Zinc in PDB 5jm6: Structure of Chaetomium Thermophilum MAPE1

The structure of Structure of Chaetomium Thermophilum MAPE1, PDB code: 5jm6 was solved by C.Bertipaglia, A.J.Jakobi, M.Wilmanns, C.Sachse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.07 / 2.76
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.019, 143.894, 201.315, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of Chaetomium Thermophilum MAPE1 (pdb code 5jm6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of Chaetomium Thermophilum MAPE1, PDB code: 5jm6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.5 occ:1.00 OD2 A:ASP306 1.8 57.0 1.0 OE2 A:GLU340 1.9 0.1 1.0 NE2 A:HIS485 1.9 73.2 1.0 CG A:ASP306 2.4 70.9 1.0 CD A:GLU340 2.4 91.7 1.0 OE1 A:GLU340 2.4 95.2 1.0 CD2 A:HIS485 2.6 66.0 1.0 OD1 A:ASP306 2.9 63.0 1.0 CE1 A:HIS485 3.1 63.0 1.0 CB A:ASP306 3.4 70.1 1.0 ZN A:ZN602 3.8 72.0 1.0 CG A:HIS485 3.9 51.8 1.0 CD1 A:LEU137 3.9 57.4 1.0 CG A:GLU340 3.9 72.7 1.0 ND1 A:HIS485 4.0 48.8 1.0 OE2 A:GLU339 4.5 77.7 1.0 CE1 A:HIS133 4.6 57.2 1.0 NE2 A:HIS133 4.8 64.1 1.0 CA A:ASP306 4.8 56.9 1.0 CG A:MET484 4.9 52.2 1.0 CB A:GLU340 4.9 73.6 1.0

Zinc binding site 2 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:72.0 occ:1.00 OD1 A:ASP306 2.0 63.0 1.0 OD1 A:ASP391 2.0 67.3 1.0 OD2 A:ASP391 2.1 70.5 1.0 NE2 A:HIS133 2.1 64.1 1.0 CG A:ASP391 2.3 60.7 1.0 CG A:ASP306 3.0 70.9 1.0 CE1 A:HIS133 3.0 57.2 1.0 OE2 A:GLU339 3.1 77.7 1.0 CD2 A:HIS133 3.2 57.7 1.0 OD2 A:ASP306 3.3 57.0 1.0 OE2 A:GLU340 3.7 0.1 1.0 ZN A:ZN601 3.8 0.5 1.0 CB A:ASP391 3.9 45.2 1.0 CD A:GLU339 3.9 73.9 1.0 CB A:ASP307 4.1 47.1 1.0 CG A:ASP307 4.1 51.6 1.0 ND1 A:HIS133 4.2 53.4 1.0 CG A:HIS133 4.3 50.9 1.0 OE1 A:GLU339 4.3 71.4 1.0 OD2 A:ASP307 4.3 53.1 1.0 CG2 A:VAL392 4.3 55.1 1.0 CB A:ASP306 4.4 70.1 1.0 N A:ASP307 4.4 64.4 1.0 C A:ASP306 4.4 60.9 1.0 CA A:ASP391 4.6 50.5 1.0 N A:VAL392 4.7 52.0 1.0 OD1 A:ASP307 4.7 54.6 1.0 CA A:ASP306 4.7 56.9 1.0 O A:ASP306 4.7 53.6 1.0 CD A:GLU340 4.8 91.7 1.0 CA A:ASP307 4.9 46.1 1.0

Zinc binding site 3 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn601 b:96.6 occ:1.00 OD2 E:ASP306 2.0 59.6 1.0 NE2 E:HIS485 2.0 67.2 1.0 CD E:GLU340 2.0 90.0 1.0 OE2 E:GLU340 2.1 88.7 1.0 OE1 E:GLU340 2.5 92.3 1.0 CG E:GLU340 2.7 88.5 1.0 CE1 E:HIS485 3.0 63.8 1.0 CD2 E:HIS485 3.0 56.8 1.0 CG E:ASP306 3.1 68.3 1.0 OD1 E:ASP306 3.7 71.0 1.0 ZN E:ZN602 3.8 73.7 1.0 ND1 E:HIS485 4.1 62.4 1.0 CB E:GLU340 4.1 79.0 1.0 CG E:HIS485 4.1 55.3 1.0 CB E:ASP306 4.2 51.8 1.0 CD2 E:LEU137 4.4 54.7 1.0 NE2 C:HIS210 4.6 49.9 1.0 SD E:MET484 4.9 52.2 1.0 CE1 E:HIS133 4.9 61.2 1.0 NE2 E:HIS133 5.0 59.8 1.0 CG E:MET484 5.0 50.8 1.0

Zinc binding site 4 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn602 b:73.7 occ:1.00 OD1 E:ASP391 2.1 68.8 1.0 NE2 E:HIS133 2.1 59.8 1.0 OD1 E:ASP306 2.1 71.0 1.0 OD2 E:ASP391 2.2 70.5 1.0 CG E:ASP391 2.4 63.1 1.0 OE2 E:GLU340 2.7 88.7 1.0 CG E:ASP306 3.0 68.3 1.0 CE1 E:HIS133 3.0 61.2 1.0 CD2 E:HIS133 3.2 57.6 1.0 OD2 E:ASP306 3.3 59.6 1.0 ZN E:ZN601 3.8 96.6 1.0 CD E:GLU340 3.9 90.0 1.0 CB E:ASP391 3.9 48.7 1.0 CB E:ASP307 4.0 46.0 1.0 CG E:ASP307 4.1 52.9 1.0 ND1 E:HIS133 4.2 55.6 1.0 OD2 E:ASP307 4.3 56.6 1.0 CG E:HIS133 4.3 53.4 1.0 CB E:ASP306 4.3 51.8 1.0 N E:ASP307 4.4 64.4 1.0 C E:ASP306 4.4 54.0 1.0 CG2 E:VAL392 4.5 53.3 1.0 OE1 E:GLU340 4.6 92.3 1.0 OD1 E:ASP307 4.6 54.1 1.0 CA E:ASP391 4.7 54.6 1.0 O E:ASP306 4.7 48.2 1.0 CA E:ASP306 4.7 48.6 1.0 N E:VAL392 4.8 49.9 1.0 CG E:GLU339 4.8 64.8 1.0 CA E:ASP307 4.9 51.4 1.0 CG E:GLU340 4.9 88.5 1.0

Zinc binding site 5 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn601 b:96.6 occ:1.00 OD2 F:ASP306 2.0 68.4 1.0 OE2 F:GLU340 2.0 88.2 1.0 NE2 F:HIS485 2.0 67.2 1.0 OE1 F:GLU340 2.2 92.3 1.0 CD F:GLU340 2.4 86.4 1.0 CE1 F:HIS485 2.9 62.2 1.0 CD2 F:HIS485 3.1 58.5 1.0 CG F:ASP306 3.2 68.4 1.0 ZN F:ZN602 3.8 74.8 1.0 OD1 F:ASP306 3.9 66.7 1.0 CG F:GLU340 3.9 71.2 1.0 ND1 F:HIS485 4.1 50.2 1.0 CG F:HIS485 4.2 49.5 1.0 CB F:ASP306 4.2 53.8 1.0 CD2 F:LEU137 4.5 62.1 1.0 CB F:GLU340 4.7 73.6 1.0 CE1 F:HIS133 4.7 57.9 1.0 NE2 F:HIS133 4.8 59.8 1.0

Zinc binding site 6 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn602 b:74.8 occ:1.00 OD1 F:ASP391 2.1 64.9 1.0 OD1 F:ASP306 2.1 66.7 1.0 NE2 F:HIS133 2.1 59.8 1.0 OD2 F:ASP391 2.2 70.5 1.0 CG F:ASP391 2.4 60.3 1.0 CG F:ASP306 2.8 68.4 1.0 OD2 F:ASP306 2.9 68.4 1.0 CE1 F:HIS133 3.0 57.9 1.0 CD2 F:HIS133 3.2 56.7 1.0 ZN F:ZN601 3.8 96.6 1.0 CB F:ASP391 3.9 53.3 1.0 CB F:ASP307 4.0 50.0 1.0 ND1 F:HIS133 4.1 59.4 1.0 CG F:ASP307 4.2 57.5 1.0 CB F:ASP306 4.3 53.8 1.0 CG F:HIS133 4.3 58.4 1.0 OD2 F:ASP307 4.4 59.5 1.0 CG2 F:VAL392 4.4 54.8 1.0 C F:ASP306 4.4 53.9 1.0 N F:ASP307 4.4 60.3 1.0 OE1 F:GLU340 4.4 92.3 1.0 OE2 F:GLU340 4.5 88.2 1.0 OD1 F:ASP307 4.6 52.0 1.0 CA F:ASP391 4.7 57.7 1.0 O F:ASP306 4.7 53.1 1.0 CA F:ASP306 4.7 48.8 1.0 N F:VAL392 4.7 59.9 1.0 CD F:GLU340 4.7 86.4 1.0 CA F:ASP307 4.8 49.0 1.0

Zinc binding site 7 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:96.6 occ:1.00 OD2 B:ASP306 2.0 58.3 1.0 NE2 B:HIS485 2.1 67.2 1.0 OE2 B:GLU340 2.1 88.1 1.0 OE1 B:GLU340 2.2 92.3 1.0 CD B:GLU340 2.5 86.4 1.0 CE1 B:HIS485 3.1 57.0 1.0 CD2 B:HIS485 3.2 54.7 1.0 CG B:ASP306 3.2 70.0 1.0 ZN B:ZN602 3.7 68.9 1.0 OD1 B:ASP306 3.8 77.8 1.0 CG B:GLU340 4.0 71.2 1.0 ND1 B:HIS485 4.2 54.7 1.0 CG B:HIS485 4.3 54.5 1.0 CB B:ASP306 4.4 54.7 1.0 OE2 B:GLU339 4.4 76.9 1.0 CB B:GLU340 4.8 76.4 1.0 SD B:MET484 4.8 55.0 1.0 CE1 B:HIS133 4.9 59.4 1.0 NE2 B:HIS133 5.0 59.8 1.0 CG B:MET484 5.0 47.6 1.0 OD2 B:ASP391 5.0 75.4 1.0

Zinc binding site 8 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:68.9 occ:1.00 OD1 B:ASP391 2.0 69.6 1.0 NE2 B:HIS133 2.1 59.8 1.0 OD1 B:ASP306 2.1 77.8 1.0 OD2 B:ASP391 2.4 75.4 1.0 CG B:ASP391 2.5 64.7 1.0 CE1 B:HIS133 2.9 59.4 1.0 CG B:ASP306 2.9 70.0 1.0 OD2 B:ASP306 3.1 58.3 1.0 CD2 B:HIS133 3.2 62.9 1.0 OD2 B:ASP307 3.6 73.3 1.0 OE2 B:GLU339 3.7 76.9 1.0 ZN B:ZN601 3.7 96.6 1.0 CB B:ASP307 4.0 52.6 1.0 OE1 B:GLU340 4.0 92.3 1.0 CB B:ASP391 4.0 47.6 1.0 ND1 B:HIS133 4.1 63.0 1.0 CG B:ASP307 4.2 65.9 1.0 CG B:HIS133 4.3 60.3 1.0 CG2 B:VAL392 4.3 52.5 1.0 CB B:ASP306 4.3 54.7 1.0 N B:ASP307 4.4 53.0 1.0 CD B:GLU339 4.4 77.1 1.0 C B:ASP306 4.4 53.2 1.0 CD B:GLU340 4.6 86.4 1.0 OE1 B:GLU339 4.6 76.2 1.0 N B:VAL392 4.7 52.3 1.0 CA B:ASP391 4.7 58.5 1.0 OE2 B:GLU340 4.7 88.1 1.0 O B:ASP306 4.7 47.1 1.0 CA B:ASP306 4.7 49.7 1.0 CA B:ASP307 4.9 47.8 1.0

Zinc binding site 9 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:96.6 occ:1.00 OD2 C:ASP306 2.1 68.4 1.0 NE2 C:HIS485 2.1 67.5 1.0 OE2 C:GLU340 2.2 88.8 1.0 OE1 C:GLU340 2.2 92.3 1.0 CD C:GLU340 2.5 86.4 1.0 CE1 C:HIS485 3.0 58.0 1.0 CD2 C:HIS485 3.2 56.8 1.0 CG C:ASP306 3.2 71.2 1.0 ZN C:ZN602 3.6 72.2 1.0 OD1 C:ASP306 3.8 69.4 1.0 CG C:GLU340 4.0 71.2 1.0 OE2 C:GLU339 4.1 79.3 1.0 ND1 C:HIS485 4.2 61.2 1.0 CG C:HIS485 4.3 53.8 1.0 CB C:ASP306 4.5 59.9 1.0 NE2 E:HIS210 4.5 57.4 1.0 OD2 C:ASP391 4.8 77.9 1.0 CB C:GLU340 4.9 73.6 1.0 SD C:MET484 4.9 55.0 1.0 NE2 C:HIS133 4.9 60.3 1.0 CE1 E:HIS210 4.9 57.9 1.0 CE1 C:HIS133 5.0 56.0 1.0

Zinc binding site 10 out of 12 in the Structure of Chaetomium Thermophilum MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Chaetomium Thermophilum MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:72.2 occ:1.00 OD1 C:ASP391 2.1 70.9 1.0 NE2 C:HIS133 2.1 60.3 1.0 OD1 C:ASP306 2.1 69.4 1.0 OD2 C:ASP391 2.1 77.9 1.0 CG C:ASP391 2.4 64.4 1.0 CE1 C:HIS133 3.0 56.0 1.0 CG C:ASP306 3.0 71.2 1.0 CD2 C:HIS133 3.2 61.2 1.0 OD2 C:ASP306 3.2 68.4 1.0 ZN C:ZN601 3.6 96.6 1.0 OE2 C:GLU339 3.7 79.3 1.0 OE1 C:GLU340 3.7 92.3 1.0 CB C:ASP391 3.9 44.6 1.0 CB C:ASP307 4.0 52.5 1.0 ND1 C:HIS133 4.1 63.0 1.0 CD C:GLU339 4.2 81.5 1.0 CG C:HIS133 4.3 59.7 1.0 OE1 C:GLU339 4.3 81.5 1.0 CB C:ASP306 4.3 59.9 1.0 CG2 C:VAL392 4.4 56.8 1.0 C C:ASP306 4.4 53.0 1.0 N C:ASP307 4.4 62.2 1.0 CD C:GLU340 4.5 86.4 1.0 CG C:ASP307 4.5 53.9 1.0 CA C:ASP391 4.7 54.8 1.0 O C:ASP306 4.7 53.3 1.0 N C:VAL392 4.7 58.9 1.0 CA C:ASP306 4.7 48.6 1.0 OE2 C:GLU340 4.8 88.8 1.0 CA C:ASP307 4.8 49.8 1.0 OD2 C:ASP307 4.9 56.2 1.0 OD1 C:ASP307 4.9 52.9 1.0

C.Bertipaglia, S.Schneider, A.J.Jakobi, A.K.Tarafder, Y.S.Bykov, A.Picco, W.Kukulski, J.Kosinski, W.J.Hagen, A.C.Ravichandran, M.Wilmanns, M.Kaksonen, J.A.Briggs, C.Sachse. Higher-Order Assemblies of Oligomeric Cargo Receptor Complexes Form the Membrane Scaffold of the Cvt Vesicle. Embo Rep. V. 17 1044 2016.
ISSN: ESSN 1469-3178
PubMed: 27266708
DOI: 10.15252/EMBR.201541960