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

Protein crystallography data

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

Other elements in 8wd3:

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

Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of JMJD2A(M1-L359) From Biortus., PDB code: 8wd3:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 8wd3

Go back to Nickel Binding Sites List in 8wd3
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:73.1
occ:1.00
OE2 A:GLU190 1.9 59.6 1.0
NE2 A:HIS276 2.0 67.9 1.0
NE2 A:HIS188 2.0 75.6 1.0
CE1 A:HIS188 2.6 70.4 1.0
CD2 A:HIS276 2.8 63.6 1.0
O A:HOH602 2.9 41.6 1.0
CD A:GLU190 3.0 58.5 1.0
CE1 A:HIS276 3.1 64.5 1.0
CD2 A:HIS188 3.2 72.3 1.0
OE1 A:GLU190 3.6 62.5 1.0
ND1 A:HIS188 3.8 67.8 1.0
CG A:HIS276 4.0 61.2 1.0
ND1 A:HIS276 4.1 63.9 1.0
CG A:HIS188 4.1 69.5 1.0
CG A:GLU190 4.2 58.4 1.0
OG A:SER196 4.3 53.6 1.0
CG2 A:THR270 4.7 66.0 1.0
CZ3 A:TRP208 4.9 65.6 1.0

Nickel binding site 2 out of 2 in 8wd3

Go back to Nickel Binding Sites List in 8wd3
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:77.9
occ:1.00
OE2 B:GLU190 1.9 78.8 1.0
NE2 B:HIS276 1.9 68.8 1.0
NE2 B:HIS188 2.0 93.0 1.0
O B:HOH601 2.3 53.8 1.0
CE1 B:HIS188 2.6 88.9 1.0
CD2 B:HIS276 2.8 63.3 1.0
CE1 B:HIS276 3.0 65.7 1.0
CD B:GLU190 3.1 82.2 1.0
CD2 B:HIS188 3.3 86.3 1.0
OE1 B:GLU190 3.7 96.7 1.0
ND1 B:HIS188 3.8 87.4 1.0
CG B:HIS276 4.0 62.0 1.0
ND1 B:HIS276 4.1 62.1 1.0
CG B:HIS188 4.2 85.4 1.0
CG B:GLU190 4.2 81.5 1.0
OG B:SER196 4.4 82.1 1.0
CG2 B:THR270 4.7 73.2 1.0
CZ3 B:TRP208 4.8 66.0 1.0

Reference:

F.Wang, W.Cheng, Z.Yuan, H.Shang. The Crystal Structure of JMJD2A(M1-L359) From Biortus. To Be Published.
Page generated: Thu Dec 28 11:57:13 2023

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