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Mercury in PDB 1ems: Crystal Structure of the C. Elegans Nitfhit Protein

Protein crystallography data

The structure of Crystal Structure of the C. Elegans Nitfhit Protein, PDB code: 1ems was solved by H.C.Pace, S.C.Hodawadekar, A.Draganescu, J.Huang, P.Bieganowski, Y.Pekarsky, C.M.Croce, C.Brenner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.750, 100.440, 158.650, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.1

Other elements in 1ems:

The structure of Crystal Structure of the C. Elegans Nitfhit Protein also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of the C. Elegans Nitfhit Protein (pdb code 1ems). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 5 binding sites of Mercury where determined in the Crystal Structure of the C. Elegans Nitfhit Protein, PDB code: 1ems:
Jump to Mercury binding site number: 1; 2; 3; 4; 5;

Mercury binding site 1 out of 5 in 1ems

Go back to Mercury Binding Sites List in 1ems
Mercury binding site 1 out of 5 in the Crystal Structure of the C. Elegans Nitfhit Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of the C. Elegans Nitfhit Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg451

b:24.1
occ:0.62
HG A:EMC451 0.0 24.1 0.6
C1 A:EMC451 2.0 24.1 0.6
SG A:CYS169 2.4 28.1 1.0
OE1 A:GLU54 2.6 27.5 1.0
C2 A:EMC451 2.8 24.1 0.6
O A:ALA194 3.1 15.3 1.0
CD A:GLU54 3.4 21.8 1.0
OE2 A:GLU54 3.4 17.6 1.0
NZ A:LYS127 3.7 6.6 1.0
C A:ALA194 3.9 14.4 1.0
CB A:CYS169 4.0 24.2 1.0
N A:ALA194 4.2 12.7 1.0
CB A:ALA194 4.4 11.8 1.0
CA A:ALA194 4.4 14.1 1.0
CG A:GLU54 4.9 18.9 1.0
N A:PHE195 4.9 15.5 1.0
CE A:LYS127 5.0 13.9 1.0

Mercury binding site 2 out of 5 in 1ems

Go back to Mercury Binding Sites List in 1ems
Mercury binding site 2 out of 5 in the Crystal Structure of the C. Elegans Nitfhit Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of the C. Elegans Nitfhit Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg453

b:25.5
occ:0.61
HG A:EMC453 0.0 25.5 0.6
C1 A:EMC453 2.0 25.5 0.6
SG A:CYS55 2.6 20.7 1.0
C2 A:EMC453 2.8 25.5 0.6
O A:GLY96 3.2 16.2 1.0
CE1 A:HIS98 3.3 7.7 1.0
CB A:CYS55 3.5 22.6 1.0
NE2 A:HIS98 3.5 8.1 1.0
ND2 A:ASN110 3.7 26.1 1.0
CA A:CYS55 3.8 22.7 1.0
ND1 A:HIS98 3.8 11.2 1.0
CD2 A:HIS98 4.1 8.4 1.0
CG A:GLU54 4.2 18.9 1.0
CG A:ASN110 4.2 19.6 1.0
N A:CYS55 4.2 24.1 1.0
OD1 A:ASN110 4.3 21.7 1.0
CG A:HIS98 4.3 9.6 1.0
C A:GLY96 4.4 19.2 1.0
C A:GLU54 4.6 26.9 1.0
O A:GLU54 4.6 33.9 1.0
CD A:GLU54 4.8 21.8 1.0
N A:HIS98 4.8 19.7 1.0
C A:LEU97 4.9 18.3 1.0
OD2 A:ASP57 4.9 22.4 1.0

Mercury binding site 3 out of 5 in 1ems

Go back to Mercury Binding Sites List in 1ems
Mercury binding site 3 out of 5 in the Crystal Structure of the C. Elegans Nitfhit Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of the C. Elegans Nitfhit Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg454

b:25.7
occ:0.55
HG A:EMC454 0.0 25.7 0.6
C1 A:EMC454 2.0 25.7 0.6
SG A:CYS75 2.3 33.7 1.0
O A:CYS75 2.7 17.1 1.0
C2 A:EMC454 2.8 25.7 0.6
C A:CYS75 3.4 20.5 1.0
CB A:CYS75 3.6 25.2 1.0
CA A:CYS75 3.7 22.1 1.0
N A:GLU76 4.5 23.8 1.0

Mercury binding site 4 out of 5 in 1ems

Go back to Mercury Binding Sites List in 1ems
Mercury binding site 4 out of 5 in the Crystal Structure of the C. Elegans Nitfhit Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of the C. Elegans Nitfhit Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg452

b:23.6
occ:0.58
HG B:EMC452 0.0 23.6 0.6
C1 B:EMC452 2.0 23.6 0.6
SG B:CYS169 2.4 25.0 1.0
OE2 B:GLU54 2.7 33.4 1.0
C2 B:EMC452 2.8 23.6 0.6
CB B:CYS169 3.3 20.5 1.0
CD B:GLU54 3.3 31.5 1.0
OE1 B:GLU54 3.3 32.6 1.0
O B:ALA194 3.4 24.1 1.0
NZ B:LYS127 3.5 34.2 1.0
C B:ALA194 4.0 21.4 1.0
N B:ALA194 4.1 20.9 1.0
CB B:ALA194 4.2 20.4 1.0
CA B:ALA194 4.4 21.4 1.0
CG B:GLU54 4.7 24.8 1.0
CE B:LYS127 4.8 34.6 1.0
CA B:CYS169 4.8 22.0 1.0
N B:PHE195 4.8 22.1 1.0
N B:TYR170 4.9 17.4 1.0

Mercury binding site 5 out of 5 in 1ems

Go back to Mercury Binding Sites List in 1ems
Mercury binding site 5 out of 5 in the Crystal Structure of the C. Elegans Nitfhit Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of the C. Elegans Nitfhit Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg455

b:24.7
occ:0.47
HG B:EMC455 0.0 24.7 0.5
C1 B:EMC455 2.0 24.7 0.5
SG B:CYS55 2.6 28.2 1.0
C2 B:EMC455 2.8 24.7 0.5
CE1 B:HIS98 3.0 38.5 1.0
O B:GLY96 3.4 32.1 1.0
ND1 B:HIS98 3.4 39.4 1.0
CA B:CYS55 3.5 28.0 1.0
NE2 B:HIS98 3.5 40.9 1.0
N B:CYS55 3.6 28.8 1.0
CB B:CYS55 3.6 28.0 1.0
OD1 B:ASN110 3.9 39.0 1.0
ND2 B:ASN110 4.1 38.9 1.0
CG B:GLU54 4.2 24.8 1.0
CG B:HIS98 4.2 39.1 1.0
CG B:ASN110 4.2 35.6 1.0
CD2 B:HIS98 4.2 38.6 1.0
C B:GLY96 4.4 33.0 1.0
C B:GLU54 4.6 26.6 1.0
OD2 B:ASP57 4.9 31.9 1.0
C B:CYS55 4.9 28.8 1.0
N B:HIS98 4.9 36.5 1.0
C B:LEU97 5.0 35.0 1.0
CD B:GLU54 5.0 31.5 1.0

Reference:

H.C.Pace, S.C.Hodawadekar, A.Draganescu, J.Huang, P.Bieganowski, Y.Pekarsky, C.M.Croce, C.Brenner. Crystal Structure of the Worm Nitfhit Rosetta Stone Protein Reveals A Nit Tetramer Binding Two Fhit Dimers. Curr.Biol. V. 10 907 2000.
ISSN: ISSN 0960-9822
PubMed: 10959838
DOI: 10.1016/S0960-9822(00)00621-7
Page generated: Sun Dec 13 19:02:35 2020

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