Zinc in PDB 9jpj: Crystal Structure of Dhdr in Complex with Dna

The structure of Crystal Structure of Dhdr in Complex with Dna, PDB code: 9jpj was solved by P.Sun, B.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.26 / 3.72
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	80.456, 87.044, 133.884, 91.48, 102.48, 117.55
R / Rfree (%)	25 / 29.9

The binding sites of Zinc atom in the Crystal Structure of Dhdr in Complex with Dna (pdb code 9jpj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Dhdr in Complex with Dna, PDB code: 9jpj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Dhdr in Complex with Dna


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 Dhdr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:230.8 occ:1.00 OD2 C:ASP143 2.3 255.8 1.0 CG C:ASP143 3.1 243.4 1.0 OD1 C:ASP143 3.5 252.2 1.0 CG1 C:VAL191 4.1 245.2 1.0 CB C:ASP143 4.3 239.5 1.0 CE1 C:HIS217 4.5 242.9 1.0 NE2 C:HIS217 4.9 249.7 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Dhdr in Complex with Dna


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 Dhdr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:191.1 occ:1.00 NE2 D:HIS147 2.0 176.9 1.0 CE1 D:HIS147 2.2 168.0 1.0 CE1 D:HIS217 2.5 196.3 1.0 NE2 D:HIS195 2.7 168.1 1.0 OD2 D:ASP143 2.7 169.4 1.0 CD2 D:HIS147 3.4 163.4 1.0 NE2 D:HIS217 3.4 203.6 1.0 ND1 D:HIS217 3.5 195.3 1.0 ND1 D:HIS147 3.5 169.5 1.0 CE1 D:HIS195 3.6 166.3 1.0 CG D:ASP143 3.7 164.5 1.0 CD2 D:HIS195 3.7 165.8 1.0 OD1 D:ASP143 3.9 163.9 1.0 CG D:HIS147 4.1 169.5 1.0 NH2 D:ARG99 4.3 195.7 1.0 CD2 D:HIS217 4.6 197.0 1.0 CG D:HIS217 4.7 196.6 1.0 ND1 D:HIS195 4.7 164.0 1.0 NH1 D:ARG99 4.8 197.7 1.0 CG D:HIS195 4.8 164.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Dhdr in Complex with Dna


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 Dhdr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:202.8 occ:1.00 OD2 E:ASP143 2.0 220.4 1.0 NE2 E:HIS147 2.0 212.9 1.0 CE1 E:HIS195 2.1 214.3 1.0 NE2 E:HIS195 2.4 217.0 1.0 CD2 E:HIS147 2.8 202.4 1.0 CG E:ASP143 2.9 208.0 1.0 CE1 E:HIS147 3.2 202.3 1.0 OD1 E:ASP143 3.2 216.7 1.0 ND1 E:HIS195 3.4 204.1 1.0 NE2 E:HIS217 3.5 209.0 1.0 CD2 E:HIS195 3.8 218.7 1.0 CE1 E:HIS217 3.9 202.2 1.0 CG E:HIS147 4.0 198.9 1.0 ND1 E:HIS147 4.2 200.2 1.0 CG E:HIS195 4.2 211.0 1.0 CB E:ASP143 4.3 204.1 1.0 CD2 E:HIS217 4.6 199.6 1.0 O E:ASP143 4.7 205.1 1.0 CA E:ASP143 5.0 208.2 1.0 C E:ASP143 5.0 210.8 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Dhdr in Complex with Dna


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 Dhdr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:204.3 occ:1.00 OD1 F:ASP143 1.9 210.3 1.0 NE2 F:HIS195 2.3 208.5 1.0 CG F:ASP143 2.6 205.5 1.0 NE2 F:HIS147 2.7 209.6 1.0 OD2 F:ASP143 2.9 204.8 1.0 CE1 F:HIS195 3.1 206.6 1.0 NE2 F:HIS217 3.1 220.1 1.0 CE1 F:HIS147 3.2 200.7 1.0 CD2 F:HIS195 3.4 206.2 1.0 CB F:ASP143 3.8 206.6 1.0 CD2 F:HIS147 3.9 196.1 1.0 CE1 F:HIS217 3.9 212.8 1.0 CD2 F:HIS217 4.0 213.5 1.0 ND1 F:HIS195 4.3 204.3 1.0 CG F:HIS195 4.5 204.8 1.0 ND1 F:HIS147 4.5 202.2 1.0 CA F:ASP143 4.7 206.9 1.0 NH2 F:ARG99 4.8 202.7 1.0 CG F:HIS147 4.8 202.2 1.0 O F:ASP143 4.9 205.8 1.0 CG1 F:VAL191 4.9 212.6 1.0 ND1 F:HIS217 4.9 211.8 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Dhdr in Complex with Dna


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 Dhdr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn301 b:261.9 occ:1.00 CE1 I:HIS195 3.0 263.3 1.0 CG1 I:VAL191 3.1 256.1 1.0 NE2 I:HIS195 3.7 266.0 1.0 OD1 I:ASP143 3.9 267.8 1.0 ND1 I:HIS195 4.0 253.1 1.0 CG I:ASP143 4.0 255.4 1.0 CB I:ASP143 4.2 251.4 1.0 OD2 I:ASP143 4.4 264.1 1.0 CB I:VAL191 4.6 263.2 1.0 CE1 I:HIS217 4.7 259.4 1.0 NH1 I:ARG224 4.8 256.8 1.0 CD2 I:HIS195 4.9 267.7 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Dhdr in Complex with Dna


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 Dhdr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn301 b:219.0 occ:1.00 OD1 J:ASP143 2.1 232.8 1.0 CG J:ASP143 3.1 227.9 1.0 NE2 J:HIS147 3.2 239.6 1.0 NE2 J:HIS217 3.4 250.9 1.0 CE1 J:HIS217 3.4 243.7 1.0 OD2 J:ASP143 3.6 227.3 1.0 CD2 J:HIS147 3.8 226.1 1.0 NE2 J:HIS195 3.8 244.7 1.0 CE1 J:HIS147 4.2 230.7 1.0 CE1 J:HIS195 4.3 242.8 1.0 CB J:ASP143 4.4 229.1 1.0 CD2 J:HIS217 4.7 244.3 1.0 ND1 J:HIS217 4.8 242.7 1.0 CD2 J:HIS195 4.8 242.4 1.0 CG1 J:VAL191 4.9 244.1 1.0 O J:ASP143 4.9 228.3 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Dhdr in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Dhdr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn301 b:152.1 occ:1.00 NE2 K:HIS195 2.0 168.3 1.0 NE2 K:HIS147 2.1 172.5 1.0 OD2 K:ASP143 2.3 180.0 1.0 CE1 K:HIS217 2.3 161.8 1.0 NE2 K:HIS217 2.6 168.6 1.0 CE1 K:HIS195 2.6 165.6 1.0 CE1 K:HIS147 3.0 161.8 1.0 CD2 K:HIS147 3.2 162.0 1.0 CD2 K:HIS195 3.2 169.9 1.0 ND1 K:HIS217 3.3 160.7 1.0 CG K:ASP143 3.4 167.6 1.0 CD2 K:HIS217 3.7 159.2 1.0 ND1 K:HIS195 3.9 155.3 1.0 OD1 K:ASP143 4.0 176.4 1.0 CG K:HIS217 4.0 157.4 1.0 ND1 K:HIS147 4.1 159.7 1.0 CG K:HIS195 4.1 162.3 1.0 CG K:HIS147 4.2 158.4 1.0 CB K:ASP143 4.6 163.7 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Dhdr in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Dhdr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:168.7 occ:1.00 OD1 L:ASP143 2.1 205.7 1.0 NE2 L:HIS217 2.3 213.0 1.0 OD2 L:ASP143 2.6 200.2 1.0 CG L:ASP143 2.7 200.9 1.0 NE2 L:HIS195 2.9 208.3 1.0 CE1 L:HIS217 3.0 205.7 1.0 CE1 L:HIS147 3.1 198.1 1.0 NE2 L:HIS147 3.2 207.0 1.0 CD2 L:HIS217 3.5 206.4 1.0 CE1 L:HIS195 3.6 206.4 1.0 CD2 L:HIS195 4.0 206.0 1.0 CB L:ASP143 4.2 202.0 1.0 ND1 L:HIS217 4.2 204.7 1.0 ND1 L:HIS147 4.3 199.6 1.0 CG L:HIS217 4.5 206.0 1.0 CD2 L:HIS147 4.5 193.5 1.0 ND1 L:HIS195 4.8 204.1 1.0 O L:ASP143 4.8 201.2 1.0 CA L:ASP143 5.0 202.3 1.0

P.Sun, B.Wang. Crystal Structure of Dhdr Inducer Binding Domain To Be Published.