Zinc in PDB 2b5l: Crystal Structure of DDB1 in Complex with Simian Virus 5 V Protein

The structure of Crystal Structure of DDB1 in Complex with Simian Virus 5 V Protein, PDB code: 2b5l was solved by T.Li, X.Chen, K.C.Garbutt, P.Zhou, N.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.80 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.758, 240.792, 117.177, 90.00, 101.79, 90.00
R / Rfree (%)	22.9 / 29.9

The binding sites of Zinc atom in the Crystal Structure of DDB1 in Complex with Simian Virus 5 V Protein (pdb code 2b5l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of DDB1 in Complex with Simian Virus 5 V Protein, PDB code: 2b5l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of DDB1 in Complex with Simian Virus 5 V Protein


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 DDB1 in Complex with Simian Virus 5 V Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3001 b:35.0 occ:1.00 SG C:CYS194 2.2 57.7 1.0 SG C:CYS208 2.2 68.3 1.0 CB C:CYS211 2.2 53.7 1.0 SG C:CYS206 2.3 0.8 1.0 SG C:CYS211 2.3 53.7 1.0 CB C:CYS194 2.5 57.7 1.0 CB C:CYS208 3.0 68.3 1.0 CA C:CYS194 3.2 71.3 1.0 N C:CYS194 3.4 71.3 1.0 CA C:CYS211 3.6 58.3 1.0 N C:CYS208 3.7 56.5 1.0 N C:CYS211 3.8 58.3 1.0 CA C:CYS208 3.8 56.5 1.0 CB C:CYS206 3.9 0.8 1.0 O C:CYS208 4.1 56.5 1.0 C C:CYS208 4.1 56.5 1.0 O C:GLY164 4.2 81.8 1.0 N C:GLY169 4.2 63.2 1.0 CA C:GLY168 4.3 59.3 1.0 CB C:PRO192 4.3 76.6 1.0 N C:THR207 4.5 61.9 1.0 C C:SER193 4.6 57.0 1.0 CA C:CYS206 4.6 76.8 1.0 C C:CYS194 4.7 71.3 1.0 N C:SER193 4.7 57.0 1.0 C C:CYS211 4.8 58.3 1.0 C C:GLY168 4.8 59.3 1.0 C C:THR207 4.9 61.9 1.0 C C:PRO192 5.0 42.0 1.0 CG C:GLN210 5.0 65.7 1.0 C C:CYS206 5.0 76.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of DDB1 in Complex with Simian Virus 5 V Protein


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 DDB1 in Complex with Simian Virus 5 V Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3002 b:35.0 occ:1.00 CB C:CYS218 2.1 36.0 1.0 SG C:CYS190 2.2 84.4 1.0 SG C:CYS215 2.3 55.3 1.0 SG C:CYS218 2.3 36.0 1.0 CA C:CYS218 2.8 74.0 1.0 ND1 C:HIS171 3.0 55.5 1.0 N C:CYS218 3.0 74.0 1.0 CB C:CYS190 3.0 84.4 1.0 CB C:CYS215 3.2 55.3 1.0 N C:CYS215 3.5 63.7 1.0 CE1 C:HIS171 3.9 55.5 1.0 CG C:HIS171 3.9 55.5 1.0 CA C:CYS215 3.9 63.7 1.0 C C:GLU217 3.9 68.4 1.0 CB C:HIS171 4.0 55.5 1.0 C C:CYS218 4.3 74.0 1.0 CA C:CYS190 4.5 52.4 1.0 C C:THR214 4.5 75.6 1.0 O C:GLU217 4.6 68.4 1.0 N C:GLU217 4.6 68.4 1.0 CA C:GLU217 4.7 68.4 1.0 CB C:GLU217 4.7 77.4 1.0 C C:CYS215 4.7 63.7 1.0 NH1 C:ARG173 4.8 45.6 1.0 O C:CYS218 5.0 74.0 1.0 NE2 C:HIS171 5.0 55.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of DDB1 in Complex with Simian Virus 5 V Protein


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 DDB1 in Complex with Simian Virus 5 V Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3003 b:35.0 occ:1.00 SG D:CYS211 2.4 76.1 1.0 SG D:CYS194 2.4 60.2 1.0 SG D:CYS208 2.4 99.7 1.0 SG D:CYS206 2.4 63.2 1.0 CB D:CYS194 2.5 60.2 1.0 CB D:CYS211 2.6 76.1 1.0 CB D:CYS208 2.6 99.7 1.0 O D:CYS208 3.0 0.2 1.0 N D:CYS208 3.1 0.2 1.0 CA D:CYS208 3.2 0.2 1.0 C D:CYS208 3.5 0.2 1.0 CB D:CYS206 3.6 63.2 1.0 N D:CYS211 3.7 87.2 1.0 CA D:CYS211 3.8 87.2 1.0 CA D:CYS194 3.9 86.8 1.0 CA D:CYS206 4.0 84.4 1.0 N D:THR207 4.0 62.9 1.0 N D:CYS194 4.1 86.8 1.0 C D:CYS206 4.2 84.4 1.0 C D:THR207 4.2 62.9 1.0 CB D:PRO192 4.3 83.9 1.0 N D:GLY169 4.4 0.4 1.0 CA D:GLY168 4.5 90.9 1.0 C D:CYS194 4.7 86.8 1.0 CA D:THR207 4.8 62.9 1.0 N D:HIS209 4.9 85.8 1.0 C D:CYS211 4.9 87.2 1.0 O D:PRO192 4.9 72.0 1.0 C D:PRO192 4.9 72.0 1.0 C D:GLY168 5.0 90.9 1.0 N D:GLN210 5.0 0.7 1.0 C D:GLN210 5.0 0.7 1.0 O D:CYS211 5.0 87.2 1.0 O D:CYS206 5.0 84.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of DDB1 in Complex with Simian Virus 5 V Protein


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 DDB1 in Complex with Simian Virus 5 V Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3004 b:35.0 occ:1.00 SG D:CYS190 2.1 0.2 1.0 SG D:CYS215 2.3 0.5 1.0 SG D:CYS218 2.4 0.5 1.0 CB D:CYS215 2.5 0.5 1.0 N D:CYS215 2.6 0.1 1.0 CB D:CYS190 2.7 0.2 1.0 CA D:CYS215 2.8 0.1 1.0 C D:CYS215 3.2 0.1 1.0 CB D:CYS218 3.4 0.5 1.0 N D:CYS218 3.5 0.1 1.0 O D:CYS215 3.6 0.1 1.0 C D:THR214 3.8 0.5 1.0 ND1 D:HIS171 3.9 0.5 1.0 N D:SER216 3.9 74.5 1.0 CA D:CYS218 4.0 0.1 1.0 N D:GLU217 4.1 0.4 1.0 CA D:CYS190 4.2 70.5 1.0 CA D:THR214 4.3 0.5 1.0 CB D:HIS171 4.5 0.5 1.0 C D:GLU217 4.5 0.4 1.0 CG D:HIS171 4.6 0.5 1.0 CA D:GLU217 4.7 0.4 1.0 C D:CYS218 4.7 0.1 1.0 O D:THR214 4.8 0.5 1.0 NH1 D:ARG173 4.8 66.1 1.0 CE1 D:HIS171 4.8 0.5 1.0 CB D:GLU217 4.9 95.1 1.0 CA D:SER216 5.0 74.5 1.0 C D:SER216 5.0 74.5 1.0

T.Li, X.Chen, K.C.Garbutt, P.Zhou, N.Zheng. Structure of DDB1 in Complex with A Paramyxovirus V Protein: Viral Hijack of A Propeller Cluster in Ubiquitin Ligase. Cell(Cambridge,Mass.) V. 124 105 2006.
ISSN: ISSN 0092-8674
PubMed: 16413485
DOI: 10.1016/J.CELL.2005.10.033