6 1.0
C C:HIS108 4.6 85.2 1.0
CG C:ARG101 4.7 79.7 1.0
NE C:ARG101 4.7 85.0 1.0
C C:GLU107 4.9 88.5 1.0
O C:GLU107 4.9 85.7 1.0
CD C:ARG101 4.9 81.5 1.0

Reference:

T.Yang, Q.Liu, B.Kloss, R.Bruni, R.C.Kalathur, Y.Guo, E.Kloppmann, B.Rost, H.M.Colecraft, W.A.Hendrickson. Structure and Selectivity in Bestrophin Ion Channels. Science V. 346 355 2014.
ISSN: ESSN 1095-9203
PubMed: 25324390
DOI: 10.1126/SCIENCE.1259723
Page generated: Wed Dec 16 05:50:54 2020

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