Iron in PDB 6mev: Structure of JMJD6 Bound to Mono-Methyl Arginine.

The structure of Structure of JMJD6 Bound to Mono-Methyl Arginine., PDB code: 6mev was solved by S.Lee, G.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	100.547, 141.906, 149.263, 90.00, 96.80, 90.00
R / Rfree (%)	22.9 / 28.7

The binding sites of Iron atom in the Structure of JMJD6 Bound to Mono-Methyl Arginine. (pdb code 6mev). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of JMJD6 Bound to Mono-Methyl Arginine., PDB code: 6mev:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Structure of JMJD6 Bound to Mono-Methyl Arginine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of JMJD6 Bound to Mono-Methyl Arginine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:35.4 occ:0.00 NE2 A:HIS187 1.5 30.5 1.0 OD1 A:ASP189 1.6 58.4 1.0 NE2 A:HIS273 1.6 30.8 1.0 O5 A:AKG401 1.8 33.7 0.0 OXT A:NMM403 2.0 43.5 1.0 C1 A:AKG401 2.2 34.4 0.0 C2 A:AKG401 2.3 33.7 0.0 O1 A:AKG401 2.3 36.6 0.0 CE1 A:HIS187 2.5 33.7 1.0 CE1 A:HIS273 2.5 30.3 1.0 CD2 A:HIS273 2.6 31.4 1.0 CD2 A:HIS187 2.7 28.8 1.0 CG A:ASP189 2.7 37.9 1.0 O2 A:AKG401 3.1 32.9 0.0 OD2 A:ASP189 3.2 41.1 1.0 C A:NMM403 3.3 48.5 1.0 ND1 A:HIS187 3.6 30.7 1.0 ND1 A:HIS273 3.6 24.4 1.0 CG A:HIS273 3.7 27.8 1.0 CG A:HIS187 3.7 26.0 1.0 C3 A:AKG401 3.8 31.1 0.0 O A:NMM403 4.0 47.1 1.0 CB A:ASP189 4.1 26.9 1.0 CA A:NMM403 4.4 53.8 1.0 N A:ASP189 4.4 22.4 1.0 CA A:ASP189 4.4 27.9 1.0 C4 A:AKG401 4.5 31.2 0.0 O A:HOH506 4.5 22.1 1.0 CB A:NMM403 4.7 42.4 1.0 O A:HOH521 4.7 40.2 1.0 O A:HOH539 4.8 37.9 1.0 N A:NMM403 4.8 42.4 1.0

Iron binding site 2 out of 8 in the Structure of JMJD6 Bound to Mono-Methyl Arginine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of JMJD6 Bound to Mono-Methyl Arginine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:33.2 occ:0.00 NE2 B:HIS187 1.4 27.7 1.0 CE1 B:HIS187 1.7 39.6 1.0 OD1 B:ASP189 1.8 25.7 1.0 NE2 B:HIS273 1.9 33.5 1.0 O5 B:AKG600 2.1 34.4 0.0 O1 B:AKG600 2.3 34.1 0.0 C2 B:AKG600 2.5 34.5 0.0 C1 B:AKG600 2.6 34.4 0.0 CD2 B:HIS273 2.7 35.9 1.0 CD2 B:HIS187 2.8 36.4 1.0 CG B:ASP189 2.9 34.2 1.0 ND1 B:HIS187 3.0 31.8 1.0 CE1 B:HIS273 3.1 31.3 1.0 OD2 B:ASP189 3.2 35.2 1.0 CG B:HIS187 3.5 30.7 1.0 C3 B:AKG600 3.7 34.8 0.0 O2 B:AKG600 3.8 34.5 0.0 CG B:HIS273 3.9 36.9 1.0 C4 B:AKG600 3.9 35.2 0.0 ND1 B:HIS273 4.0 35.0 1.0 O B:HOH709 4.4 34.3 1.0 CB B:ASP189 4.4 23.8 1.0 O B:HOH716 4.5 42.4 1.0 CA B:ASP189 5.0 35.7 1.0

Iron binding site 3 out of 8 in the Structure of JMJD6 Bound to Mono-Methyl Arginine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of JMJD6 Bound to Mono-Methyl Arginine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:28.7 occ:0.00 NE2 C:HIS187 1.3 20.3 1.0 CE1 C:HIS187 1.7 37.0 1.0 OD1 C:ASP189 1.8 26.5 1.0 NE2 C:HIS273 1.8 32.4 1.0 C2 C:AKG600 2.2 30.6 0.0 O5 C:AKG600 2.2 30.4 0.0 O2 C:AKG600 2.4 29.4 0.0 C1 C:AKG600 2.5 30.0 0.0 CD2 C:HIS187 2.7 31.5 1.0 CD2 C:HIS273 2.8 28.2 1.0 CG C:ASP189 2.9 33.0 1.0 CE1 C:HIS273 2.9 27.6 1.0 ND1 C:HIS187 3.0 26.8 1.0 C3 C:AKG600 3.2 31.1 0.0 OD2 C:ASP189 3.3 31.0 1.0 CG C:HIS187 3.4 25.2 1.0 O1 C:AKG600 3.5 30.2 0.0 CG C:HIS273 3.9 28.7 1.0 ND1 C:HIS273 3.9 26.1 1.0 O C:HOH733 4.3 31.5 1.0 CB C:ASP189 4.4 18.9 1.0 C4 C:AKG600 4.5 32.4 0.0 CA C:ASP189 4.9 26.6 1.0 N C:ASP189 5.0 27.9 1.0 CB C:HIS187 5.0 25.9 1.0

Iron binding site 4 out of 8 in the Structure of JMJD6 Bound to Mono-Methyl Arginine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of JMJD6 Bound to Mono-Methyl Arginine. within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:41.0 occ:0.00 NE2 D:HIS187 1.0 34.8 1.0 CE1 D:HIS187 1.6 46.9 1.0 NE2 D:HIS273 1.7 40.2 1.0 O2 D:AKG600 1.9 42.7 0.0 C1 D:AKG600 2.1 42.4 0.0 OD1 D:ASP189 2.1 53.4 1.0 CD2 D:HIS187 2.3 42.9 1.0 O5 D:AKG600 2.4 42.5 0.0 C2 D:AKG600 2.4 42.4 0.0 CD2 D:HIS273 2.5 41.0 1.0 ND1 D:HIS187 2.8 41.3 1.0 CE1 D:HIS273 2.8 39.9 1.0 O1 D:AKG600 3.0 42.6 0.0 CG D:HIS187 3.1 38.7 1.0 CG D:ASP189 3.3 45.4 1.0 CG D:HIS273 3.6 38.0 1.0 C3 D:AKG600 3.7 41.6 0.0 ND1 D:HIS273 3.8 36.7 1.0 OD2 D:ASP189 3.9 49.2 1.0 C4 D:AKG600 4.1 41.0 0.0 CB D:ASP189 4.6 34.5 1.0 CB D:HIS187 4.6 37.4 1.0 N D:ASP189 4.8 37.4 1.0 CA D:ASP189 4.9 39.5 1.0

Iron binding site 5 out of 8 in the Structure of JMJD6 Bound to Mono-Methyl Arginine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of JMJD6 Bound to Mono-Methyl Arginine. within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe402 b:32.5 occ:0.00 NE2 E:HIS273 1.5 28.9 1.0 OXT E:NMM403 1.7 35.2 1.0 NE2 E:HIS187 1.8 23.3 1.0 O1 E:AKG401 1.8 31.9 0.0 OD1 E:ASP189 1.9 41.5 1.0 O5 E:AKG401 2.2 31.5 0.0 C1 E:AKG401 2.4 31.4 0.0 CE1 E:HIS273 2.5 32.5 1.0 CE1 E:HIS187 2.5 37.0 1.0 C2 E:AKG401 2.5 31.6 0.0 CD2 E:HIS273 2.7 33.4 1.0 C E:NMM403 2.9 45.8 1.0 CG E:ASP189 3.0 31.0 1.0 CD2 E:HIS187 3.1 32.8 1.0 OD2 E:ASP189 3.4 30.1 1.0 O E:NMM403 3.5 41.7 1.0 ND1 E:HIS273 3.6 27.2 1.0 O2 E:AKG401 3.6 30.2 0.0 CG E:HIS273 3.7 26.6 1.0 ND1 E:HIS187 3.7 27.2 1.0 O E:HOH538 3.8 33.3 1.0 C3 E:AKG401 3.9 30.5 0.0 CG E:HIS187 4.0 32.5 1.0 O E:HOH558 4.2 31.6 1.0 CA E:NMM403 4.3 52.4 1.0 CB E:ASP189 4.4 25.3 1.0 C4 E:AKG401 4.7 29.0 0.0 CB E:ALA195 4.7 29.1 1.0 CB E:NMM403 4.8 50.7 1.0 CA E:ASP189 4.8 29.4 1.0

Iron binding site 6 out of 8 in the Structure of JMJD6 Bound to Mono-Methyl Arginine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of JMJD6 Bound to Mono-Methyl Arginine. within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe601 b:31.3 occ:0.00 NE2 F:HIS187 1.7 15.1 1.0 NE2 F:HIS273 1.8 37.5 1.0 CE1 F:HIS187 2.0 25.7 1.0 OD1 F:ASP189 2.1 34.7 1.0 O5 F:AKG600 2.2 31.7 0.0 O1 F:AKG600 2.3 32.4 0.0 OD2 F:ASP189 2.6 34.5 1.0 CG F:ASP189 2.7 30.3 1.0 CD2 F:HIS273 2.7 36.4 1.0 C2 F:AKG600 2.9 32.1 0.0 CE1 F:HIS273 2.9 31.9 1.0 C1 F:AKG600 2.9 32.5 0.0 CD2 F:HIS187 3.0 32.9 1.0 ND1 F:HIS187 3.2 44.4 1.0 CG F:HIS187 3.7 33.0 1.0 CG F:HIS273 3.9 27.7 1.0 ND1 F:HIS273 3.9 30.1 1.0 O2 F:AKG600 4.1 33.0 0.0 CB F:ASP189 4.2 24.7 1.0 C3 F:AKG600 4.4 32.4 0.0 CG1 F:VAL267 4.4 33.8 1.0 CB F:ALA195 4.6 37.9 1.0 C4 F:AKG600 4.8 31.8 0.0 CB F:VAL267 4.9 38.4 1.0 O F:HOH712 4.9 41.8 1.0

Iron binding site 7 out of 8 in the Structure of JMJD6 Bound to Mono-Methyl Arginine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of JMJD6 Bound to Mono-Methyl Arginine. within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe402 b:30.2 occ:0.00 NE2 G:HIS273 1.3 27.6 1.0 NE2 G:HIS187 1.4 31.7 1.0 CE1 G:HIS187 1.7 35.7 1.0 CD2 G:HIS273 2.0 29.3 1.0 O2 G:AKG401 2.0 29.0 0.0 OXT G:NMM403 2.1 30.5 1.0 O5 G:AKG401 2.1 30.4 0.0 OD1 G:ASP189 2.2 31.1 1.0 CE1 G:HIS273 2.4 26.8 1.0 C1 G:AKG401 2.7 29.3 0.0 C2 G:AKG401 2.7 29.7 0.0 CD2 G:HIS187 2.8 31.6 1.0 ND1 G:HIS187 2.9 25.5 1.0 CG G:HIS273 3.1 23.0 1.0 ND1 G:HIS273 3.3 23.7 1.0 C G:NMM403 3.3 44.0 1.0 CG G:ASP189 3.3 31.2 1.0 CG G:HIS187 3.4 27.4 1.0 OD2 G:ASP189 3.7 30.9 1.0 O1 G:AKG401 3.9 28.3 0.0 O G:NMM403 4.0 40.3 1.0 C3 G:AKG401 4.2 28.6 0.0 CA G:NMM403 4.4 42.9 1.0 CB G:HIS273 4.5 21.8 1.0 N G:NMM403 4.6 38.4 1.0 CB G:ASP189 4.7 14.6 1.0 O G:HIS273 4.9 26.3 1.0 C4 G:AKG401 4.9 26.3 0.0 O G:HIS187 4.9 26.3 1.0 CB G:HIS187 4.9 25.2 1.0 N G:ASP189 5.0 28.4 1.0

Iron binding site 8 out of 8 in the Structure of JMJD6 Bound to Mono-Methyl Arginine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of JMJD6 Bound to Mono-Methyl Arginine. within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe402 b:37.0 occ:0.00 NE2 H:HIS187 1.7 19.0 1.0 NE2 H:HIS273 1.9 41.1 1.0 O1 H:AKG401 2.0 37.1 0.0 OD2 H:ASP189 2.2 42.9 1.0 CE1 H:HIS273 2.6 37.3 1.0 CD2 H:HIS187 2.6 35.5 1.0 O5 H:AKG401 2.7 39.5 0.0 O H:NMM403 2.7 45.5 1.0 CE1 H:HIS187 2.7 39.4 1.0 C1 H:AKG401 2.9 36.8 0.0 CG H:ASP189 3.0 39.5 1.0 CD2 H:HIS273 3.1 34.6 1.0 C2 H:AKG401 3.2 38.2 0.0 OD1 H:ASP189 3.3 46.0 1.0 ND1 H:HIS187 3.8 31.9 1.0 CG H:HIS187 3.8 29.6 1.0 ND1 H:HIS273 3.8 38.0 1.0 C H:NMM403 3.8 47.0 1.0 O2 H:AKG401 4.1 35.7 0.0 CG H:HIS273 4.1 31.9 1.0 CB H:ASP189 4.2 32.9 1.0 O H:HOH513 4.3 35.9 1.0 CA H:ASP189 4.3 32.1 1.0 N H:ASP189 4.4 30.2 1.0 CB H:ALA195 4.5 31.9 1.0 O H:HOH501 4.5 23.7 1.0 OXT H:NMM403 4.6 47.0 1.0 C3 H:AKG401 4.7 37.0 0.0 CB H:NMM403 4.7 51.3 1.0 CA H:NMM403 4.8 54.9 1.0 CG1 H:VAL267 4.8 26.4 1.0 O H:HOH544 4.9 24.7 1.0

S.Lee, H.Liu, R.Hill, X.Hong, X.Liu, F.Crawford, Q.Zhang, Z.Chen, A.Lengeling, K.Bernet, P.Marrack, J.Kappler, K.Hansen, C.Li, G.Zhang. JMJD6 Bridges BRD4, CDK9, and Rna Polymerase II To Be Published.