Nickel in PDB 2xxz: Crystal Structure of the Human JMJD3 Jumonji Domain

The structure of Crystal Structure of the Human JMJD3 Jumonji Domain, PDB code: 2xxz was solved by K.H.Che, W.W.Yue, T.Krojer, J.R.C.Muniz, S.S.Ng, A.Tumber, M.Daniel, N.Burgess-Brown, P.Savitsky, E.Ugochukwu, P.Filippakopoulos, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.16 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.757, 71.431, 159.698, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.6

The structure of Crystal Structure of the Human JMJD3 Jumonji Domain also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Nickel atom in the Crystal Structure of the Human JMJD3 Jumonji Domain (pdb code 2xxz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of the Human JMJD3 Jumonji Domain, PDB code: 2xxz:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of the Human JMJD3 Jumonji Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Human JMJD3 Jumonji Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2494 b:20.7 occ:1.00 NE2 A:HIS1387 2.0 15.3 1.0 OAC A:8XQ3001 2.1 19.9 1.0 O A:HOH2098 2.1 11.9 1.0 OE2 A:GLU1389 2.1 24.0 1.0 NAI A:8XQ3001 2.2 18.4 1.0 O A:HOH2103 2.4 18.0 1.0 CAK A:8XQ3001 2.8 15.9 1.0 CAN A:8XQ3001 2.8 18.1 1.0 CD2 A:HIS1387 3.0 19.6 1.0 CE1 A:HIS1387 3.0 21.1 1.0 CD A:GLU1389 3.1 23.7 1.0 CAE A:8XQ3001 3.2 20.9 1.0 OE1 A:GLU1389 3.3 24.0 1.0 NE2 A:HIS1467 3.8 20.4 1.0 ND1 A:HIS1387 4.1 16.1 1.0 CAF A:8XQ3001 4.1 16.1 1.0 CG A:HIS1387 4.1 18.7 1.0 CAM A:8XQ3001 4.2 12.1 1.0 CE1 A:HIS1467 4.3 19.2 1.0 O A:HOH2104 4.3 18.3 1.0 CG A:GLU1389 4.5 24.9 1.0 CAD A:8XQ3001 4.5 21.6 1.0 O A:HOH2110 4.5 19.1 1.0 CAH A:8XQ3001 4.8 13.4 1.0 O A:HOH2102 4.9 26.6 1.0 CD2 A:HIS1467 4.9 18.5 1.0 O A:HOH2088 4.9 31.0 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of the Human JMJD3 Jumonji Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Human JMJD3 Jumonji Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2500 b:33.8 occ:0.50 O A:HOH2059 2.0 8.0 1.0 O A:HOH2054 2.2 6.5 1.0 O A:HOH2060 2.2 7.0 1.0 O1 A:EDO2498 4.1 29.9 1.0 O A:HOH2032 4.2 13.4 1.0 O A:HOH2034 4.2 20.4 1.0 O A:HOH2053 4.2 8.6 1.0 O A:ASN1328 4.3 27.6 1.0 OD1 A:ASN1371 4.3 22.5 1.0 ND2 A:ASN1371 4.4 24.8 1.0 O A:HOH2057 4.6 2.5 1.0 C1 A:EDO2498 4.7 45.9 1.0 CG A:ASN1371 4.8 25.4 1.0 O A:HOH2087 4.8 23.3 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of the Human JMJD3 Jumonji Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Human JMJD3 Jumonji Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni2500 b:22.9 occ:1.00 OE2 B:GLU1389 2.0 20.5 1.0 NE2 B:HIS1387 2.1 16.7 1.0 OAC B:8XQ3001 2.1 24.0 1.0 NAI B:8XQ3001 2.1 28.2 1.0 O B:HOH2155 2.2 19.6 1.0 O B:HOH2083 2.2 9.1 1.0 CAK B:8XQ3001 2.9 21.0 1.0 CAN B:8XQ3001 2.9 20.9 1.0 CD B:GLU1389 3.0 26.9 1.0 CE1 B:HIS1387 3.1 22.5 1.0 CD2 B:HIS1387 3.1 19.8 1.0 CAE B:8XQ3001 3.1 25.6 1.0 OE1 B:GLU1389 3.3 31.4 1.0 NE2 B:HIS1467 3.7 21.3 1.0 O B:HOH2079 4.1 25.4 1.0 ND1 B:HIS1387 4.2 19.4 1.0 CG B:HIS1387 4.2 20.1 1.0 CAF B:8XQ3001 4.3 18.9 1.0 CE1 B:HIS1467 4.3 19.3 1.0 CAM B:8XQ3001 4.3 21.7 1.0 CG B:GLU1389 4.3 25.7 1.0 O B:HOH2139 4.4 28.5 1.0 CAD B:8XQ3001 4.4 20.7 1.0 O B:HOH2091 4.6 27.7 1.0 OG B:SER1395 4.6 41.9 1.0 CD2 B:HIS1467 4.9 19.1 1.0 CAH B:8XQ3001 4.9 24.2 1.0 OD1 B:ASN1481 4.9 34.0 1.0

K.H.Che, W.W.Yue, T.Krojer, J.R.C.Muniz, S.S.Ng, A.Tumber, M.Daniel, N.Burgess-Brown, P.Savitsky, F.Von Delft, E.Ugochukwu, P.Filippakopoulos, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, U.Oppermann. Crystal Structure of the Human JMJD3 Jumonji Domain To Be Published.