Zinc in PDB 3rzu: The Crystal Structure of the Catalytic Domain of Amsh

The structure of The Crystal Structure of the Catalytic Domain of Amsh, PDB code: 3rzu was solved by C.W.Davies, C.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.15 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	203.491, 67.362, 113.165, 90.00, 112.44, 90.00
R / Rfree (%)	19.3 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of the Catalytic Domain of Amsh (pdb code 3rzu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the The Crystal Structure of the Catalytic Domain of Amsh, PDB code: 3rzu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:36.1 occ:1.00 O A:HOH14 2.2 31.9 1.0 OD2 A:ASP348 2.2 48.4 1.0 NE2 A:HIS337 2.3 29.2 1.0 NE2 A:HIS335 2.3 36.7 1.0 OD1 A:ASP348 2.8 27.0 1.0 CG A:ASP348 2.8 44.9 1.0 CD2 A:HIS337 3.1 32.8 1.0 CD2 A:HIS335 3.2 29.6 1.0 CE1 A:HIS337 3.4 33.8 1.0 CE1 A:HIS335 3.4 31.8 1.0 OE2 A:GLU280 4.0 53.2 1.0 OG A:SER345 4.1 41.4 1.0 O A:PHE343 4.3 43.2 1.0 CB A:ASP348 4.3 43.0 1.0 CG A:HIS337 4.3 36.7 1.0 CG A:HIS335 4.4 28.8 1.0 ND1 A:HIS337 4.4 38.5 1.0 ND1 A:HIS335 4.4 33.6 1.0 OE1 A:GLU280 4.4 55.2 1.0 N A:SER345 4.5 38.3 1.0 CD A:GLU280 4.6 52.2 1.0 CB A:SER345 4.7 39.5 1.0

Zinc binding site 2 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:53.1 occ:1.00 NE2 A:HIS398 2.3 37.3 1.0 NE2 A:HIS350 2.4 47.1 1.0 NE2 A:HIS396 2.4 51.6 1.0 SG A:CYS390 2.6 54.4 1.0 CD2 A:HIS396 3.0 49.3 1.0 CE1 A:HIS398 3.0 44.7 1.0 CD2 A:HIS350 3.2 45.2 1.0 CD2 A:HIS398 3.4 44.7 1.0 CE1 A:HIS350 3.4 53.2 1.0 CE1 A:HIS396 3.5 54.4 1.0 CB A:CYS390 3.5 60.6 1.0 ND1 A:HIS398 4.2 49.8 1.0 CG A:HIS396 4.3 55.2 1.0 CD1 A:ILE387 4.3 47.2 1.0 CG A:HIS350 4.4 48.7 1.0 CG A:HIS398 4.5 52.4 1.0 ND1 A:HIS350 4.5 54.8 1.0 ND1 A:HIS396 4.5 55.0 1.0 OG A:SER346 4.7 51.1 1.0 O A:GLN392 4.8 79.8 1.0 CA A:CYS390 4.9 64.4 1.0 CB A:GLN392 4.9 81.3 1.0

Zinc binding site 3 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:45.1 occ:1.00 OD2 B:ASP348 2.1 35.3 1.0 NE2 B:HIS337 2.3 32.6 1.0 NE2 B:HIS335 2.3 43.7 1.0 CG B:ASP348 2.8 39.7 1.0 OD1 B:ASP348 2.8 38.7 1.0 CD2 B:HIS337 3.0 37.6 1.0 CD2 B:HIS335 3.2 40.6 1.0 CE1 B:HIS335 3.3 44.4 1.0 CE1 B:HIS337 3.4 37.3 1.0 OE2 B:GLU280 3.8 57.1 1.0 OG B:SER345 4.1 57.7 1.0 O B:PHE343 4.2 46.0 1.0 CB B:ASP348 4.2 41.6 1.0 CG B:HIS337 4.3 37.4 1.0 ND1 B:HIS337 4.4 36.9 1.0 ND1 B:HIS335 4.4 44.7 1.0 CG B:HIS335 4.4 42.0 1.0 CD B:GLU280 4.5 54.4 1.0 N B:SER345 4.6 57.8 1.0 CB B:SER345 4.6 52.6 1.0 OE1 B:GLU280 4.6 53.9 1.0 O B:HOH25 5.0 51.1 1.0

Zinc binding site 4 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:73.8 occ:1.00 NE2 B:HIS398 2.3 60.5 1.0 NE2 B:HIS350 2.4 60.3 1.0 NE2 B:HIS396 2.6 79.8 1.0 SG B:CYS390 2.7 95.5 1.0 CE1 B:HIS398 3.1 59.5 1.0 CD2 B:HIS396 3.2 81.8 1.0 CD2 B:HIS350 3.3 59.1 1.0 CE1 B:HIS350 3.4 62.2 1.0 CD2 B:HIS398 3.5 65.2 1.0 CB B:CYS390 3.8 95.2 1.0 CE1 B:HIS396 3.8 81.4 1.0 ND1 B:HIS398 4.3 63.1 1.0 CG B:HIS396 4.5 86.2 1.0 CG B:HIS398 4.5 69.3 1.0 CG B:HIS350 4.5 58.9 1.0 ND1 B:HIS350 4.5 60.9 1.0 ND1 B:HIS396 4.8 84.4 1.0 CB B:GLN392 4.8 0.3 1.0 OG B:SER346 4.9 53.6 1.0 CD B:GLN392 5.0 0.1 1.0

Zinc binding site 5 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn5 b:35.7 occ:1.00 OD2 C:ASP348 2.2 38.6 1.0 NE2 C:HIS337 2.3 31.9 1.0 O C:HOH134 2.3 38.6 1.0 NE2 C:HIS335 2.3 31.9 1.0 OD1 C:ASP348 2.7 31.6 1.0 CG C:ASP348 2.8 40.3 1.0 CD2 C:HIS337 3.0 39.4 1.0 CD2 C:HIS335 3.3 31.7 1.0 CE1 C:HIS335 3.3 33.9 1.0 CE1 C:HIS337 3.4 47.1 1.0 OE2 C:GLU280 3.8 47.0 1.0 OG C:SER345 4.1 37.4 1.0 O C:PHE343 4.1 40.6 1.0 CB C:ASP348 4.2 41.6 1.0 CG C:HIS337 4.3 47.7 1.0 ND1 C:HIS337 4.4 49.7 1.0 ND1 C:HIS335 4.4 33.5 1.0 CG C:HIS335 4.4 34.4 1.0 OE1 C:GLU280 4.5 44.4 1.0 CD C:GLU280 4.5 40.6 1.0 N C:SER345 4.5 47.1 1.0 CB C:SER345 4.7 37.0 1.0

Zinc binding site 6 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn6 b:45.2 occ:1.00 NE2 C:HIS350 2.3 32.0 1.0 NE2 C:HIS398 2.3 44.3 1.0 NE2 C:HIS396 2.4 41.5 1.0 SG C:CYS390 2.6 56.5 1.0 CD2 C:HIS396 3.0 35.2 1.0 CD2 C:HIS350 3.1 31.9 1.0 CE1 C:HIS398 3.2 44.4 1.0 CE1 C:HIS350 3.3 44.4 1.0 CD2 C:HIS398 3.4 47.8 1.0 CE1 C:HIS396 3.5 47.4 1.0 CB C:CYS390 3.5 55.7 1.0 CG C:HIS396 4.3 45.9 1.0 CG C:HIS350 4.3 32.0 1.0 CD1 C:ILE387 4.3 40.4 1.0 ND1 C:HIS350 4.4 39.6 1.0 ND1 C:HIS398 4.4 47.2 1.0 CG C:HIS398 4.5 51.1 1.0 ND1 C:HIS396 4.5 54.8 1.0 CB C:GLN392 4.6 58.9 1.0 O C:GLN392 4.7 75.1 1.0 OG C:SER346 4.7 58.7 1.0 CA C:CYS390 4.9 56.6 1.0 N C:GLN392 5.0 58.5 1.0

Zinc binding site 7 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn7 b:40.3 occ:1.00 NE2 D:HIS337 2.3 36.5 1.0 OD2 D:ASP348 2.3 51.4 1.0 NE2 D:HIS335 2.3 39.8 1.0 OD1 D:ASP348 2.8 36.4 1.0 CG D:ASP348 2.8 48.2 1.0 CD2 D:HIS337 3.0 38.6 1.0 CD2 D:HIS335 3.2 35.3 1.0 CE1 D:HIS335 3.3 39.2 1.0 CE1 D:HIS337 3.4 40.3 1.0 OE2 D:GLU280 4.0 54.4 1.0 OG D:SER345 4.1 43.4 1.0 O D:PHE343 4.2 48.9 1.0 CG D:HIS337 4.3 42.8 1.0 CB D:ASP348 4.3 44.8 1.0 ND1 D:HIS335 4.4 39.4 1.0 ND1 D:HIS337 4.4 44.6 1.0 CG D:HIS335 4.4 41.1 1.0 N D:SER345 4.5 51.3 1.0 OE1 D:GLU280 4.6 48.4 1.0 CD D:GLU280 4.6 53.1 1.0 CB D:SER345 4.7 46.1 1.0

Zinc binding site 8 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn8 b:65.9 occ:1.00 NE2 D:HIS398 2.3 59.2 1.0 O D:HOH136 2.3 48.2 1.0 NE2 D:HIS396 2.5 81.7 1.0 NE2 D:HIS350 2.5 55.8 1.0 SG D:CYS390 2.8 77.7 1.0 CD2 D:HIS396 2.9 81.8 1.0 CE1 D:HIS398 3.0 64.7 1.0 CD2 D:HIS350 3.3 56.6 1.0 CD2 D:HIS398 3.4 64.0 1.0 CE1 D:HIS350 3.6 56.8 1.0 CE1 D:HIS396 3.7 82.4 1.0 CB D:CYS390 3.8 0.8 1.0 CD1 D:ILE387 4.0 55.1 1.0 CG D:HIS396 4.2 84.0 1.0 ND1 D:HIS398 4.2 69.9 1.0 CG D:HIS398 4.5 70.5 1.0 CG D:HIS350 4.5 55.7 1.0 ND1 D:HIS396 4.5 83.5 1.0 ND1 D:HIS350 4.7 58.7 1.0 OG D:SER346 4.9 62.2 1.0

Zinc binding site 9 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn9 b:46.7 occ:1.00 OD2 E:ASP348 2.2 36.5 1.0 NE2 E:HIS337 2.3 41.5 1.0 O E:HOH135 2.3 48.6 1.0 NE2 E:HIS335 2.4 40.9 1.0 OD1 E:ASP348 2.7 43.1 1.0 CG E:ASP348 2.8 41.9 1.0 CD2 E:HIS337 3.1 45.4 1.0 CD2 E:HIS335 3.3 41.1 1.0 CE1 E:HIS337 3.4 45.2 1.0 CE1 E:HIS335 3.4 46.3 1.0 OG E:SER345 4.0 56.9 1.0 OE2 E:GLU280 4.1 57.8 1.0 O E:PHE343 4.2 52.8 1.0 CG E:HIS337 4.3 44.6 1.0 CB E:ASP348 4.3 40.4 1.0 N E:SER345 4.4 60.2 1.0 ND1 E:HIS337 4.4 46.8 1.0 CG E:HIS335 4.4 42.1 1.0 ND1 E:HIS335 4.5 50.3 1.0 CB E:SER345 4.5 59.0 1.0 OE1 E:GLU280 4.6 54.6 1.0 CD E:GLU280 4.7 52.7 1.0 O E:HOH121 4.8 50.9 1.0

Zinc binding site 10 out of 14 in the The Crystal Structure of the Catalytic Domain of Amsh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of the Catalytic Domain of Amsh within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn10 b:90.2 occ:1.00 NE2 E:HIS398 2.3 80.6 1.0 O E:HOH103 2.4 60.3 1.0 NE2 E:HIS350 2.7 91.7 1.0 NE2 E:HIS396 2.7 95.6 1.0 SG E:CYS390 2.8 0.7 1.0 CE1 E:HIS398 3.0 80.2 1.0 CD2 E:HIS396 3.3 96.3 1.0 CD2 E:HIS350 3.4 87.9 1.0 CD2 E:HIS398 3.5 85.5 1.0 CB E:CYS390 3.7 99.9 1.0 CE1 E:HIS350 3.8 92.5 1.0 CE1 E:HIS396 3.9 97.8 1.0 ND1 E:HIS398 4.2 83.8 1.0 CG E:HIS398 4.5 87.6 1.0 CG E:HIS396 4.6 97.9 1.0 CG E:HIS350 4.6 87.0 1.0 OG E:SER346 4.7 55.9 1.0 ND1 E:HIS350 4.8 89.9 1.0 ND1 E:HIS396 4.8 99.2 1.0 NE2 E:GLN392 4.9 98.0 1.0 CG1 E:ILE387 4.9 93.3 1.0 CD E:GLN392 5.0 99.5 1.0

C.W.Davies, L.N.Paul, M.I.Kim, C.Das. Structural and Thermodynamic Comparison of the Catalytic Domain of Amsh and Amsh-Lp: Nearly Identical Fold But Different Stability. J.Mol.Biol. V. 413 416 2011.
ISSN: ISSN 0022-2836
PubMed: 21888914
DOI: 10.1016/J.JMB.2011.08.029