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Mercury in PDB 3ldb: Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment.

Protein crystallography data

The structure of Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment., PDB code: 3ldb 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) 47.28 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 138.381, 138.381, 183.622, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 28.5

Other elements in 3ldb:

The structure of Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment. also contains other interesting chemical elements:

Iron (Fe) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment. (pdb code 3ldb). 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 Complexd with Alpha-Ketoglutarate and Fab Fragment., PDB code: 3ldb:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 3ldb

Go back to Mercury Binding Sites List in 3ldb
Mercury binding site 1 out of 2 in the Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment.


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 Complexd with Alpha-Ketoglutarate and Fab Fragment. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg352

b:98.2
occ:0.80
SG A:CYS207 2.9 63.0 1.0
CB A:CYS207 2.9 60.6 1.0
O A:TRP206 3.6 58.2 1.0
C A:TRP206 3.7 58.8 1.0
N A:CYS207 3.7 58.8 1.0
CA A:CYS207 3.8 59.0 1.0
CZ3 A:TRP235 3.9 47.4 1.0
CG A:ARG205 4.3 61.9 1.0
CG2 A:VAL274 4.3 63.6 1.0
CD1 A:TYR240 4.4 55.4 1.0
CD1 A:PHE236 4.4 67.8 1.0
CA A:TRP206 4.5 57.7 1.0
NE A:ARG205 4.5 66.7 1.0
O A:VAL274 4.6 65.3 1.0
CD A:ARG205 4.6 61.1 1.0
CE3 A:TRP235 4.6 49.5 1.0
CE1 A:TYR240 4.6 57.2 1.0
N A:TRP206 4.7 59.3 1.0
CH2 A:TRP235 4.7 48.8 1.0
CE1 A:PHE236 4.8 66.4 1.0
O A:ARG205 4.9 59.6 1.0
C A:ARG205 4.9 59.4 1.0

Mercury binding site 2 out of 2 in 3ldb

Go back to Mercury Binding Sites List in 3ldb
Mercury binding site 2 out of 2 in the Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment.


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 Complexd with Alpha-Ketoglutarate and Fab Fragment. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg353

b:0.1
occ:0.80
SG A:CYS101 2.7 84.7 1.0
SD A:MET112 3.5 74.8 1.0
CB A:CYS101 3.6 82.1 1.0
CG A:MET112 3.9 78.7 1.0
CD1 A:LEU130 4.0 66.0 1.0
CD1 A:TYR117 4.1 80.5 1.0
CB A:ALA12 4.1 97.2 1.0
CE A:MET112 4.3 71.3 1.0
CE1 A:TYR117 4.3 79.5 1.0
CB A:LEU130 4.3 67.6 1.0
O A:CYS101 4.8 82.4 1.0
CG A:LEU130 4.8 67.7 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: Wed Oct 28 18:42:49 2020

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