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Zinc in PDB 2p5b: The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide

Protein crystallography data

The structure of The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide, PDB code: 2p5b was solved by G.Zhang, Z.Chen, J.Zang, X.Hong, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.34 / 1.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.915, 150.844, 57.346, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 26.3

Other elements in 2p5b:

The structure of The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide (pdb code 2p5b). 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 Complex Structure of JMJD2A and Trimethylated H3K36 Peptide, PDB code: 2p5b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2p5b

Go back to Zinc Binding Sites List in 2p5b
Zinc binding site 1 out of 2 in the The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn351

b:26.1
occ:0.60
NE2 A:HIS240 2.1 30.7 1.0
SG A:CYS306 2.2 40.5 1.0
SG A:CYS234 2.3 37.9 1.0
SG A:CYS308 2.4 50.9 1.0
CE1 A:HIS240 3.1 29.2 1.0
CD2 A:HIS240 3.1 28.3 1.0
CB A:CYS306 3.1 43.5 1.0
CB A:CYS234 3.2 44.8 1.0
CB A:CYS308 3.5 54.4 1.0
N A:CYS308 3.8 56.5 1.0
CA A:CYS306 3.9 43.5 1.0
CA A:CYS308 4.1 55.8 1.0
CG A:ARG309 4.1 58.3 1.0
N A:ARG309 4.2 58.5 1.0
ND1 A:HIS240 4.2 27.7 1.0
N A:SER307 4.2 50.9 1.0
CG A:HIS240 4.3 27.8 1.0
C A:CYS306 4.3 46.8 1.0
O A:HOH640 4.4 51.7 1.0
C A:CYS308 4.4 57.1 1.0
CD A:ARG309 4.4 56.8 1.0
CA A:CYS234 4.6 46.8 1.0
O A:ALA236 4.6 33.6 1.0
CB A:ARG309 4.7 59.4 1.0
O A:HOH577 4.8 38.1 1.0
C A:SER307 4.8 57.4 1.0
NE A:ARG309 4.8 55.7 1.0
CA A:PHE237 4.9 31.5 1.0
C A:ALA236 5.0 35.1 1.0

Zinc binding site 2 out of 2 in 2p5b

Go back to Zinc Binding Sites List in 2p5b
Zinc binding site 2 out of 2 in the The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn351

b:45.3
occ:1.00
NE2 B:HIS240 2.2 36.2 1.0
SG B:CYS306 2.3 41.9 1.0
SG B:CYS234 2.3 42.7 1.0
SG B:CYS308 2.5 49.9 1.0
CB B:CYS306 3.0 46.4 1.0
CD2 B:HIS240 3.2 33.8 1.0
CE1 B:HIS240 3.2 33.8 1.0
CB B:CYS234 3.2 48.9 1.0
CB B:CYS308 3.5 57.0 1.0
CA B:CYS306 3.8 47.4 1.0
N B:CYS308 3.8 59.2 1.0
CA B:CYS308 4.1 59.4 1.0
N B:SER307 4.1 54.2 1.0
C B:CYS306 4.2 50.7 1.0
CG B:ARG309 4.2 64.5 1.0
N B:ARG309 4.2 63.0 1.0
ND1 B:HIS240 4.3 33.9 1.0
CG B:HIS240 4.3 34.8 1.0
C B:CYS308 4.5 61.4 1.0
O B:ALA236 4.5 36.5 1.0
O B:HOH550 4.5 57.6 1.0
CD B:ARG309 4.6 63.6 1.0
O B:HOH627 4.6 47.7 1.0
CA B:CYS234 4.7 51.4 1.0
CB B:ARG309 4.7 64.7 1.0
C B:SER307 4.8 59.6 1.0
CA B:PHE237 4.8 35.9 1.0
C B:ALA236 4.9 38.2 1.0
NE B:ARG309 5.0 63.1 1.0

Reference:

Z.Chen, J.Zang, J.Kappler, X.Hong, F.Crawford, Q.Wang, F.Lan, C.Jiang, J.Whetstine, S.Dai, K.Hansen, Y.Shi, G.Zhang. Structural Basis of the Recognition of A Methylated Histone Tail By JMJD2A. Proc.Natl.Acad.Sci.Usa V. 104 10818 2007.
ISSN: ISSN 0027-8424
PubMed: 17567753
DOI: 10.1073/PNAS.0704525104
Page generated: Wed Dec 16 03:47:47 2020

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