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Zinc in PDB 3h90: Structural Basis For the Autoregulation of the Zinc Transporter Yiip

Protein crystallography data

The structure of Structural Basis For the Autoregulation of the Zinc Transporter Yiip, PDB code: 3h90 was solved by M.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.657, 130.704, 115.757, 90.00, 93.28, 90.00
R / Rfree (%) 26.1 / 27.7

Other elements in 3h90:

The structure of Structural Basis For the Autoregulation of the Zinc Transporter Yiip also contains other interesting chemical elements:

Mercury (Hg) 8 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip (pdb code 3h90). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip, PDB code: 3h90:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 3h90

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Zinc binding site 1 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:69.5
occ:1.00
OD2 A:ASP157 2.0 63.3 1.0
NE2 A:HIS153 2.4 51.5 1.0
OD2 A:ASP49 2.6 72.4 1.0
CG A:ASP157 2.7 63.2 1.0
OD1 A:ASP45 2.8 98.8 1.0
OD1 A:ASP157 2.9 63.6 1.0
CE1 A:HIS153 2.9 52.1 1.0
OD1 A:ASP49 3.0 70.8 1.0
CG A:ASP49 3.1 72.4 1.0
CG A:ASP45 3.1 0.4 1.0
OD2 A:ASP45 3.3 0.3 1.0
CD2 A:HIS153 3.6 49.3 1.0
O A:ASP45 3.6 99.2 1.0
C A:ASP45 4.1 0.9 1.0
ND1 A:HIS153 4.2 51.3 1.0
CB A:ASP157 4.2 61.6 1.0
CB A:ASP45 4.2 0.5 1.0
CG A:HIS153 4.5 48.7 1.0
CB A:ASP49 4.6 74.1 1.0
CA A:ASP45 4.7 0.6 1.0
N A:SER46 4.7 0.3 1.0
CA A:SER46 4.9 98.4 1.0

Zinc binding site 2 out of 16 in 3h90

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Zinc binding site 2 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn291

b:5.8
occ:1.00
NE2 C:HIS261 1.8 8.9 1.0
OD1 A:ASP285 2.1 17.4 1.0
NE2 A:HIS283 2.2 5.1 1.0
CE1 C:HIS261 2.6 10.7 1.0
O A:HOH298 2.8 2.0 1.0
CD2 C:HIS261 3.0 10.0 1.0
CE1 A:HIS283 3.0 3.8 1.0
CG A:ASP285 3.2 17.9 1.0
CD2 A:HIS283 3.3 3.6 1.0
OD2 A:ASP285 3.6 16.4 1.0
O C:HOH343 3.6 13.0 1.0
O A:HOH333 3.7 88.9 1.0
ND1 C:HIS261 3.8 12.2 1.0
O C:HOH345 3.9 2.0 1.0
CG C:HIS261 4.0 12.5 1.0
ZN A:ZN293 4.1 10.8 1.0
ND1 A:HIS283 4.2 3.0 1.0
O C:HOH344 4.3 0.9 1.0
CG A:HIS283 4.3 3.0 1.0
OD2 C:ASP265 4.4 16.4 1.0
CB A:ASP285 4.5 18.7 1.0
O C:HOH355 4.6 4.0 1.0
ND1 A:HIS248 4.8 1.2 1.0
CA A:ASP285 4.8 18.6 1.0
CE1 A:HIS248 4.9 2.4 1.0
O A:HOH294 4.9 2.0 1.0

Zinc binding site 3 out of 16 in 3h90

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Zinc binding site 3 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn292

b:26.2
occ:1.00
OD2 A:ASP68 1.9 41.6 1.0
ND1 A:HIS71 1.9 31.9 1.0
CG A:ASP68 2.2 39.2 1.0
NE2 A:HIS75 2.3 21.3 1.0
CE1 A:HIS71 2.7 32.8 1.0
OD1 A:ASP68 2.7 39.6 1.0
CB A:ASP68 2.9 37.7 1.0
O A:HOH295 2.9 2.0 1.0
CG A:HIS71 3.0 30.8 1.0
CE1 A:HIS75 3.0 20.5 1.0
CD2 A:HIS75 3.4 20.1 1.0
CB A:HIS71 3.5 30.4 1.0
OH A:TYR62 3.7 32.7 1.0
NE2 A:HIS71 3.9 32.1 1.0
O A:HOH310 3.9 34.5 1.0
CD2 A:HIS71 4.0 30.7 1.0
N A:HIS71 4.2 33.7 1.0
ND1 A:HIS75 4.2 19.7 1.0
CA A:ASP68 4.3 37.2 1.0
OD1 A:ASN70 4.4 44.0 1.0
O A:HOH319 4.4 23.8 1.0
CG A:HIS75 4.4 18.7 1.0
CA A:HIS71 4.5 30.8 1.0
CZ A:TYR62 4.6 32.3 1.0
CE2 A:TYR62 4.8 33.3 1.0
C A:ASN70 4.9 36.5 1.0
N A:ASP68 5.0 35.6 1.0

Zinc binding site 4 out of 16 in 3h90

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Zinc binding site 4 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn293

b:10.8
occ:1.00
OD2 A:ASP285 1.8 16.4 1.0
NE2 A:HIS232 1.9 15.2 1.0
ND1 A:HIS248 2.1 1.2 1.0
CE1 A:HIS232 2.5 15.5 1.0
O A:HOH294 2.6 2.0 1.0
O A:HOH298 2.9 2.0 1.0
CE1 A:HIS248 2.9 2.4 1.0
CG A:ASP285 3.0 17.9 1.0
CD2 A:HIS232 3.1 15.6 1.0
CG A:HIS248 3.2 0.8 1.0
O A:HOH331 3.5 31.8 1.0
OD1 A:ASP285 3.6 17.4 1.0
CB A:HIS248 3.6 0.4 1.0
ND1 A:HIS232 3.8 15.4 1.0
CD2 A:HIS283 4.0 3.6 1.0
CG A:HIS232 4.1 15.6 1.0
ZN A:ZN291 4.1 5.8 1.0
NE2 A:HIS248 4.1 1.2 1.0
CB A:ASP285 4.2 18.7 1.0
CD2 A:HIS248 4.3 0.6 1.0
NE2 A:HIS283 4.4 5.1 1.0
O A:HOH315 4.6 6.3 1.0
CG1 A:VAL289 4.8 67.6 1.0
O A:HOH333 4.8 88.9 1.0

Zinc binding site 5 out of 16 in 3h90

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Zinc binding site 5 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn291

b:42.6
occ:1.00
OD2 B:ASP157 2.0 41.5 1.0
OD2 B:ASP49 2.2 60.3 1.0
OD1 B:ASP45 2.3 89.0 1.0
NE2 B:HIS153 2.6 31.9 1.0
CG B:ASP49 2.8 61.2 1.0
CG B:ASP157 2.9 42.9 1.0
OD1 B:ASP49 2.9 61.0 1.0
CG B:ASP45 2.9 89.4 1.0
OD1 B:ASP157 3.0 44.2 1.0
OD2 B:ASP45 3.0 89.5 1.0
CE1 B:HIS153 3.1 32.9 1.0
O B:ASP45 3.5 87.0 1.0
CD2 B:HIS153 3.9 29.9 1.0
C B:ASP45 3.9 87.6 1.0
CB B:ASP45 4.2 90.0 1.0
CB B:ASP49 4.2 62.2 1.0
CB B:ASP157 4.3 42.2 1.0
ND1 B:HIS153 4.4 32.7 1.0
N B:SER46 4.5 85.3 1.0
CD2 B:LEU24 4.5 75.4 1.0
CA B:ASP45 4.6 89.8 1.0
CA B:SER46 4.6 82.8 1.0
CG B:HIS153 4.8 30.5 1.0
CE2 B:TYR154 4.8 27.0 1.0

Zinc binding site 6 out of 16 in 3h90

Go back to Zinc Binding Sites List in 3h90
Zinc binding site 6 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn292

b:17.2
occ:1.00
O B:HOH300 2.0 2.0 1.0
OD1 B:ASP285 2.1 17.7 1.0
NE2 D:HIS261 2.1 7.9 1.0
NE2 B:HIS283 2.1 6.2 1.0
CE1 D:HIS261 2.9 9.1 1.0
CE1 B:HIS283 3.1 6.1 1.0
CG B:ASP285 3.1 17.6 1.0
CD2 B:HIS283 3.1 5.1 1.0
CD2 D:HIS261 3.1 9.2 1.0
OD2 B:ASP285 3.4 16.1 1.0
OD2 D:ASP265 4.0 16.3 1.0
ND1 D:HIS261 4.1 9.8 1.0
ZN B:ZN294 4.1 10.0 1.0
ND1 B:HIS283 4.2 5.3 1.0
CG D:HIS261 4.2 10.3 1.0
CG B:HIS283 4.2 4.8 1.0
O D:HOH327 4.3 31.4 1.0
CB B:ASP285 4.4 17.9 1.0
O B:HOH295 4.6 2.0 1.0
ND1 B:HIS248 4.6 2.8 1.0
CE1 B:HIS248 4.7 2.9 1.0
CA B:ASP285 4.7 18.3 1.0
O D:HOH331 4.8 23.3 1.0

Zinc binding site 7 out of 16 in 3h90

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Zinc binding site 7 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn293

b:21.8
occ:1.00
OD2 B:ASP68 1.8 39.0 1.0
NE2 B:HIS75 2.0 20.1 1.0
CG B:ASP68 2.1 39.0 1.0
ND1 B:HIS71 2.2 31.3 1.0
CB B:ASP68 2.4 38.0 1.0
CE1 B:HIS75 2.7 20.4 1.0
O B:HOH296 2.8 2.0 1.0
OD1 B:ASP68 3.1 41.2 1.0
CE1 B:HIS71 3.1 31.9 1.0
CG B:HIS71 3.2 30.3 1.0
CD2 B:HIS75 3.2 19.8 1.0
CB B:HIS71 3.6 30.5 1.0
O B:HOH314 3.8 13.8 1.0
CA B:ASP68 3.9 38.4 1.0
ND1 B:HIS75 3.9 20.2 1.0
OH B:TYR62 3.9 30.5 1.0
NE2 B:HIS71 4.2 30.8 1.0
CG B:HIS75 4.2 19.2 1.0
CD2 B:HIS71 4.2 29.7 1.0
N B:HIS71 4.3 32.4 1.0
OD1 B:ASN70 4.5 40.2 1.0
N B:ASP68 4.5 37.7 1.0
O B:HOH313 4.6 6.4 1.0
CA B:HIS71 4.6 30.3 1.0
O B:HOH341 4.6 45.7 1.0
CZ B:TYR62 4.7 30.9 1.0
C B:ASP68 4.9 38.5 1.0
C B:ASN70 4.9 33.9 1.0

Zinc binding site 8 out of 16 in 3h90

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Zinc binding site 8 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn294

b:10.0
occ:1.00
NE2 B:HIS232 1.8 13.3 1.0
OD2 B:ASP285 2.0 16.1 1.0
ND1 B:HIS248 2.2 2.8 1.0
O B:HOH300 2.5 2.0 1.0
CE1 B:HIS232 2.7 13.9 1.0
O B:HOH295 2.8 2.0 1.0
CD2 B:HIS232 3.0 14.1 1.0
CE1 B:HIS248 3.1 2.9 1.0
CG B:ASP285 3.1 17.6 1.0
CG B:HIS248 3.3 1.8 1.0
CB B:HIS248 3.7 1.1 1.0
OD1 B:ASP285 3.7 17.7 1.0
ND1 B:HIS232 3.9 14.0 1.0
O B:HOH299 4.0 8.7 1.0
CG B:HIS232 4.0 14.1 1.0
ZN B:ZN292 4.1 17.2 1.0
NE2 B:HIS248 4.3 1.4 1.0
CB B:ASP285 4.3 17.9 1.0
O B:HOH331 4.3 16.1 1.0
CD2 B:HIS248 4.4 0.8 1.0
CD2 B:HIS283 4.4 5.1 1.0
O B:HOH362 4.5 14.6 1.0
NE2 B:HIS283 4.8 6.2 1.0
CG1 B:VAL289 5.0 65.4 1.0

Zinc binding site 9 out of 16 in 3h90

Go back to Zinc Binding Sites List in 3h90
Zinc binding site 9 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:2.0
occ:1.00
OD1 C:ASP285 2.1 18.5 1.0
NE2 A:HIS261 2.2 6.9 1.0
NE2 C:HIS283 2.2 6.1 1.0
CE1 A:HIS261 2.8 8.2 1.0
O C:HOH294 2.9 2.0 1.0
CG C:ASP285 3.1 18.9 1.0
CE1 C:HIS283 3.2 5.0 1.0
CD2 C:HIS283 3.3 4.2 1.0
CD2 A:HIS261 3.3 8.2 1.0
OD2 C:ASP285 3.4 17.4 1.0
O A:HOH334 3.8 10.5 1.0
ZN C:ZN3 3.8 5.7 1.0
ND1 A:HIS261 4.0 9.7 1.0
CG A:HIS261 4.3 10.3 1.0
O A:HOH336 4.3 24.9 1.0
ND1 C:HIS283 4.3 3.9 1.0
O A:HOH335 4.4 16.9 1.0
CG C:HIS283 4.4 3.6 1.0
O A:HOH344 4.4 2.0 1.0
CB C:ASP285 4.4 19.5 1.0
O C:HOH346 4.4 41.7 1.0
ND1 C:HIS248 4.6 2.6 1.0
OD2 A:ASP265 4.6 14.2 1.0
CE1 C:HIS248 4.6 3.6 1.0
CA C:ASP285 4.8 19.5 1.0

Zinc binding site 10 out of 16 in 3h90

Go back to Zinc Binding Sites List in 3h90
Zinc binding site 10 out of 16 in the Structural Basis For the Autoregulation of the Zinc Transporter Yiip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structural Basis For the Autoregulation of the Zinc Transporter Yiip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2

b:23.9
occ:1.00
OD2 C:ASP68 1.9 40.6 1.0
ND1 C:HIS71 1.9 29.5 1.0
CG C:ASP68 2.1 38.7 1.0
NE2 C:HIS75 2.2 20.8 1.0
O C:HOH293 2.6 2.0 1.0
OD1 C:ASP68 2.7 39.8 1.0
CE1 C:HIS71 2.8 29.9 1.0
CB C:ASP68 2.8 37.3 1.0
CG C:HIS71 3.0 28.6 1.0
CE1 C:HIS75 3.0 20.8 1.0
CD2 C:HIS75 3.4 19.3 1.0
CB C:HIS71 3.4 29.0 1.0
OH C:TYR62 3.8 30.3 1.0
NE2 C:HIS71 3.9 29.1 1.0
CD2 C:HIS71 4.0 28.1 1.0
O C:HOH327 4.1 10.0 1.0
ND1 C:HIS75 4.2 20.3 1.0
N C:HIS71 4.2 31.6 1.0
CA C:ASP68 4.2 38.0 1.0
O C:HOH317 4.2 35.8 1.0
O C:HOH308 4.4 11.8 1.0
CG C:HIS75 4.4 18.7 1.0
CA C:HIS71 4.4 29.1 1.0
OD1 C:ASN70 4.5 41.0 1.0
CZ C:TYR62 4.6 30.0 1.0
CE2 C:TYR62 4.8 31.4 1.0
N C:ASP68 4.9 37.0 1.0
C C:ASN70 4.9 33.5 1.0

Reference:

M.Lu, J.Chai, D.Fu. Structural Basis For Autoregulation of the Zinc Transporter Yiip. Nat.Struct.Mol.Biol. V. 16 1063 2009.
ISSN: ISSN 1545-9993
PubMed: 19749753
DOI: 10.1038/NSMB.1662
Page generated: Wed Dec 16 04:23:17 2020

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