Zinc in PDB 6obd: Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic

The structure of Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic, PDB code: 6obd was solved by R.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.53 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.400, 131.200, 133.800, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 30.7

The binding sites of Zinc atom in the Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic (pdb code 6obd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic, PDB code: 6obd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic


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 Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:30.0 occ:1.00 OE2 A:GLU86 1.4 27.3 1.0 OE2 L:GLU84 1.7 33.0 1.0 OE2 A:GLU84 1.7 29.3 1.0 OE2 L:GLU86 1.8 32.4 1.0 CD A:GLU86 2.5 29.7 1.0 CD L:GLU86 2.6 32.2 1.0 CD L:GLU84 2.9 30.0 1.0 CD A:GLU84 2.9 26.5 1.0 OE1 L:GLU86 3.0 30.5 1.0 OE1 A:GLU86 3.1 28.5 1.0 OE1 A:GLU84 3.6 29.0 1.0 CB L:GLU84 3.7 25.7 1.0 CG L:GLU84 3.7 29.4 1.0 OE1 L:GLU84 3.8 33.2 1.0 CG A:GLU86 3.8 26.9 1.0 NH1 L:ARG66 3.8 23.0 1.0 CG L:GLU86 3.9 29.7 1.0 CG A:GLU84 4.0 26.0 1.0 CB A:GLU84 4.0 25.8 1.0 NH1 A:ARG66 4.0 26.3 1.0 CZ L:ARG66 4.7 27.8 1.0 CZ A:ARG66 4.9 28.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic


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 Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.0 occ:0.50 O3 E:OPE101 2.1 51.1 1.0 P E:OPE101 3.6 51.7 1.0 O2 E:OPE101 4.2 50.7 1.0 O4 E:OPE101 4.3 49.6 1.0 O1 E:OPE101 4.6 49.3 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic


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 Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:30.0 occ:1.00 OE2 B:GLU1 1.1 33.8 1.0 OD1 L:ASN142 1.7 35.1 1.0 CE1 H:HIS165 1.9 20.0 1.0 ND2 L:ASN141 2.3 21.0 1.0 CD B:GLU1 2.4 33.4 1.0 CG L:ASN142 2.9 32.3 1.0 ND1 H:HIS165 2.9 19.8 1.0 NE2 H:HIS165 2.9 25.3 1.0 OE1 B:GLU1 3.2 33.2 1.0 CG L:ASN141 3.2 25.9 1.0 OD1 L:ASN141 3.4 25.5 1.0 ND2 L:ASN142 3.5 34.7 1.0 CG B:GLU1 3.5 33.6 1.0 OG L:SER178 3.9 24.7 1.0 CD2 H:HIS165 4.1 23.8 1.0 CG H:HIS165 4.1 24.6 1.0 O H:GLY163 4.1 24.8 1.0 CB L:ASN142 4.1 27.0 1.0 OG1 H:THR184 4.5 28.6 1.0 CB L:ASN141 4.6 24.2 1.0 C H:GLY163 4.7 25.4 1.0 CA H:GLY163 4.7 26.0 1.0 N L:ASN142 4.8 25.9 1.0 O L:HOH478 4.8 30.4 1.0 CB B:GLU1 4.9 31.4 1.0 CA L:ASN142 5.0 25.9 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic


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 Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:30.0 occ:1.00 OE1 H:GLU1 1.5 40.0 1.0 NE2 B:HIS165 2.0 21.5 1.0 ND2 A:ASN141 2.3 17.4 1.0 ND2 A:ASN142 2.6 30.4 1.0 CD H:GLU1 2.7 36.0 1.0 CD2 B:HIS165 2.9 23.0 1.0 CE1 B:HIS165 3.0 20.9 1.0 OD1 A:ASN142 3.0 40.0 1.0 CG A:ASN142 3.2 33.8 1.0 CG A:ASN141 3.2 23.4 1.0 OE2 H:GLU1 3.4 38.4 1.0 OD1 A:ASN141 3.5 23.1 1.0 CG H:GLU1 3.9 36.4 1.0 OG A:SER178 4.0 22.0 1.0 ND1 B:HIS165 4.0 17.8 1.0 CG B:HIS165 4.1 22.9 1.0 O B:GLY163 4.4 23.5 1.0 O A:HOH478 4.4 19.5 1.0 CG2 B:THR184 4.5 24.1 1.0 CB A:ASN142 4.6 27.3 1.0 CB A:ASN141 4.7 24.2 1.0 N A:ASN142 4.7 24.8 1.0 C B:GLY163 4.8 23.6 1.0 CA B:GLY163 4.8 24.3 1.0 CB B:THR184 4.9 26.1 1.0 CB H:GLU1 4.9 33.5 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic


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 Anti-GLD52 Fab Complex with Human GLD52 Peptide Mimetic within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn102 b:30.0 occ:0.50 O1 E:OPE101 1.9 49.3 1.0 P E:OPE101 3.3 51.7 1.0 O2 E:OPE101 3.7 50.7 1.0 O4 E:OPE101 4.3 49.6 1.0 O3 E:OPE101 4.4 51.1 1.0 CA E:OPE101 4.4 49.8 1.0 O E:SER12 4.9 25.2 1.0

H.Qiu, R.Wei, J.Jaworski, E.Boudanova, H.Hughes, S.Vanpatten, A.Lund, J.Day, Y.Zhou, T.Mcsherry, C.Q.Pan, R.Sendak. Engineering An Anti-CD52 Antibody For Enhanced Deamidation Stability. Mabs V. 11 1266 2019.
ISSN: ESSN 1942-0870
PubMed: 31199181
DOI: 10.1080/19420862.2019.1631117