Zinc in PDB 8wd3: The Crystal Structure of JMJD2A(M1-L359) From Biortus.

The structure of The Crystal Structure of JMJD2A(M1-L359) From Biortus., PDB code: 8wd3 was solved by F.Wang, W.Cheng, Z.Lv, C.Ju, C.Bao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 3.30
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.641, 97.111, 141.083, 90, 90, 90
R / Rfree (%)	24.4 / 29.3

The structure of The Crystal Structure of JMJD2A(M1-L359) From Biortus. also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the The Crystal Structure of JMJD2A(M1-L359) From Biortus. (pdb code 8wd3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of JMJD2A(M1-L359) From Biortus., PDB code: 8wd3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Crystal Structure of JMJD2A(M1-L359) From Biortus.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of JMJD2A(M1-L359) From Biortus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:105.0 occ:1.00 NE2 A:HIS240 2.0 114.9 1.0 SG A:CYS308 2.3 150.6 1.0 SG A:CYS306 2.3 118.8 1.0 SG A:CYS234 2.3 122.5 1.0 CE1 A:HIS240 2.9 112.5 1.0 CD2 A:HIS240 3.0 106.2 1.0 CB A:CYS234 3.4 113.6 1.0 CB A:CYS306 3.4 117.7 1.0 CB A:CYS308 3.5 161.8 1.0 N A:CYS308 3.9 162.6 1.0 CA A:CYS306 4.0 119.5 1.0 ND1 A:HIS240 4.1 105.6 1.0 O A:ALA236 4.1 95.3 1.0 CG A:HIS240 4.1 100.8 1.0 CA A:CYS308 4.2 165.1 1.0 N A:ARG309 4.2 152.8 1.0 CG A:ARG309 4.3 147.6 1.0 N A:SER307 4.5 136.5 1.0 C A:CYS308 4.5 160.7 1.0 C A:CYS306 4.6 127.9 1.0 CD A:ARG309 4.6 140.7 1.0 CA A:CYS234 4.7 109.9 1.0 C A:ALA236 4.7 95.0 1.0 CA A:PHE237 4.9 87.1 1.0 CB A:ARG309 4.9 151.1 1.0 NE A:ARG309 5.0 134.1 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of JMJD2A(M1-L359) From Biortus.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of JMJD2A(M1-L359) From Biortus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:92.2 occ:1.00 NE2 B:HIS240 2.0 104.3 1.0 SG B:CYS308 2.3 115.5 1.0 SG B:CYS306 2.3 95.5 1.0 SG B:CYS234 2.3 110.9 1.0 CE1 B:HIS240 3.0 101.5 1.0 CD2 B:HIS240 3.1 95.7 1.0 CB B:CYS234 3.2 111.3 1.0 CB B:CYS306 3.4 100.2 1.0 CB B:CYS308 3.5 116.5 1.0 N B:CYS308 3.7 122.2 1.0 CA B:CYS306 3.8 100.0 1.0 N B:SER307 4.0 125.2 1.0 ND1 B:HIS240 4.1 94.4 1.0 CA B:CYS308 4.1 122.4 1.0 CG B:HIS240 4.2 87.7 1.0 CA B:CYS234 4.2 116.4 1.0 C B:CYS306 4.2 113.7 1.0 N B:ARG309 4.2 121.8 1.0 O B:CYS234 4.4 121.4 1.0 O B:ALA236 4.5 85.4 1.0 CG B:ARG309 4.5 131.8 1.0 CD B:ARG309 4.5 128.1 1.0 C B:CYS308 4.5 124.9 1.0 C B:SER307 4.8 129.2 1.0 C B:CYS234 4.8 115.5 1.0 NE B:ARG309 4.9 126.2 1.0 CB B:ARG309 4.9 127.7 1.0

F.Wang, W.Cheng, Z.Yuan, H.Shang. The Crystal Structure of JMJD2A(M1-L359) From Biortus. To Be Published.