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Mercury in PDB 2jhn: 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus

Enzymatic activity of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus

All present enzymatic activity of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus:
3.2.2.21;

Protein crystallography data

The structure of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus, PDB code: 2jhn was solved by I.Leiros, M.P.Nabong, K.Grosvik, J.Ringvoll, G.T.Haugland, L.Uldal, K.Reite, I.K.Olsbu, I.Knaevelsrud, E.Moe, O.A.Andersen, N.K.Birkeland, P.Ruoff, A.Klungland, S.Bjelland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 1.8
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.494, 49.968, 105.798, 90.00, 107.43, 90.00
R / Rfree (%) 18.5 / 22.3

Other elements in 2jhn:

The structure of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus (pdb code 2jhn). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus, PDB code: 2jhn:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 2jhn

Go back to Mercury Binding Sites List in 2jhn
Mercury binding site 1 out of 4 in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1296

b:24.6
occ:0.70
HG A:MBO1296 0.0 24.6 0.7
CE1 A:MBO1296 2.3 23.9 0.7
SG A:CYS178 2.3 21.5 1.0
CE6 A:MBO1296 3.2 22.7 0.7
CE2 A:MBO1296 3.2 22.7 0.7
O A:LYS142 3.2 16.8 1.0
CB A:CYS178 3.2 22.9 1.0
O B:HOH2173 3.4 30.8 1.0
NH1 A:ARG146 3.6 24.0 1.0
CZ A:ARG146 3.6 22.4 1.0
C A:LYS142 3.7 17.8 1.0
CA A:CYS178 3.7 23.8 1.0
CB A:LYS142 3.7 20.6 1.0
NE A:ARG146 3.8 21.1 1.0
CB A:ARG146 3.9 19.8 1.0
CA A:LYS142 4.0 18.6 1.0
CD A:ARG146 4.1 21.9 1.0
NH2 A:ARG146 4.2 25.3 1.0
CD A:LYS142 4.3 27.0 1.0
CE3 A:MBO1296 4.5 24.1 0.7
N A:ILE143 4.5 16.8 1.0
CE5 A:MBO1296 4.5 24.3 0.7
N A:CYS178 4.5 23.9 1.0
CG A:ARG146 4.6 19.5 1.0
CG A:LYS142 4.7 23.2 1.0
C A:CYS178 4.8 24.1 1.0
O A:CYS178 4.9 24.5 1.0
CA A:ILE143 4.9 16.5 1.0
OE2 B:GLU177 4.9 24.6 1.0
N A:ARG146 5.0 18.6 1.0

Mercury binding site 2 out of 4 in 2jhn

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Mercury binding site 2 out of 4 in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1297

b:44.9
occ:0.30
N A:MET1 2.7 29.0 1.0
O A:MET1 2.9 26.9 1.0
C A:MET1 3.4 27.1 1.0
CE2 A:TRP2 3.6 23.9 1.0
CA A:MET1 3.6 28.2 1.0
CZ2 A:TRP2 3.7 24.5 1.0
CD2 A:TRP2 3.8 23.1 1.0
CH2 A:TRP2 3.9 24.9 1.0
CE3 A:TRP2 4.1 22.8 1.0
CZ3 A:TRP2 4.1 24.4 1.0
NE1 A:TRP2 4.1 23.1 1.0
N A:TRP2 4.4 24.5 1.0
CB A:MET1 4.4 29.2 1.0
CG A:TRP2 4.4 23.3 1.0
O A:HOH2001 4.6 30.0 1.0
CD1 A:TRP2 4.6 24.8 1.0
OD1 A:ASN66 4.7 41.1 1.0

Mercury binding site 3 out of 4 in 2jhn

Go back to Mercury Binding Sites List in 2jhn
Mercury binding site 3 out of 4 in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1296

b:21.2
occ:0.70
HG B:MBO1296 0.0 21.2 0.7
CE1 B:MBO1296 2.3 21.8 0.7
SG B:CYS178 2.4 20.5 1.0
CE2 B:MBO1296 3.2 20.7 0.7
O B:LYS142 3.2 13.0 1.0
CE6 B:MBO1296 3.2 20.4 0.7
O A:HOH2125 3.2 27.9 1.0
CB B:CYS178 3.4 17.4 1.0
CB B:ARG146 3.6 16.1 1.0
C B:LYS142 3.7 14.2 1.0
CA B:CYS178 3.7 18.3 1.0
CB B:LYS142 3.9 16.5 1.0
CA B:LYS142 4.1 14.8 1.0
OE2 A:GLU177 4.1 28.0 1.0
NE B:ARG146 4.3 24.0 1.0
NH2 B:ARG146 4.3 25.8 1.0
CD B:LYS142 4.4 24.5 1.0
CG B:ARG146 4.4 17.9 1.0
CZ B:ARG146 4.5 24.4 1.0
OE1 A:GLU177 4.5 30.0 1.0
N B:ILE143 4.5 12.5 1.0
CE3 B:MBO1296 4.5 22.8 0.7
CE5 B:MBO1296 4.5 21.3 0.7
N B:CYS178 4.6 17.7 1.0
CD A:GLU177 4.7 27.7 1.0
CG B:LYS142 4.7 18.1 1.0
C B:CYS178 4.8 17.5 1.0
N B:ARG146 4.8 15.0 1.0
O B:CYS178 4.8 18.5 1.0
CA B:ARG146 4.8 15.5 1.0
O B:HOH2171 4.8 22.8 1.0
O B:HOH2144 4.9 34.1 1.0
CA B:ILE143 4.9 12.9 1.0
CD B:ARG146 5.0 20.7 1.0

Mercury binding site 4 out of 4 in 2jhn

Go back to Mercury Binding Sites List in 2jhn
Mercury binding site 4 out of 4 in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1297

b:42.8
occ:0.30
N B:MET1 2.8 27.7 1.0
O B:MET1 2.9 26.4 1.0
O B:HOH2029 3.2 42.2 1.0
C B:MET1 3.3 25.5 1.0
CA B:MET1 3.4 26.4 1.0
CE2 B:TRP2 3.7 21.2 1.0
CZ2 B:TRP2 3.8 23.5 1.0
CD2 B:TRP2 3.9 22.0 1.0
CH2 B:TRP2 3.9 23.1 1.0
CE3 B:TRP2 4.0 20.6 1.0
CZ3 B:TRP2 4.1 21.7 1.0
NE1 B:TRP2 4.3 21.1 1.0
O B:HOH2066 4.3 22.7 1.0
N B:TRP2 4.4 22.9 1.0
CG B:TRP2 4.5 22.1 1.0
CD1 B:TRP2 4.7 21.9 1.0
OD1 B:ASN66 4.7 30.8 0.5
CB B:MET1 4.9 26.8 1.0

Reference:

I.Leiros, M.P.Nabong, K.Grosvik, J.Ringvoll, G.T.Haugland, L.Uldal, K.Reite, I.K.Olsbu, I.Knaevelsrud, E.Moe, O.A.Andersen, N.K.Birkeland, P.Ruoff, A.Klungland, S.Bjelland. Structural Basis For Enzymatic Excision of N1- Methyladenine and N3-Methylcytosine From Dna Embo J. V. 26 2206 2007.
ISSN: ISSN 0261-4189
PubMed: 17396151
DOI: 10.1038/SJ.EMBOJ.7601662
Page generated: Wed Oct 28 18:41:42 2020

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