Zinc in PDB 3vdp: Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway

The structure of Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway, PDB code: 3vdp was solved by Q.Tang, X.X.Yan, D.C.Liang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.260, 68.325, 94.056, 90.00, 92.95, 90.00
R / Rfree (%)	19.6 / 22.7

The binding sites of Zinc atom in the Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway (pdb code 3vdp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway, PDB code: 3vdp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:39.5 occ:1.00 SG A:CYS70 2.2 42.7 1.0 SG A:CYS67 2.3 36.5 1.0 SG A:CYS58 2.4 36.5 1.0 SG A:CYS55 2.5 40.8 1.0 CB A:CYS55 3.2 36.6 1.0 CB A:CYS70 3.3 42.3 1.0 CB A:CYS58 3.4 35.7 1.0 CB A:CYS67 3.5 18.8 1.0 N A:CYS58 3.7 40.3 1.0 N A:CYS67 3.9 28.6 1.0 O A:HOH304 4.0 29.6 1.0 CA A:CYS58 4.1 37.4 1.0 N A:CYS70 4.2 39.5 1.0 CA A:CYS67 4.2 38.4 1.0 CA A:CYS70 4.3 43.8 1.0 CB A:ILE57 4.6 32.4 1.0 CA A:CYS55 4.7 33.0 1.0 O A:CYS67 4.7 44.2 1.0 C A:CYS58 4.7 32.6 1.0 CB A:ASN60 4.8 41.1 1.0 C A:ILE57 4.8 38.0 1.0 N A:PHE59 4.8 32.5 1.0 C A:CYS67 4.9 46.2 1.0 N A:ASN60 4.9 29.6 1.0 C A:VAL66 5.0 38.9 1.0

Zinc binding site 2 out of 4 in the Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:36.2 occ:1.00 SG B:CYS58 2.3 32.5 1.0 SG B:CYS70 2.4 36.7 1.0 SG B:CYS67 2.4 40.7 1.0 SG B:CYS55 2.4 35.4 1.0 CB B:CYS55 3.0 30.0 1.0 CB B:CYS58 3.2 39.3 1.0 CB B:CYS70 3.3 41.6 1.0 CB B:CYS67 3.4 45.2 1.0 N B:CYS58 3.7 37.0 1.0 N B:CYS67 3.9 48.7 1.0 CA B:CYS58 4.0 36.9 1.0 O B:HOH318 4.0 36.4 1.0 O B:HOH322 4.0 31.5 1.0 N B:CYS70 4.1 53.2 1.0 CA B:CYS67 4.2 43.9 1.0 O B:HOH374 4.3 30.0 1.0 CA B:CYS70 4.4 44.0 1.0 CA B:CYS55 4.5 37.6 1.0 C B:CYS58 4.7 33.0 1.0 O B:CYS67 4.8 43.4 1.0 C B:CYS67 4.8 47.6 1.0 C B:ILE57 4.8 35.0 1.0 N B:PHE59 4.8 33.4 1.0 CB B:ILE57 4.9 39.8 1.0 CB B:ASN60 4.9 35.6 1.0

Zinc binding site 3 out of 4 in the Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:36.3 occ:1.00 SG C:CYS70 2.3 34.9 1.0 SG C:CYS58 2.3 37.7 1.0 SG C:CYS67 2.4 38.7 1.0 SG C:CYS55 2.4 39.6 1.0 CB C:CYS55 3.1 32.5 1.0 CB C:CYS70 3.3 39.8 1.0 CB C:CYS67 3.4 31.2 1.0 CB C:CYS58 3.4 29.3 1.0 N C:CYS58 3.8 41.1 1.0 N C:CYS67 3.9 30.6 1.0 O C:HOH302 3.9 28.0 1.0 O C:HOH347 4.0 55.5 1.0 CA C:CYS58 4.2 34.4 1.0 N C:CYS70 4.2 43.7 1.0 CA C:CYS67 4.2 33.1 1.0 CA C:CYS70 4.3 40.6 1.0 O C:HOH310 4.6 49.1 1.0 CA C:CYS55 4.6 26.9 1.0 CB C:ILE57 4.7 32.6 1.0 O C:CYS67 4.7 42.7 1.0 C C:CYS58 4.8 32.9 1.0 C C:CYS67 4.8 37.5 1.0 CB C:ASN60 4.8 29.8 1.0 C C:ILE57 4.8 37.5 1.0 N C:ASN60 4.9 27.8 1.0 N C:PHE59 4.9 38.1 1.0 N C:ILE57 5.0 39.1 1.0 C C:VAL66 5.0 41.6 1.0

Zinc binding site 4 out of 4 in the Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure and Biochemical Studies of the Recombination Mediator Protein Recr in Recfor Pathway within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:40.8 occ:1.00 SG D:CYS70 2.3 35.8 1.0 SG D:CYS67 2.3 49.8 1.0 SG D:CYS58 2.3 38.7 1.0 SG D:CYS55 2.4 41.4 1.0 CB D:CYS58 3.1 36.5 1.0 CB D:CYS55 3.1 42.6 1.0 CB D:CYS67 3.3 41.0 1.0 CB D:CYS70 3.4 41.7 1.0 N D:CYS58 3.6 30.1 1.0 O D:HOH311 3.8 30.1 1.0 CA D:CYS58 3.9 32.4 1.0 O D:HOH315 3.9 38.0 1.0 N D:CYS67 3.9 46.9 1.0 CA D:CYS67 4.2 44.5 1.0 N D:CYS70 4.2 49.0 1.0 CA D:CYS70 4.4 47.1 1.0 O D:HOH321 4.4 45.8 1.0 C D:CYS58 4.5 33.0 1.0 CA D:CYS55 4.6 39.9 1.0 N D:PHE59 4.7 39.7 1.0 C D:CYS67 4.8 48.0 1.0 O D:CYS67 4.8 45.9 1.0 C D:ILE57 4.8 31.6 1.0 CB D:ASN60 4.8 44.8 1.0 CB D:ILE57 4.8 29.6 1.0 N D:ASN60 5.0 49.5 1.0

Q.Tang, P.Gao, Y.P.Liu, A.Gao, X.M.An, S.Liu, X.X.Yan, D.C.Liang. Recor Complex Including Recr N-N Dimer and Reco Monomer Displays A High Affinity For Ssdna Nucleic Acids Res. V. 40 11115 2012.
ISSN: ISSN 0305-1048
PubMed: 23019218
DOI: 10.1093/NAR/GKS889