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Mercury in PDB 3ld8: Structure of JMJD6 and Fab Fragments

Protein crystallography data

The structure of Structure of JMJD6 and Fab Fragments, PDB code: 3ld8 was solved by X.Hong, J.Zang, J.White, J.W.Kappler, C.Wang, G.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.89 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 138.281, 138.281, 183.554, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 26

Other elements in 3ld8:

The structure of Structure of JMJD6 and Fab Fragments also contains other interesting chemical elements:

Iron (Fe) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Structure of JMJD6 and Fab Fragments (pdb code 3ld8). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the Structure of JMJD6 and Fab Fragments, PDB code: 3ld8:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 3ld8

Go back to Mercury Binding Sites List in 3ld8
Mercury binding site 1 out of 2 in the Structure of JMJD6 and Fab Fragments


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Structure of JMJD6 and Fab Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg335

b:92.3
occ:0.80
CB A:CYS207 2.9 52.6 1.0
SG A:CYS207 2.9 54.7 1.0
N A:CYS207 3.6 52.2 1.0
C A:TRP206 3.6 53.0 1.0
O A:TRP206 3.7 53.3 1.0
CA A:CYS207 3.7 52.8 1.0
CZ3 A:TRP235 3.8 52.4 1.0
CG1 A:VAL274 4.2 55.3 1.0
CG A:ARG205 4.3 53.4 1.0
CA A:TRP206 4.3 51.6 1.0
CD1 A:TYR240 4.4 47.3 1.0
CD1 A:PHE236 4.5 61.6 1.0
CH2 A:TRP235 4.5 52.7 1.0
CD A:ARG205 4.5 53.9 1.0
NE A:ARG205 4.6 60.6 1.0
N A:TRP206 4.6 52.4 1.0
CE3 A:TRP235 4.6 51.6 1.0
O A:VAL274 4.6 56.1 1.0
CE1 A:TYR240 4.6 46.9 1.0
C A:ARG205 4.9 52.2 1.0
CE1 A:PHE236 4.9 59.7 1.0
O A:ARG205 4.9 50.8 1.0
C A:CYS207 5.0 52.4 1.0

Mercury binding site 2 out of 2 in 3ld8

Go back to Mercury Binding Sites List in 3ld8
Mercury binding site 2 out of 2 in the Structure of JMJD6 and Fab Fragments


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Structure of JMJD6 and Fab Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg336

b:0.2
occ:0.80
SG A:CYS101 2.8 84.6 1.0
SD A:MET112 3.6 68.4 1.0
CB A:CYS101 3.7 82.8 1.0
CD1 A:LEU130 3.8 64.7 1.0
CG A:MET112 3.9 72.7 1.0
CB A:ALA12 4.0 94.5 1.0
CD1 A:TYR117 4.1 76.8 1.0
CE A:MET112 4.2 65.0 1.0
CB A:LEU130 4.3 63.5 1.0
CE1 A:TYR117 4.4 76.1 1.0
O A:CYS101 4.4 82.9 1.0
CG A:LEU130 4.7 64.0 1.0

Reference:

X.Hong, J.Zang, J.White, C.Wang, C.H.Pan, R.Zhao, R.C.Murphy, S.Dai, P.Henson, J.W.Kappler, J.Hagman, G.Zhang. Interaction of JMJD6 with Single-Stranded Rna. Proc.Natl.Acad.Sci.Usa V. 107 14568 2010.
ISSN: ISSN 0027-8424
PubMed: 20679243
DOI: 10.1073/PNAS.1008832107
Page generated: Sun Dec 13 19:09:57 2020

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