Zinc in PDB 5w0r: Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid

All present enzymatic activity of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid:
3.5.4.38;

The structure of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid, PDB code: 5w0r was solved by Q.Qiao, L.Wang, H.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.81 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.960, 179.070, 188.080, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 23.9

The structure of Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid also contains other interesting chemical elements:

Arsenic	(As)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid (pdb code 5w0r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid, PDB code: 5w0r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid


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 Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:36.3 occ:1.00 O1 B:CAC2002 2.0 30.1 1.0 ND1 B:HIS1056 2.2 43.1 1.0 SG B:CYS1090 2.3 42.5 1.0 SG B:CYS1087 2.4 40.1 1.0 CG B:HIS1056 3.1 41.5 1.0 CE1 B:HIS1056 3.1 45.2 1.0 CB B:CYS1090 3.2 41.9 1.0 CB B:HIS1056 3.4 39.1 1.0 AS B:CAC2002 3.4 43.2 1.0 CB B:CYS1087 3.5 45.8 1.0 N B:CYS1087 3.9 42.2 1.0 O B:HOH2127 3.9 24.1 1.0 C1 B:CAC2002 4.0 29.8 1.0 NE2 B:HIS1056 4.1 45.4 1.0 CD2 B:HIS1056 4.1 43.0 1.0 O2 B:CAC2002 4.2 39.4 1.0 N B:CYS1090 4.2 45.5 1.0 CA B:CYS1090 4.3 43.2 1.0 CA B:CYS1087 4.3 44.9 1.0 C B:CYS1087 4.9 46.2 1.0 CA B:HIS1056 4.9 38.8 1.0 C2 B:CAC2002 4.9 26.6 1.0 O B:CYS1087 5.0 44.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid


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 Mbp Fused Activation-Induced Cytidine Deaminase (Aid) in Complex with Cacodylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:42.1 occ:1.00 O1 A:CAC2002 2.0 58.3 1.0 ND1 A:HIS1056 2.0 46.6 1.0 SG A:CYS1090 2.4 37.4 1.0 SG A:CYS1087 2.4 47.7 1.0 CG A:HIS1056 3.0 45.7 1.0 CE1 A:HIS1056 3.0 48.9 1.0 AS A:CAC2002 3.3 49.2 1.0 CB A:HIS1056 3.3 44.3 1.0 CB A:CYS1090 3.4 38.9 1.0 CB A:CYS1087 3.4 43.7 1.0 C1 A:CAC2002 3.7 33.7 1.0 O A:HOH2131 3.9 31.6 1.0 N A:CYS1087 3.9 39.5 1.0 O2 A:CAC2002 4.0 53.1 1.0 NE2 A:HIS1056 4.1 49.2 1.0 CD2 A:HIS1056 4.1 47.0 1.0 CA A:CYS1087 4.2 42.8 1.0 N A:CYS1090 4.2 41.9 1.0 CA A:CYS1090 4.4 40.4 1.0 O A:CYS1087 4.6 41.6 1.0 C A:CYS1087 4.7 43.6 1.0 CA A:HIS1056 4.9 44.8 1.0 C2 A:CAC2002 4.9 33.7 1.0

Q.Qiao, L.Wang, F.L.Meng, J.K.Hwang, F.W.Alt, H.Wu. Aid Recognizes Structured Dna For Class Switch Recombination. Mol. Cell V. 67 361 2017.
ISSN: ISSN 1097-4164
PubMed: 28757211
DOI: 10.1016/J.MOLCEL.2017.06.034