Atomistry » Zinc » PDB 8u2q-9atc » 8wd3
Atomistry »
  Zinc »
    PDB 8u2q-9atc »
      8wd3 »

Zinc 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:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

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 8wd3

Go back to Zinc Binding Sites List in 8wd3
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 8wd3

Go back to Zinc Binding Sites List in 8wd3
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

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 13:48:02 2023

Last articles

Cl in 4NHT
Cl in 4NO7
Cl in 4NML
Cl in 4NN3
Cl in 4NMW
Cl in 4NM7
Cl in 4NM5
Cl in 4NM3
Cl in 4NM0
Cl in 4NHQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy