Zinc in PDB 9myp: Structure of Patiria Miniata HOP1 Chromatin Binding Region

The structure of Structure of Patiria Miniata HOP1 Chromatin Binding Region, PDB code: 9myp was solved by A.R.Rodriguez, Q.Ye, J.Nguyen, K.Chau, K.D.Corbett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.95 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.654, 106.955, 131.402, 90, 90, 90
R / Rfree (%)	19.8 / 23.5

The structure of Structure of Patiria Miniata HOP1 Chromatin Binding Region also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Zinc atom in the Structure of Patiria Miniata HOP1 Chromatin Binding Region (pdb code 9myp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Patiria Miniata HOP1 Chromatin Binding Region, PDB code: 9myp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of Patiria Miniata HOP1 Chromatin Binding Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Patiria Miniata HOP1 Chromatin Binding Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:37.2 occ:1.00 SG A:CYS370 2.3 27.5 1.0 SG A:CYS399 2.3 29.1 1.0 SG A:CYS373 2.4 26.0 1.0 SG A:CYS396 2.4 25.7 1.0 HB2 A:CYS399 2.8 32.1 1.0 H A:CYS373 3.0 33.4 1.0 HB3 A:CYS373 3.0 36.5 1.0 HB3 A:CYS370 3.1 29.0 1.0 HH22 A:ARG355 3.1 36.4 1.0 CB A:CYS399 3.1 26.8 1.0 CB A:CYS370 3.2 24.1 1.0 HB3 A:CYS396 3.2 30.3 1.0 CB A:CYS373 3.2 30.4 1.0 HB2 A:CYS370 3.3 29.0 1.0 H A:CYS396 3.3 27.9 1.0 CB A:CYS396 3.4 25.3 1.0 HB3 A:GLU372 3.6 38.5 1.0 H A:CYS399 3.6 31.1 1.0 N A:CYS373 3.7 27.9 1.0 HH12 A:ARG355 3.7 33.4 1.0 HB3 A:CYS399 3.7 32.1 1.0 NH2 A:ARG355 4.0 30.4 1.0 HB2 A:CYS373 4.0 36.5 1.0 N A:CYS396 4.0 23.2 1.0 CA A:CYS373 4.1 27.1 1.0 HB2 A:CYS396 4.2 30.3 1.0 N A:CYS399 4.2 25.9 1.0 HB2 A:GLN398 4.2 43.1 1.0 H A:GLU372 4.2 32.0 1.0 CA A:CYS399 4.3 29.1 1.0 CA A:CYS396 4.3 26.0 1.0 HE22 A:GLN377 4.3 29.0 1.0 NH1 A:ARG355 4.5 27.9 1.0 HH21 A:ARG355 4.5 36.4 1.0 CB A:GLU372 4.5 32.1 1.0 CA A:CYS370 4.6 24.5 1.0 H A:LEU375 4.7 27.3 1.0 HA A:CYS399 4.7 34.9 1.0 HA A:VAL395 4.7 27.3 1.0 CZ A:ARG355 4.7 32.8 1.0 C A:GLU372 4.8 34.8 1.0 H A:LYS374 4.8 26.4 1.0 HA A:CYS373 4.8 32.5 1.0 C A:CYS396 4.8 24.4 1.0 NE2 A:GLN377 4.9 24.1 1.0 N A:GLU372 4.9 26.7 1.0 C A:CYS373 4.9 23.3 1.0 HA A:CYS370 5.0 29.4 1.0 HB2 A:LEU375 5.0 25.9 1.0 CA A:GLU372 5.0 31.8 1.0

Zinc binding site 2 out of 6 in the Structure of Patiria Miniata HOP1 Chromatin Binding Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Patiria Miniata HOP1 Chromatin Binding Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:31.2 occ:1.00 ND1 A:HIS378 2.2 19.9 1.0 SG A:CYS381 2.3 23.6 1.0 SG A:CYS356 2.3 21.4 1.0 SG A:CYS358 2.3 24.8 1.0 HB2 A:HIS378 2.8 26.8 1.0 HB3 A:CYS356 2.9 29.2 1.0 HB3 A:CYS358 3.1 28.2 1.0 CE1 A:HIS378 3.1 26.6 1.0 CG A:HIS378 3.1 25.2 1.0 CB A:CYS356 3.2 24.4 1.0 HB2 A:CYS381 3.2 26.0 1.0 H A:HIS378 3.2 25.8 1.0 CB A:CYS381 3.3 21.7 1.0 H A:CYS358 3.3 27.6 1.0 HD2 A:ARG430 3.3 30.3 1.0 HE1 A:HIS378 3.3 31.9 1.0 CB A:CYS358 3.3 23.5 1.0 CB A:HIS378 3.4 22.4 1.0 HB3 A:CYS381 3.5 26.0 1.0 HB2 A:CYS356 3.7 29.2 1.0 N A:HIS378 4.0 21.5 1.0 N A:CYS358 4.0 23.0 1.0 HB2 A:CYS358 4.0 28.2 1.0 HB3 A:HIS378 4.2 26.8 1.0 CD A:ARG430 4.2 25.2 1.0 HB3 A:CYS426 4.3 28.7 1.0 NE2 A:HIS378 4.3 24.1 1.0 CA A:CYS358 4.3 22.0 1.0 CA A:HIS378 4.3 21.0 1.0 CD2 A:HIS378 4.3 20.6 1.0 HD2 A:PRO357 4.4 30.4 1.0 CA A:CYS356 4.4 20.0 1.0 H A:CYS381 4.5 25.5 1.0 HB3 A:CYS360 4.5 34.7 1.0 HG3 A:ARG430 4.6 31.8 1.0 O A:HIS378 4.6 20.6 1.0 HG2 A:ARG430 4.6 31.8 1.0 C A:CYS356 4.6 24.5 1.0 H A:CYS360 4.6 29.9 1.0 CA A:CYS381 4.6 21.1 1.0 CG A:ARG430 4.7 26.5 1.0 HD3 A:ARG430 4.8 30.3 1.0 N A:PRO357 4.8 23.5 1.0 HA A:CYS356 4.8 24.1 1.0 NE A:ARG430 4.9 26.2 1.0 HA A:GLN377 4.9 24.5 1.0 HA A:CYS381 4.9 25.3 1.0 H A:GLY359 4.9 31.0 1.0 HB3 A:GLN377 4.9 30.2 1.0 C A:HIS378 5.0 19.4 1.0 HE A:ARG430 5.0 31.4 1.0 O A:CYS360 5.0 26.3 1.0 N A:CYS381 5.0 21.2 1.0 HA A:CYS358 5.0 26.4 1.0

Zinc binding site 3 out of 6 in the Structure of Patiria Miniata HOP1 Chromatin Binding Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Patiria Miniata HOP1 Chromatin Binding Region within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:47.7 occ:1.00 SG C:CYS373 2.3 37.1 1.0 SG C:CYS396 2.3 39.4 1.0 SG C:CYS370 2.4 36.5 1.0 SG C:CYS399 2.4 38.7 1.0 H C:CYS373 2.9 47.4 1.0 HH22 C:ARG355 3.0 55.3 1.0 HB3 C:CYS373 3.1 50.6 1.0 HB3 C:CYS370 3.1 41.4 1.0 HB2 C:CYS399 3.1 60.4 1.0 CB C:CYS370 3.2 34.5 1.0 HB3 C:CYS396 3.2 49.5 1.0 H C:CYS396 3.2 31.6 1.0 CB C:CYS373 3.3 42.2 1.0 HB2 C:CYS370 3.3 41.4 1.0 CB C:CYS396 3.4 41.3 1.0 CB C:CYS399 3.4 50.3 1.0 HH11 C:ARG355 3.6 86.3 1.0 H C:CYS399 3.6 69.3 1.0 N C:CYS373 3.6 39.5 1.0 HB3 C:GLU372 3.7 53.4 1.0 NH2 C:ARG355 3.9 46.1 1.0 N C:CYS396 4.0 26.3 1.0 CA C:CYS373 4.0 38.1 1.0 HB2 C:CYS373 4.1 50.6 1.0 HB3 C:CYS399 4.1 60.4 1.0 HB2 C:CYS396 4.1 49.5 1.0 CA C:CYS396 4.2 37.0 1.0 N C:CYS399 4.3 57.8 1.0 H C:GLU372 4.3 46.9 1.0 NH1 C:ARG355 4.3 71.9 1.0 HE22 C:GLN377 4.4 42.5 1.0 HH21 C:ARG355 4.4 55.3 1.0 HB2 C:GLN398 4.4 83.2 1.0 CA C:CYS399 4.5 56.8 1.0 H C:LEU375 4.6 33.7 1.0 CB C:GLU372 4.6 44.5 1.0 CZ C:ARG355 4.6 63.6 1.0 CA C:CYS370 4.6 30.1 1.0 H C:LYS374 4.6 42.3 1.0 C C:GLU372 4.8 35.1 1.0 HA C:VAL395 4.8 43.2 1.0 HA C:CYS373 4.8 45.7 1.0 C C:CYS373 4.8 38.4 1.0 C C:CYS396 4.9 44.9 1.0 HB2 C:LEU375 4.9 38.3 1.0 NE2 C:GLN377 4.9 35.4 1.0 HA C:CYS370 5.0 36.1 1.0 N C:LYS374 5.0 35.2 1.0 HA C:CYS399 5.0 68.2 1.0 N C:GLU372 5.0 39.0 1.0

Zinc binding site 4 out of 6 in the Structure of Patiria Miniata HOP1 Chromatin Binding Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Patiria Miniata HOP1 Chromatin Binding Region within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:46.8 occ:1.00 ND1 C:HIS378 2.1 34.2 1.0 SG C:CYS356 2.2 32.2 1.0 SG C:CYS381 2.3 33.1 1.0 SG C:CYS358 2.4 38.1 1.0 HB3 C:CYS358 2.9 51.0 1.0 HB2 C:HIS378 2.9 40.3 1.0 HB3 C:CYS356 3.0 38.5 1.0 CE1 C:HIS378 3.0 38.4 1.0 HD2 C:ARG430 3.1 48.0 1.0 HB2 C:CYS381 3.1 31.8 1.0 CG C:HIS378 3.1 32.9 1.0 HE1 C:HIS378 3.2 46.0 1.0 H C:HIS378 3.2 36.7 1.0 CB C:CYS356 3.2 32.0 1.0 CB C:CYS358 3.3 42.5 1.0 CB C:CYS381 3.3 26.5 1.0 H C:CYS358 3.3 52.9 1.0 HB3 C:CYS381 3.5 31.8 1.0 CB C:HIS378 3.5 33.6 1.0 HB2 C:CYS356 3.7 38.5 1.0 HB2 C:CYS358 3.9 51.0 1.0 N C:HIS378 4.0 30.6 1.0 N C:CYS358 4.0 44.1 1.0 CD C:ARG430 4.0 40.0 1.0 NE2 C:HIS378 4.2 36.4 1.0 CD2 C:HIS378 4.2 34.0 1.0 CA C:CYS358 4.3 41.4 1.0 HB3 C:HIS378 4.3 40.3 1.0 HB3 C:CYS426 4.3 44.5 1.0 CA C:HIS378 4.3 27.4 1.0 H C:CYS381 4.4 38.1 1.0 HB3 C:CYS360 4.5 54.4 1.0 HD3 C:ARG430 4.5 48.0 1.0 HD2 C:PRO357 4.5 47.9 1.0 CA C:CYS356 4.5 36.6 1.0 HG2 C:ARG430 4.5 42.5 1.0 C C:CYS356 4.6 42.2 1.0 HG3 C:ARG430 4.6 42.5 1.0 O C:HIS378 4.6 27.8 1.0 CA C:CYS381 4.7 31.2 1.0 H C:CYS360 4.7 53.5 1.0 CG C:ARG430 4.7 35.5 1.0 NE C:ARG430 4.8 46.0 1.0 N C:PRO357 4.8 44.3 1.0 HA C:GLN377 4.8 38.3 1.0 O C:CYS356 4.9 35.3 1.0 HB3 C:GLN377 4.9 36.6 1.0 HE2 C:HIS378 4.9 43.7 1.0 HA C:CYS381 4.9 37.4 1.0 HA C:CYS356 5.0 44.0 1.0 HE C:ARG430 5.0 55.2 1.0 N C:CYS381 5.0 31.7 1.0 HA C:CYS358 5.0 49.7 1.0 C C:HIS378 5.0 31.2 1.0 O C:CYS360 5.0 43.4 1.0

Zinc binding site 5 out of 6 in the Structure of Patiria Miniata HOP1 Chromatin Binding Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Patiria Miniata HOP1 Chromatin Binding Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:42.2 occ:1.00 SG B:CYS370 2.3 31.8 1.0 SG B:CYS373 2.4 31.7 1.0 SG B:CYS396 2.4 29.6 1.0 SG B:CYS399 2.4 30.1 1.0 H B:CYS373 2.8 39.7 1.0 HB2 B:CYS399 2.9 38.3 1.0 HB3 B:CYS370 3.1 33.5 1.0 HB3 B:CYS373 3.1 41.6 1.0 O B:HOH665 3.1 51.6 1.0 CB B:CYS370 3.2 27.9 1.0 CB B:CYS399 3.2 31.9 1.0 HH22 B:ARG355 3.3 48.8 1.0 HB2 B:CYS370 3.3 33.5 1.0 CB B:CYS373 3.3 34.7 1.0 H B:CYS396 3.3 31.8 1.0 HB3 B:CYS396 3.3 30.2 1.0 H B:CYS399 3.5 48.5 1.0 HB3 B:GLU372 3.5 53.3 1.0 CB B:CYS396 3.5 25.2 1.0 N B:CYS373 3.6 33.1 1.0 HH12 B:ARG355 3.7 40.4 1.0 HB3 B:CYS399 3.8 38.3 1.0 CA B:CYS373 4.0 33.2 1.0 N B:CYS396 4.1 26.5 1.0 NH2 B:ARG355 4.1 40.6 1.0 HB2 B:CYS373 4.1 41.6 1.0 N B:CYS399 4.1 40.5 1.0 H B:GLU372 4.1 43.5 1.0 HB2 B:CYS396 4.2 30.2 1.0 CA B:CYS399 4.3 42.4 1.0 CA B:CYS396 4.3 27.9 1.0 HB2 B:GLN398 4.3 56.1 1.0 CB B:GLU372 4.4 44.4 1.0 HE22 B:GLN377 4.4 31.9 1.0 H B:LYS374 4.5 39.5 1.0 NH1 B:ARG355 4.5 33.7 1.0 H B:LEU375 4.6 36.8 1.0 CA B:CYS370 4.6 27.8 1.0 C B:GLU372 4.7 37.9 1.0 HH21 B:ARG355 4.7 48.8 1.0 HA B:CYS399 4.7 50.9 1.0 N B:GLU372 4.8 36.3 1.0 HA B:VAL395 4.8 33.5 1.0 HA B:CYS373 4.8 39.8 1.0 CZ B:ARG355 4.8 39.7 1.0 C B:CYS373 4.9 29.8 1.0 CA B:GLU372 4.9 32.1 1.0 C B:CYS396 4.9 32.4 1.0 N B:LYS374 4.9 32.9 1.0 HB2 B:GLU372 4.9 53.3 1.0 HB2 B:LEU375 4.9 35.6 1.0

Zinc binding site 6 out of 6 in the Structure of Patiria Miniata HOP1 Chromatin Binding Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Patiria Miniata HOP1 Chromatin Binding Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:39.4 occ:1.00 ND1 B:HIS378 2.1 28.6 1.0 SG B:CYS381 2.3 30.1 1.0 SG B:CYS356 2.3 27.5 1.0 SG B:CYS358 2.3 31.0 1.0 HB3 B:CYS356 2.9 34.2 1.0 HB2 B:HIS378 2.9 33.5 1.0 CE1 B:HIS378 3.0 32.2 1.0 HB3 B:CYS358 3.0 39.6 1.0 CG B:HIS378 3.1 29.9 1.0 HE1 B:HIS378 3.2 38.6 1.0 CB B:CYS356 3.2 28.5 1.0 HB2 B:CYS381 3.2 32.9 1.0 HD2 B:ARG430 3.2 45.7 1.0 H B:HIS378 3.3 32.4 1.0 CB B:CYS381 3.3 27.4 1.0 H B:CYS358 3.3 39.2 1.0 CB B:CYS358 3.3 33.0 1.0 CB B:HIS378 3.5 27.9 1.0 HB3 B:CYS381 3.5 32.9 1.0 HB2 B:CYS356 3.7 34.2 1.0 HB2 B:CYS358 4.0 39.6 1.0 N B:HIS378 4.0 27.0 1.0 N B:CYS358 4.1 32.6 1.0 CD B:ARG430 4.2 38.0 1.0 NE2 B:HIS378 4.2 33.5 1.0 HB3 B:CYS426 4.2 39.9 1.0 HB3 B:HIS378 4.2 33.5 1.0 CD2 B:HIS378 4.2 27.2 1.0 HD2 B:PRO357 4.3 32.4 1.0 CA B:CYS358 4.3 32.6 1.0 CA B:HIS378 4.3 29.1 1.0 CA B:CYS356 4.4 32.4 1.0 H B:CYS381 4.5 33.8 1.0 HG2 B:ARG430 4.5 36.5 1.0 HG3 B:ARG430 4.5 36.5 1.0 O B:HIS378 4.6 25.1 1.0 C B:CYS356 4.6 31.5 1.0 CG B:ARG430 4.7 30.4 1.0 HB3 B:CYS360 4.7 40.2 1.0 CA B:CYS381 4.7 27.9 1.0 HD3 B:ARG430 4.7 45.7 1.0 N B:PRO357 4.7 27.0 1.0 H B:CYS360 4.8 44.7 1.0 HA B:CYS356 4.8 38.9 1.0 HB3 B:GLN377 4.8 34.3 1.0 HA B:GLN377 4.9 34.6 1.0 NE B:ARG430 4.9 36.3 1.0 O B:CYS360 4.9 33.7 1.0 CD B:PRO357 4.9 27.0 1.0 HA B:CYS381 4.9 33.5 1.0 C B:HIS378 4.9 30.0 1.0 HE2 B:HIS378 4.9 40.3 1.0 N B:CYS381 5.0 28.1 1.0

A.A.Rodriguez, K.D.Corbett. Structure of Patiria Miniata HOP1 Chromatin Binding Region To Be Published.