Zinc in PDB 4kis: Crystal Structure of A Lsr-Dna Complex

The structure of Crystal Structure of A Lsr-Dna Complex, PDB code: 4kis was solved by K.Rutherford, P.Yuan, K.Perry, G.D.Van Duyne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.86 / 3.20
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	290.750, 290.750, 290.750, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 25.6

The structure of Crystal Structure of A Lsr-Dna Complex also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Zinc atom in the Crystal Structure of A Lsr-Dna Complex (pdb code 4kis). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Lsr-Dna Complex, PDB code: 4kis:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of A Lsr-Dna Complex


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 A Lsr-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.8 occ:1.00 SG A:CYS302 2.3 81.9 1.0 SG A:CYS274 2.3 96.9 1.0 SG A:CYS277 2.3 96.6 1.0 O A:LYS276 2.3 97.1 1.0 SG A:CYS314 2.4 0.0 1.0 CB A:CYS274 2.9 96.9 1.0 CB A:CYS302 3.4 81.9 1.0 C A:LYS276 3.4 97.1 1.0 CB A:CYS314 3.4 0.0 1.0 CB A:CYS277 3.6 96.6 1.0 OG1 A:THR304 4.0 0.1 1.0 CB A:LYS276 4.2 0.8 1.0 N A:CYS277 4.3 0.4 1.0 CA A:LYS276 4.3 97.1 1.0 CA A:CYS274 4.4 93.9 1.0 CA A:CYS277 4.4 0.4 1.0 CG2 A:THR304 4.4 0.1 1.0 N A:LYS276 4.6 97.1 1.0 N A:GLY278 4.7 92.7 1.0 CA A:CYS302 4.7 78.3 1.0 C A:CYS277 4.7 0.4 1.0 C A:CYS274 4.8 93.9 1.0 O A:CYS274 4.8 93.9 1.0 CB A:THR304 4.8 0.1 1.0 CB A:ASN316 4.9 0.1 1.0 N A:LEU279 4.9 90.9 1.0 CA A:CYS314 4.9 0.8 1.0 O A:LEU279 4.9 90.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of A Lsr-Dna Complex


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 A Lsr-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:87.5 occ:1.00 ND1 A:HIS455 2.0 94.7 1.0 OD2 D:ASP330 2.1 81.3 1.0 CE1 A:HIS457 2.1 0.1 1.0 NE2 A:HIS459 2.2 97.1 1.0 ND1 A:HIS457 2.4 0.1 1.0 CG D:ASP330 2.9 81.3 1.0 CG A:HIS455 3.0 94.7 1.0 OD1 D:ASP330 3.0 81.3 1.0 CE1 A:HIS459 3.1 97.1 1.0 CE1 A:HIS455 3.1 94.7 1.0 CB A:HIS455 3.2 94.7 1.0 NE2 A:HIS457 3.4 0.1 1.0 CD2 A:HIS459 3.4 97.1 1.0 CG A:HIS457 3.8 0.1 1.0 CD2 A:HIS455 4.2 94.7 1.0 CD2 A:HIS457 4.2 0.1 1.0 CD D:ARG331 4.2 86.5 1.0 NE2 A:HIS455 4.2 94.7 1.0 CB D:ASP330 4.3 81.3 1.0 ND1 A:HIS459 4.3 97.1 1.0 CG A:HIS459 4.5 97.1 1.0 O D:ASP330 4.6 82.6 1.0 C D:ASP330 4.7 82.6 1.0 NE D:ARG331 4.7 86.5 1.0 CA A:HIS455 4.7 89.1 1.0 N D:ARG331 4.9 89.2 1.0 CB A:HIS457 4.9 0.1 1.0 CE2 D:TYR335 4.9 0.3 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of A Lsr-Dna Complex


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 A Lsr-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:0.8 occ:1.00 CE1 A:HIS460 2.0 86.7 1.0 NE2 A:HIS458 2.1 0.9 1.0 ND1 D:HIS455 2.2 0.2 1.0 CE1 D:HIS459 2.5 0.7 1.0 NE2 A:HIS460 2.8 86.7 1.0 CE1 A:HIS458 2.9 0.9 1.0 ND1 D:HIS459 3.0 0.7 1.0 ND1 A:HIS460 3.1 86.7 1.0 CE1 D:HIS455 3.1 0.2 1.0 CG D:HIS455 3.2 0.2 1.0 CD2 A:HIS458 3.3 0.9 1.0 CB D:HIS455 3.6 0.2 1.0 NE2 D:HIS459 3.6 0.7 1.0 O D:HIS458 4.0 0.5 1.0 CD2 A:HIS460 4.0 86.7 1.0 CG A:HIS460 4.1 86.7 1.0 ND1 A:HIS458 4.2 0.9 1.0 N D:HIS456 4.2 0.0 1.0 NE2 D:HIS455 4.3 0.2 1.0 CG D:HIS459 4.3 0.7 1.0 CA D:HIS455 4.3 0.7 1.0 CD2 D:HIS455 4.3 0.2 1.0 CG A:HIS458 4.3 0.9 1.0 C D:HIS455 4.4 0.7 1.0 O A:HIS459 4.5 87.5 1.0 CD2 D:HIS459 4.6 0.7 1.0 CD1 D:LEU436 4.7 82.7 1.0 CZ3 D:TRP451 4.9 81.8 1.0 CA D:HIS456 4.9 0.0 1.0 CE3 D:TRP451 4.9 81.8 1.0 C D:HIS458 5.0 0.5 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of A Lsr-Dna Complex


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 A Lsr-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:94.5 occ:1.00 SG B:CYS302 2.2 70.5 1.0 SG B:CYS274 2.3 89.1 1.0 SG B:CYS277 2.3 80.6 1.0 SG B:CYS314 2.3 96.5 1.0 O B:LYS276 2.6 82.8 1.0 CB B:CYS274 3.0 89.1 1.0 CB B:CYS302 3.2 70.5 1.0 CB B:CYS314 3.4 96.5 1.0 CG2 B:THR304 3.7 81.5 1.0 CB B:CYS277 3.7 80.6 1.0 C B:LYS276 3.9 82.8 1.0 OG1 B:THR304 4.3 81.5 1.0 CA B:CYS274 4.5 76.2 1.0 CA B:CYS302 4.6 68.1 1.0 CA B:CYS277 4.6 82.0 1.0 C B:CYS277 4.7 82.0 1.0 N B:CYS277 4.7 82.0 1.0 O B:CYS277 4.7 82.0 1.0 CB B:THR304 4.7 81.5 1.0 CA B:CYS314 4.8 0.9 1.0 N B:LEU279 4.8 78.0 1.0 CB B:LEU279 4.8 79.2 1.0 CA B:LYS276 4.9 82.8 1.0 CB B:LYS276 4.9 88.6 1.0 O B:LEU279 4.9 78.0 1.0 CE2 B:PHE281 5.0 84.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of A Lsr-Dna Complex


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 A Lsr-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:0.1 occ:1.00 SG C:CYS277 2.3 0.8 1.0 SG C:CYS314 2.3 0.8 1.0 SG C:CYS302 2.4 0.7 1.0 SG C:CYS274 2.4 0.3 1.0 O C:LYS276 2.6 0.2 1.0 CB C:CYS274 2.8 0.3 1.0 CB C:CYS302 3.5 0.7 1.0 CB C:CYS314 3.6 0.8 1.0 CB C:CYS277 3.6 0.8 1.0 C C:LYS276 3.7 0.2 1.0 CG2 C:THR304 4.0 0.5 1.0 CA C:CYS274 4.3 0.5 1.0 CA C:CYS277 4.5 0.7 1.0 N C:CYS277 4.5 0.7 1.0 O C:CYS274 4.5 0.5 1.0 OG1 C:THR304 4.6 0.5 1.0 CB C:LYS276 4.6 0.9 1.0 N C:GLY278 4.6 1.0 1.0 CA C:LYS276 4.7 0.2 1.0 C C:CYS274 4.7 0.5 1.0 O C:LEU279 4.8 0.9 1.0 N C:LEU279 4.8 0.9 1.0 C C:CYS277 4.8 0.7 1.0 CA C:CYS302 4.9 0.5 1.0 N C:LYS276 4.9 0.2 1.0 CB C:THR304 4.9 0.5 1.0 CA C:CYS314 4.9 0.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of A Lsr-Dna Complex


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 A Lsr-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:0.4 occ:1.00 SG D:CYS274 2.3 94.0 1.0 SG D:CYS314 2.3 0.8 1.0 SG D:CYS302 2.3 84.1 1.0 SG D:CYS277 2.4 97.6 1.0 O D:LYS276 2.6 0.1 1.0 CB D:CYS274 3.0 94.0 1.0 CB D:CYS302 3.2 84.1 1.0 CB D:CYS314 3.6 0.8 1.0 C D:LYS276 3.8 0.1 1.0 CG2 D:THR304 3.9 0.9 1.0 CB D:CYS277 3.9 97.6 1.0 OG1 D:THR304 4.1 0.9 1.0 CA D:CYS274 4.4 91.1 1.0 CA D:CYS302 4.6 90.0 1.0 CB D:LEU279 4.6 85.0 1.0 CA D:CYS277 4.7 0.6 1.0 CB D:THR304 4.7 0.9 1.0 N D:CYS277 4.7 0.6 1.0 CB D:LYS276 4.7 0.3 1.0 N D:LEU279 4.7 85.2 1.0 C D:CYS277 4.7 0.6 1.0 CA D:LYS276 4.8 0.1 1.0 CB D:ASN316 4.8 0.1 1.0 C D:CYS274 4.9 91.1 1.0 O D:CYS274 4.9 91.1 1.0 O D:CYS277 4.9 0.6 1.0 N D:LYS276 5.0 0.1 1.0 CA D:CYS314 5.0 0.6 1.0

K.Rutherford, P.Yuan, K.Perry, R.Sharp, G.D.Van Duyne. Attachment Site Recognition and Regulation of Directionality By the Serine Integrases. Nucleic Acids Res. V. 41 8341 2013.
ISSN: ISSN 0305-1048
PubMed: 23821671
DOI: 10.1093/NAR/GKT580