Zinc in PDB 1t4k: Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab

The structure of Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab, PDB code: 1t4k was solved by X.Zhu, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.701, 81.228, 149.496, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.1

The binding sites of Zinc atom in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab (pdb code 1t4k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab, PDB code: 1t4k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:58.1 occ:0.79 OE2 A:GLU185 2.1 37.9 1.0 NE2 A:HIS189 2.4 39.1 1.0 O D:HOH309 2.6 32.8 1.0 CD A:GLU185 2.7 44.4 1.0 OE1 A:GLU185 2.8 48.1 1.0 CE1 A:HIS189 3.2 37.4 1.0 O D:HOH318 3.4 33.5 1.0 CD2 A:HIS189 3.5 36.0 1.0 OG D:SER168 3.8 40.8 1.0 CB D:SER168 4.2 34.7 1.0 CG A:GLU185 4.2 37.9 1.0 NH2 A:ARG155 4.4 61.3 1.0 ND1 A:HIS189 4.4 36.6 1.0 CD D:PRO194 4.6 32.4 1.0 CG A:HIS189 4.6 36.2 1.0 O D:THR192 4.8 31.6 1.0 O D:SER168 4.9 28.6 1.0 CG D:PRO194 4.9 35.9 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:64.9 occ:0.41 NE2 B:HIS172 2.4 48.4 1.0 OD1 A:ASN138 2.4 46.7 1.0 CE1 B:HIS172 3.0 49.3 1.0 OD2 A:ASP167 3.1 57.9 1.0 CD2 B:HIS172 3.6 46.3 1.0 OD2 A:ASP170 3.6 65.1 1.0 CG A:ASN138 3.6 41.2 1.0 CG A:ASP167 4.0 56.8 1.0 ND1 B:HIS172 4.3 49.4 1.0 ND2 A:ASN138 4.4 47.8 1.0 CB A:ASP167 4.4 53.3 1.0 OG1 A:THR172 4.5 27.5 1.0 O A:HOH333 4.5 34.6 1.0 CG A:ASP170 4.5 60.6 1.0 CG B:HIS172 4.5 45.2 1.0 OG A:SER174 4.6 35.8 1.0 CB A:ASN138 4.7 39.2 1.0 OD1 A:ASP170 4.7 63.3 1.0 OD1 A:ASP167 4.9 60.1 1.0 CA A:ASN138 5.0 38.1 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:61.9 occ:0.75 OD2 B:ASP54 1.8 30.9 1.0 O B:HOH381 2.5 38.9 1.0 CG B:ASP54 2.9 41.2 1.0 OD1 B:ASP54 3.4 41.2 1.0 OG B:SER56 4.0 43.3 1.0 CB B:ASP54 4.1 38.0 1.0 CB B:SER56 4.4 40.0 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn308 b:50.7 occ:1.00 NE2 B:HIS83 2.1 42.0 1.0 O B:HOH336 2.4 29.9 1.0 CD2 B:HIS83 2.9 37.7 1.0 CE1 B:HIS83 3.1 40.5 1.0 O B:PHE65 4.0 54.4 1.0 CG B:HIS83 4.1 35.5 1.0 OG B:SER83A 4.1 42.7 1.0 ND1 B:HIS83 4.2 37.2 1.0 C B:PHE65 4.9 53.3 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn309 b:54.7 occ:0.79 OD2 B:ASP72 2.2 54.0 1.0 OD1 B:ASP72 2.6 49.6 1.0 CG B:ASP72 2.8 49.8 1.0 CB B:SER74 3.5 56.4 1.0 OG B:SER74 3.8 62.2 1.0 CB B:ASP72 4.3 48.0 1.0 CG B:LYS75 4.4 49.8 1.0 CE B:LYS75 4.4 56.7 1.0 CD B:LYS75 4.4 52.8 1.0 N B:LYS75 4.7 53.5 1.0 CA B:SER74 4.7 55.5 1.0 N B:SER74 4.9 53.3 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:61.9 occ:0.51 ND2 C:ASN138 2.2 41.4 1.0 O D:HOH379 2.3 51.9 1.0 NE2 D:HIS172 2.4 45.8 1.0 CE1 D:HIS172 3.0 45.2 1.0 OD2 C:ASP167 3.2 65.0 1.0 CG C:ASN138 3.3 39.4 1.0 CD2 D:HIS172 3.5 42.8 1.0 OD1 C:ASN138 3.6 46.2 1.0 OD2 C:ASP170 3.8 66.0 1.0 OG C:SER174 4.2 37.2 1.0 OG1 C:THR172 4.2 38.6 1.0 CG C:ASP167 4.2 63.4 1.0 ND1 D:HIS172 4.2 43.2 1.0 CG D:HIS172 4.5 41.8 1.0 CB C:ASN138 4.5 37.9 1.0 CB C:ASP167 4.5 60.3 1.0 CG C:ASP170 4.7 64.5 1.0 OD1 C:ASP170 4.8 62.6 1.0 CA C:ASN138 4.9 39.9 1.0 N C:ASN138 5.0 38.1 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:69.1 occ:0.42 ND1 C:HIS189 2.4 76.0 1.0 OD2 C:ASP151 2.6 55.4 1.0 CE1 C:HIS189 2.8 77.2 1.0 CB C:ASP151 3.0 62.3 1.0 CG C:ASP151 3.2 60.3 1.0 CG C:HIS189 3.7 75.7 1.0 NE2 C:HIS189 4.1 75.4 1.0 O C:ILE150 4.1 70.5 1.0 CB C:HIS189 4.4 73.4 1.0 CA C:ASP151 4.4 65.1 1.0 OD1 C:ASP151 4.5 55.6 1.0 CD2 C:HIS189 4.5 74.6 1.0 O C:ASP151 4.7 67.8 1.0 C C:ILE150 4.8 68.0 1.0 CA C:HIS189 4.9 72.6 1.0 N C:ASP151 5.0 66.9 1.0 C C:ASP151 5.0 66.3 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn306 b:66.0 occ:0.38 OE2 C:GLU185 2.3 87.7 1.0 CD C:GLU185 2.9 86.0 1.0 OE1 C:GLU185 3.1 90.4 1.0 NH2 C:ARG155 3.4 76.3 1.0 NE2 C:HIS189 3.4 75.4 1.0 NH2 C:ARG188 4.0 80.5 1.0 CG C:GLU185 4.0 81.5 1.0 CZ C:ARG155 4.1 78.0 1.0 CE1 C:HIS189 4.1 77.2 1.0 NH1 C:ARG155 4.5 77.4 1.0 CD2 C:HIS189 4.6 74.6 1.0 NE C:ARG155 4.8 79.1 1.0 CZ C:ARG188 5.0 79.0 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab


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 Unliganded Aldolase Antibody 93F3 Fab within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn307 b:65.1 occ:0.47 OE1 D:GLU204 2.4 66.6 1.0 OE1 A:GLU187 3.4 57.0 1.0 CD D:GLU204 3.5 66.4 1.0 OE2 D:GLU204 3.9 70.5 1.0 NZ A:LYS183 3.9 60.9 1.0 CD A:GLU187 4.5 54.3 1.0 CG D:GLU204 4.7 61.2 1.0

X.Zhu, F.Tanaka, Y.Hu, A.Heine, R.Fuller, G.Zhong, A.J.Olson, R.A.Lerner, C.F.Barbas, I.A.Wilson. The Origin of Enantioselectivity in Aldolase Antibodies: Crystal Structure, Site-Directed Mutagenesis, and Computational Analysis J.Mol.Biol. V. 343 1269 2004.
ISSN: ISSN 0022-2836
PubMed: 15491612
DOI: 10.1016/J.JMB.2004.08.102