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Mercury in PDB 3f7f: Structure of NUP120

Protein crystallography data

The structure of Structure of NUP120, PDB code: 3f7f was solved by H.S.Seo, Y.Ma, E.W.Debler, G.Blobel, A.Hoelz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.680, 117.478, 146.287, 89.94, 89.77, 89.89
R / Rfree (%) 23.2 / 25.4

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Mercury atom in the Structure of NUP120 (pdb code 3f7f). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 12 binding sites of Mercury where determined in the Structure of NUP120, PDB code: 3f7f:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 12 in 3f7f

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Mercury binding site 1 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg801

b:0.6
occ:1.00
SG A:CYS475 2.7 61.4 1.0
O A:ASN458 3.0 53.5 1.0
OG A:SER482 3.3 50.0 1.0
CB A:SER482 3.7 46.5 1.0
C A:ASN458 3.8 52.4 1.0
CB A:CYS475 3.9 55.1 1.0
CG1 A:VAL473 3.9 44.0 1.0
NH2 A:ARG6 3.9 47.3 1.0
OD1 A:ASN458 4.1 49.5 1.0
CA A:ASN458 4.2 50.6 1.0
CB A:ASN458 4.2 51.0 1.0
CA A:CYS475 4.4 52.4 1.0
CA A:ALA460 4.4 57.1 1.0
N A:ALA460 4.5 56.4 1.0
C A:GLU459 4.5 56.5 1.0
O A:GLU459 4.5 55.8 1.0
CG A:ASN458 4.6 51.9 1.0
CB A:VAL473 4.6 43.8 1.0
N A:CYS475 4.6 49.6 1.0
N A:SER482 4.6 45.1 1.0
O A:VAL473 4.7 45.7 1.0
CZ A:ARG6 4.7 51.2 1.0
CA A:SER482 4.8 46.9 1.0
CB A:ALA460 4.8 56.9 1.0
C A:ASN474 4.9 49.6 1.0
N A:GLU459 4.9 55.1 1.0
C A:HIS481 5.0 46.0 1.0
C A:VAL473 5.0 45.8 1.0

Mercury binding site 2 out of 12 in 3f7f

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Mercury binding site 2 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg802

b:0.6
occ:1.00
SG A:CYS3 3.3 71.6 1.0
N A:MET1 3.4 74.8 1.0
O A:ALA2 3.8 62.6 1.0
OD1 A:ASN492 4.0 55.6 1.0
ND2 A:ASN496 4.0 64.5 1.0
C A:ALA2 4.1 63.7 1.0
N A:ALA2 4.2 69.7 1.0
C A:MET1 4.2 74.3 1.0
CA A:MET1 4.4 76.2 1.0
CG A:ASN492 4.4 55.2 1.0
N A:CYS3 4.4 63.0 1.0
CA A:CYS3 4.5 60.9 1.0
CB A:CYS3 4.6 63.1 1.0
OE1 A:GLU500 4.6 0.5 1.0
CG A:ASN496 4.6 65.6 1.0
CA A:ALA2 4.8 65.4 1.0
O A:MET1 4.8 75.3 1.0
ND2 A:ASN343 4.8 0.3 1.0
CB A:ASN492 4.9 53.7 1.0
ND2 A:ASN492 4.9 54.2 1.0
OD1 A:ASN343 5.0 0.5 1.0
CG A:ASN343 5.0 0.2 1.0
OD1 A:ASN496 5.0 66.7 1.0

Mercury binding site 3 out of 12 in 3f7f

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Mercury binding site 3 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg803

b:90.5
occ:1.00
SG A:CYS673 2.6 54.6 1.0
CB A:CYS673 3.3 45.9 1.0
O A:CYS673 3.3 39.9 1.0
CA A:CYS673 3.4 45.0 1.0
C A:CYS673 3.6 41.4 1.0
CG A:TYR14 3.8 45.9 1.0
CD2 A:TYR14 3.8 47.6 1.0
CB A:TYR14 4.0 48.9 1.0
CD1 A:TYR14 4.4 43.7 1.0
CE2 A:TYR14 4.4 47.9 1.0
CB A:ALA676 4.5 43.8 1.0
N A:LEU674 4.7 39.5 1.0
N A:GLU677 4.7 49.5 1.0
N A:CYS673 4.7 45.8 1.0
CB A:GLU677 4.8 52.5 1.0
CE1 A:TYR14 4.8 46.0 1.0
CZ A:TYR14 4.9 48.4 1.0

Mercury binding site 4 out of 12 in 3f7f

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Mercury binding site 4 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg801

b:0.1
occ:1.00
SG B:CYS475 2.7 62.7 1.0
O B:ASN458 2.9 54.6 1.0
OG B:SER482 3.3 50.5 1.0
CB B:SER482 3.7 46.5 1.0
C B:ASN458 3.8 53.2 1.0
CB B:CYS475 3.9 54.9 1.0
CG1 B:VAL473 3.9 44.9 1.0
NH2 B:ARG6 4.0 48.5 1.0
OD1 B:ASN458 4.1 50.4 1.0
CA B:ASN458 4.2 50.8 1.0
CB B:ASN458 4.3 50.4 1.0
CA B:ALA460 4.4 56.5 1.0
CA B:CYS475 4.4 51.9 1.0
N B:ALA460 4.4 56.3 1.0
O B:GLU459 4.5 57.6 1.0
C B:GLU459 4.5 56.9 1.0
CB B:VAL473 4.5 44.7 1.0
N B:CYS475 4.6 48.6 1.0
CG B:ASN458 4.6 51.7 1.0
N B:SER482 4.7 46.3 1.0
O B:VAL473 4.7 46.9 1.0
CZ B:ARG6 4.7 51.2 1.0
CB B:ALA460 4.8 55.9 1.0
CA B:SER482 4.9 47.7 1.0
C B:ASN474 4.9 48.4 1.0
N B:GLU459 4.9 55.5 1.0
C B:VAL473 5.0 46.0 1.0

Mercury binding site 5 out of 12 in 3f7f

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Mercury binding site 5 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg802

b:0.6
occ:1.00
N B:MET1 3.3 74.2 1.0
SG B:CYS3 3.5 68.9 1.0
O B:ALA2 3.7 61.7 1.0
ND2 B:ASN496 3.8 66.3 1.0
OD1 B:ASN492 4.0 55.4 1.0
C B:ALA2 4.1 63.4 1.0
N B:ALA2 4.1 70.0 1.0
C B:MET1 4.3 74.0 1.0
CA B:MET1 4.3 75.9 1.0
OE1 B:GLU500 4.4 0.8 1.0
CG B:ASN492 4.4 54.8 1.0
CG B:ASN496 4.4 65.7 1.0
N B:CYS3 4.5 62.9 1.0
CA B:CYS3 4.6 60.6 1.0
OD1 B:ASN496 4.7 67.9 1.0
CA B:ALA2 4.8 65.6 1.0
CB B:CYS3 4.8 62.2 1.0
CB B:ASN492 4.8 53.3 1.0
O B:MET1 4.9 75.9 1.0
ND2 B:ASN343 4.9 0.6 1.0
CD B:GLU500 4.9 0.9 1.0
ND2 B:ASN492 5.0 52.1 1.0

Mercury binding site 6 out of 12 in 3f7f

Go back to Mercury Binding Sites List in 3f7f
Mercury binding site 6 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg803

b:90.4
occ:1.00
SG B:CYS673 2.6 56.0 1.0
CB B:CYS673 3.3 46.4 1.0
O B:CYS673 3.3 40.4 1.0
CA B:CYS673 3.4 45.0 1.0
C B:CYS673 3.6 41.2 1.0
CG B:TYR14 3.8 46.1 1.0
CD2 B:TYR14 3.8 47.7 1.0
CB B:TYR14 4.0 48.9 1.0
CD1 B:TYR14 4.4 44.5 1.0
CE2 B:TYR14 4.4 47.7 1.0
CB B:ALA676 4.5 45.1 1.0
N B:GLU677 4.7 49.1 1.0
N B:LEU674 4.7 38.7 1.0
N B:CYS673 4.8 45.4 1.0
CB B:GLU677 4.8 53.9 1.0
CE1 B:TYR14 4.9 46.9 1.0
CZ B:TYR14 4.9 49.7 1.0

Mercury binding site 7 out of 12 in 3f7f

Go back to Mercury Binding Sites List in 3f7f
Mercury binding site 7 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg801

b:0.8
occ:1.00
SG C:CYS475 2.6 60.6 1.0
O C:ASN458 2.9 54.3 1.0
OG C:SER482 3.3 50.8 1.0
CB C:SER482 3.7 46.9 1.0
C C:ASN458 3.8 53.1 1.0
CB C:CYS475 3.8 53.9 1.0
NH2 C:ARG6 3.9 48.5 1.0
CG1 C:VAL473 3.9 44.7 1.0
OD1 C:ASN458 4.0 52.8 1.0
CA C:ASN458 4.1 51.0 1.0
CB C:ASN458 4.2 50.5 1.0
CA C:CYS475 4.4 51.4 1.0
CA C:ALA460 4.5 56.5 1.0
N C:ALA460 4.5 56.6 1.0
O C:GLU459 4.5 56.9 1.0
CG C:ASN458 4.5 51.3 1.0
C C:GLU459 4.5 56.6 1.0
CB C:VAL473 4.6 44.3 1.0
N C:CYS475 4.6 49.5 1.0
N C:SER482 4.6 45.0 1.0
CZ C:ARG6 4.7 52.6 1.0
O C:VAL473 4.7 46.6 1.0
CA C:SER482 4.8 47.2 1.0
CB C:ALA460 4.9 56.5 1.0
N C:GLU459 4.9 54.7 1.0
C C:ASN474 5.0 49.3 1.0
C C:HIS481 5.0 45.2 1.0
NE C:ARG6 5.0 50.9 1.0

Mercury binding site 8 out of 12 in 3f7f

Go back to Mercury Binding Sites List in 3f7f
Mercury binding site 8 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg802

b:0.6
occ:1.00
N C:MET1 3.0 75.1 1.0
SG C:CYS3 3.5 71.6 1.0
O C:ALA2 3.8 64.9 1.0
ND2 C:ASN496 3.9 65.6 1.0
N C:ALA2 4.0 70.8 1.0
C C:MET1 4.0 75.0 1.0
CA C:MET1 4.0 76.5 1.0
C C:ALA2 4.1 65.3 1.0
OD1 C:ASN492 4.3 55.6 1.0
OE1 C:GLU500 4.4 0.1 1.0
CG C:ASN496 4.5 66.1 1.0
N C:CYS3 4.5 63.9 1.0
O C:MET1 4.6 76.2 1.0
CA C:ALA2 4.7 67.0 1.0
CG C:ASN492 4.7 53.9 1.0
CA C:CYS3 4.7 61.9 1.0
OD1 C:ASN496 4.8 67.5 1.0
CB C:CYS3 4.8 64.3 1.0

Mercury binding site 9 out of 12 in 3f7f

Go back to Mercury Binding Sites List in 3f7f
Mercury binding site 9 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg803

b:91.3
occ:1.00
SG C:CYS673 2.6 54.8 1.0
O C:CYS673 3.3 40.7 1.0
CB C:CYS673 3.3 45.5 1.0
CA C:CYS673 3.3 44.5 1.0
C C:CYS673 3.6 41.5 1.0
CD2 C:TYR14 3.8 48.0 1.0
CG C:TYR14 3.8 46.2 1.0
CB C:TYR14 4.0 48.9 1.0
CD1 C:TYR14 4.4 44.2 1.0
CE2 C:TYR14 4.4 48.0 1.0
CB C:ALA676 4.5 43.4 1.0
N C:LEU674 4.7 39.5 1.0
N C:GLU677 4.7 49.6 1.0
N C:CYS673 4.7 46.2 1.0
CB C:GLU677 4.8 54.5 1.0
CE1 C:TYR14 4.9 47.7 1.0
CZ C:TYR14 4.9 49.4 1.0

Mercury binding site 10 out of 12 in 3f7f

Go back to Mercury Binding Sites List in 3f7f
Mercury binding site 10 out of 12 in the Structure of NUP120


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Structure of NUP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg801

b:0.2
occ:1.00
SG D:CYS475 2.6 62.7 1.0
O D:ASN458 3.1 53.6 1.0
OG D:SER482 3.2 50.5 1.0
CB D:SER482 3.6 47.5 1.0
CG1 D:VAL473 3.8 45.9 1.0
CB D:CYS475 3.8 55.0 1.0
C D:ASN458 4.0 52.3 1.0
NH2 D:ARG6 4.0 47.9 1.0
OD1 D:ASN458 4.1 51.0 1.0
CA D:ASN458 4.3 50.8 1.0
CA D:CYS475 4.3 52.0 1.0
CB D:ASN458 4.4 50.3 1.0
CB D:VAL473 4.4 44.7 1.0
CA D:ALA460 4.4 56.0 1.0
N D:CYS475 4.5 48.8 1.0
O D:VAL473 4.5 45.0 1.0
N D:SER482 4.5 45.4 1.0
N D:ALA460 4.5 55.8 1.0
O D:GLU459 4.5 57.5 1.0
C D:GLU459 4.6 56.8 1.0
CG D:ASN458 4.7 51.0 1.0
CZ D:ARG6 4.7 52.2 1.0
CA D:SER482 4.7 47.5 1.0
C D:ASN474 4.8 48.2 1.0
CB D:ALA460 4.8 55.3 1.0
C D:VAL473 4.8 45.4 1.0
C D:HIS481 4.9 46.7 1.0

Reference:

H.S.Seo, Y.Ma, E.W.Debler, D.Wacker, S.Kutik, G.Blobel, A.Hoelz. Structural and Functional Analysis of NUP120 Suggests Ring Formation of the NUP84 Complex. Proc.Natl.Acad.Sci.Usa V. 106 14281 2009.
ISSN: ISSN 0027-8424
PubMed: 19706512
DOI: 10.1073/PNAS.0907453106
Page generated: Wed Oct 28 18:42:34 2020

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