Zinc in PDB 9f40: Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound

The structure of Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound, PDB code: 9f40 was solved by L.Nel, E.Olesen, K.M.Frain, B.P.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.05 / 2.44
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.76, 109.58, 151.81, 90, 90, 90
R / Rfree (%)	21.4 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound (pdb code 9f40). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 29 binding sites of Zinc where determined in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound, PDB code: 9f40:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:74.1 occ:1.00 OD2 A:ASP218 2.0 68.1 1.0 OD1 A:ASN107 2.0 78.9 1.0 O A:HOH405 2.1 91.8 1.0 NE2 A:HIS111 2.3 73.4 1.0 O A:HOH410 2.8 68.1 1.0 OE2 A:GLU67 2.8 95.9 1.0 CG A:ASN107 2.9 67.2 1.0 OE1 A:GLU67 3.1 115.1 1.0 CD2 A:HIS111 3.2 56.5 1.0 CG A:ASP218 3.2 75.1 1.0 ND2 A:ASN107 3.2 64.8 1.0 CE1 A:HIS111 3.3 66.8 1.0 CD A:GLU67 3.3 104.6 1.0 OD1 A:ASP218 3.7 84.2 1.0 CG A:HIS111 4.3 67.4 1.0 ND1 A:HIS111 4.3 63.8 1.0 CB A:ASN107 4.3 61.0 1.0 CB A:ASP218 4.4 65.8 1.0 OE2 A:GLU219 4.7 116.7 1.0 CG A:GLU67 4.7 93.3 1.0 O A:HOH431 4.8 76.1 1.0 NZ A:LYS103 4.8 102.1 1.0 O A:ASN107 5.0 63.3 1.0 CG A:GLU219 5.0 94.5 1.0

Zinc binding site 2 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:70.2 occ:1.00 OE1 A:GLU38 2.1 55.5 1.0 O1 A:SO4302 2.1 73.8 1.0 OD2 A:ASP79 2.1 72.6 1.0 OE2 A:GLU38 2.6 75.6 1.0 CD A:GLU38 2.6 75.2 1.0 CG A:ASP79 3.1 72.2 1.0 S A:SO4302 3.2 68.2 1.0 O2 A:SO4302 3.2 58.7 1.0 CB A:ASP79 3.4 47.5 1.0 ND2 A:ASN28 4.0 63.5 1.0 CG A:GLU38 4.1 65.9 1.0 O3 A:SO4302 4.1 82.4 1.0 O4 A:SO4302 4.2 69.2 1.0 OD1 A:ASP79 4.2 82.5 1.0 CB A:ASN28 4.5 62.4 1.0 CG A:ASN28 4.7 61.7 1.0 CB A:GLU38 4.8 56.7 1.0 CA A:ASP79 5.0 51.3 1.0

Zinc binding site 3 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:70.4 occ:1.00 OE2 B:GLU212 1.9 62.1 1.0 OE1 B:GLU210 1.9 66.8 1.0 OE2 A:GLU212 2.0 70.3 1.0 OE1 A:GLU210 2.0 70.5 1.0 CD B:GLU210 2.6 62.9 1.0 OE2 B:GLU210 2.7 71.5 1.0 CD A:GLU210 2.7 71.3 1.0 OE2 A:GLU210 2.8 72.7 1.0 CD B:GLU212 2.9 64.7 1.0 CD A:GLU212 3.0 65.8 1.0 CG B:GLU212 3.4 63.0 1.0 CG A:GLU212 3.5 65.3 1.0 NE1 B:TRP213 4.0 68.7 1.0 CD1 B:TRP213 4.0 64.6 1.0 NE1 A:TRP213 4.0 68.9 1.0 OE1 B:GLU212 4.0 64.5 1.0 CG B:GLU210 4.1 71.6 1.0 CD1 A:TRP213 4.1 56.4 1.0 OE1 A:GLU212 4.1 80.2 1.0 CG A:GLU210 4.2 67.8 1.0 CB B:GLU210 4.6 70.1 1.0 CB A:GLU210 4.8 74.6 1.0 CB B:GLU212 4.9 51.4 1.0 CA B:GLU210 4.9 77.5 1.0 CB A:GLU212 5.0 63.9 1.0

Zinc binding site 4 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn312 b:113.4 occ:1.00 OE2 A:GLU215 2.6 84.6 1.0 OE1 A:GLU215 3.0 67.5 1.0 CD A:GLU215 3.2 60.5 1.0 O1 A:SO4315 3.3 144.7 1.0 O A:TYR204 3.4 74.7 1.0 N A:SER146 3.9 68.2 1.0 OG A:SER146 3.9 84.1 1.0 O A:MET144 4.0 59.6 1.0 CA A:ASN145 4.3 67.1 1.0 C A:TYR204 4.4 74.6 1.0 CB A:SER146 4.4 66.1 1.0 S A:SO4315 4.5 196.6 1.0 O3 A:SO4315 4.5 160.4 1.0 C A:ASN145 4.6 62.9 1.0 C8 F:NAG1 4.6 101.3 1.0 CG A:GLU215 4.7 64.4 1.0 CA A:SER146 4.8 70.1 1.0 CA A:TYR204 4.8 68.5 1.0 C A:MET144 5.0 64.0 1.0

Zinc binding site 5 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn313 b:110.2 occ:1.00 OE2 A:GLU139 2.1 102.6 1.0 O A:HOH428 2.6 92.2 1.0 O A:HOH440 2.9 111.8 1.0 CD A:GLU139 3.1 83.1 1.0 OE1 A:GLU139 3.5 88.6 1.0 ND2 A:ASN201 3.6 70.3 1.0 OD1 A:ASN201 4.2 57.3 1.0 CG A:ASN201 4.3 58.7 1.0 CG A:GLU139 4.5 77.5 1.0 CG A:GLN199 4.8 53.5 1.0

Zinc binding site 6 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:87.9 occ:1.00 OD2 B:ASP218 2.0 66.6 1.0 CE1 B:HIS111 2.1 87.1 1.0 OD1 B:ASN107 2.2 91.3 1.0 NE2 B:HIS111 2.3 89.0 1.0 O B:HOH403 2.6 75.4 1.0 CG B:ASN107 3.0 73.1 1.0 OE2 B:GLU67 3.0 107.0 1.0 OE1 B:GLU67 3.1 109.6 1.0 CG B:ASP218 3.1 84.1 1.0 ND2 B:ASN107 3.2 80.1 1.0 ND1 B:HIS111 3.2 79.5 1.0 CD B:GLU67 3.4 106.3 1.0 CD2 B:HIS111 3.5 70.8 1.0 OD1 B:ASP218 3.6 85.9 1.0 CG B:HIS111 4.0 79.1 1.0 OE2 B:GLU219 4.1 119.6 1.0 CB B:ASP218 4.4 78.7 1.0 CB B:ASN107 4.4 68.1 1.0 CG B:GLU219 4.7 112.0 1.0 CG B:GLU67 4.8 94.2 1.0 NZ B:LYS103 4.8 96.7 1.0 CD B:GLU219 4.8 140.5 1.0 O B:ASN107 4.9 73.1 1.0

Zinc binding site 7 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:74.1 occ:1.00 O2 B:SO4302 1.9 82.7 1.0 OD2 B:ASP79 2.0 82.4 1.0 OE2 B:GLU38 2.1 82.1 1.0 OE1 B:GLU38 2.4 66.8 1.0 CD B:GLU38 2.6 78.6 1.0 CG B:ASP79 3.1 80.5 1.0 S B:SO4302 3.1 71.8 1.0 O1 B:SO4302 3.4 74.9 1.0 CB B:ASP79 3.5 62.0 1.0 O4 B:SO4302 3.7 71.3 1.0 ND2 B:ASN28 4.0 71.2 1.0 CG B:GLU38 4.1 75.4 1.0 OD1 B:ASP79 4.2 81.9 1.0 O3 B:SO4302 4.3 65.1 1.0 O B:HOH412 4.3 92.8 1.0 CB B:ASN28 4.5 72.3 1.0 CG B:ASN28 4.7 77.3 1.0 CB B:GLU38 4.9 68.5 1.0

Zinc binding site 8 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:106.0 occ:1.00 O B:HOH432 2.2 86.4 1.0 OE2 B:GLU151 2.4 108.3 1.0 OE1 B:GLU151 2.5 101.8 1.0 OD2 B:ASP154 2.6 97.0 1.0 CD B:GLU151 2.8 108.7 1.0 CG B:ASP154 3.5 88.9 1.0 OE2 B:GLU237 3.9 85.9 1.0 ZN B:ZN306 4.1 100.4 1.0 OD1 B:ASP154 4.3 105.5 1.0 CB B:ASP154 4.3 83.8 1.0 CG B:GLU151 4.3 94.7 1.0 CB B:ALA222 4.6 74.9 1.0 CD B:GLU237 4.9 99.5 1.0

Zinc binding site 9 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn306 b:100.4 occ:1.00 OE2 B:GLU237 2.1 85.9 1.0 O B:HOH404 2.1 89.2 1.0 OD1 B:ASP154 2.2 105.5 1.0 OD2 B:ASP154 2.8 97.0 1.0 CG B:ASP154 2.8 88.9 1.0 CD B:GLU237 3.0 99.5 1.0 OE1 B:GLU237 3.4 116.9 1.0 ZN B:ZN305 4.1 106.0 1.0 NZ B:LYS157 4.2 89.5 1.0 O B:HOH432 4.2 86.4 1.0 CB B:ASP154 4.3 83.8 1.0 CE B:LYS157 4.3 86.4 1.0 CG B:GLU237 4.4 96.6 1.0 O B:ASP154 4.6 98.8 1.0

Zinc binding site 10 out of 29 in the Crystal Structure of the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound


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 the Ntd Domain From S. Cerevisia Niemann-Pick Type C Protein NCR1 with Ergosterol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn313 b:108.8 occ:1.00 OE2 B:GLU215 2.5 105.6 1.0 OE1 B:GLU215 2.9 86.8 1.0 CD B:GLU215 3.1 95.0 1.0 O2 B:SO4315 3.3 122.1 1.0 O B:TYR204 3.3 72.1 1.0 C8 I:NAG1 3.8 123.2 1.0 OG B:SER146 4.0 90.7 1.0 O B:MET144 4.1 70.5 1.0 N B:SER146 4.1 75.1 1.0 C B:TYR204 4.3 74.0 1.0 S B:SO4315 4.3 134.8 1.0 O3 B:SO4315 4.4 132.4 1.0 CA B:ASN145 4.5 76.4 1.0 CG B:GLU215 4.6 78.3 1.0 CB B:SER146 4.6 67.7 1.0 O4 B:SO4315 4.7 137.6 1.0 C7 I:NAG1 4.7 124.7 1.0 N2 I:NAG1 4.7 122.2 1.0 CA B:TYR204 4.8 72.4 1.0 C B:ASN145 4.8 73.6 1.0 CA B:SER146 5.0 77.9 1.0

D.Jamecna, K.Thaysen, L.Nel, E.Olesen, K.M.Frain, M.Szomek, J.Langer, B.P.Pedersen, D.Wustner, D.Hoglinger. Structural and Biochemical Analysis of Ligand Binding in Yeast Niemann-Pick Type C 1-Related Protein To Be Published.