Zinc in PDB 2gp5: Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate

The structure of Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate, PDB code: 2gp5 was solved by Z.Chen, J.Zang, J.Whetstine, X.Hong, F.Davrazou, T.G.Kutateladze, M.Simpson, S.Dai, J.Hagman, Y.Shi, G.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.67 / 2.28
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.107, 149.524, 57.028, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 28.5

The structure of Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate (pdb code 2gp5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate, PDB code: 2gp5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate


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 Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.7 occ:0.60 NE2 A:HIS240 2.3 45.6 1.0 SG A:CYS234 2.3 42.6 1.0 SG A:CYS306 2.4 59.4 1.0 SG A:CYS308 2.6 68.6 1.0 CB A:CYS306 3.0 56.3 1.0 CD2 A:HIS240 3.1 45.9 1.0 CB A:CYS234 3.2 44.9 1.0 CE1 A:HIS240 3.4 45.7 1.0 CA A:CYS306 3.8 47.9 1.0 N A:ARG309 3.9 82.0 1.0 N A:CYS308 4.0 81.0 1.0 CB A:CYS308 4.0 72.1 1.0 N A:SER307 4.0 61.1 1.0 CG A:ARG309 4.0 81.2 1.0 C A:CYS306 4.1 51.8 1.0 CG A:HIS240 4.3 45.7 1.0 CA A:CYS308 4.4 78.9 1.0 ND1 A:HIS240 4.4 46.0 1.0 CB A:ARG309 4.4 81.1 1.0 CD A:ARG309 4.5 81.4 1.0 CA A:CYS234 4.5 52.7 1.0 C A:SER307 4.7 74.7 1.0 C A:CYS308 4.7 80.2 1.0 O A:ALA236 4.7 49.0 1.0 CA A:ARG309 4.8 88.3 1.0 O A:CYS306 4.9 44.0 1.0 NE A:ARG309 4.9 81.1 1.0 CA A:SER307 4.9 72.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate


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 Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:39.4 occ:0.60 SG B:CYS306 2.3 62.8 1.0 SG B:CYS234 2.3 45.9 1.0 NE2 B:HIS240 2.4 42.6 1.0 SG B:CYS308 2.7 70.7 1.0 CB B:CYS306 2.8 61.9 1.0 CD2 B:HIS240 3.1 42.6 1.0 CB B:CYS234 3.3 53.9 1.0 CE1 B:HIS240 3.5 42.1 1.0 CA B:CYS306 3.6 63.1 1.0 N B:SER307 3.9 79.9 1.0 C B:CYS306 3.9 67.4 1.0 N B:ARG309 3.9 80.4 1.0 N B:CYS308 4.0 0.6 1.0 CG B:ARG309 4.1 78.7 1.0 CB B:CYS308 4.2 76.2 1.0 CG B:HIS240 4.4 42.1 1.0 CB B:ARG309 4.4 80.1 1.0 CA B:CYS308 4.5 0.6 1.0 CD B:ARG309 4.5 77.9 1.0 ND1 B:HIS240 4.5 42.4 1.0 O B:ALA236 4.5 50.6 1.0 CA B:CYS234 4.7 60.1 1.0 C B:SER307 4.7 87.7 1.0 O B:CYS306 4.7 65.3 1.0 C B:CYS308 4.7 0.9 1.0 CA B:ARG309 4.8 79.7 1.0 CA B:SER307 4.9 83.9 1.0 NE B:ARG309 5.0 77.5 1.0 N B:CYS306 5.0 53.8 1.0

Z.Chen, J.Zang, J.Whetstine, X.Hong, F.Davrazou, T.G.Kutateladze, M.Simpson, Q.Mao, C.H.Pan, S.Dai, J.Hagman, K.Hansen, Y.Shi, G.Zhang. Structural Insights Into Histone Demethylation By JMJD2 Family Members Cell(Cambridge,Mass.) V. 125 691 2006.
ISSN: ISSN 0092-8674
PubMed: 16677698
DOI: 10.1016/J.CELL.2006.04.024