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Mercury in PDB 1jop: Yhch Protein (HI0227)

Protein crystallography data

The structure of Yhch Protein (HI0227), PDB code: 1jop was solved by A.Teplyakov, G.Obmolova, G.L.Gilliland, Structure 2 Functionproject (S2F), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.100, 152.300, 53.400, 90.00, 113.60, 90.00
R / Rfree (%) 18.5 / n/a

Mercury Binding Sites:

Pages:

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

Binding sites:

The binding sites of Mercury atom in the Yhch Protein (HI0227) (pdb code 1jop). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 12 binding sites of Mercury where determined in the Yhch Protein (HI0227), PDB code: 1jop:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 12 in 1jop

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Mercury binding site 1 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg201

b:49.9
occ:0.50
O A:HOH209 2.4 41.8 1.0
SG A:CYS23 2.7 57.9 1.0
O A:ILE19 2.8 45.2 1.0
CG1 A:VAL22 2.8 76.5 1.0
N A:CYS23 3.3 45.8 1.0
CG2 A:ILE19 3.5 22.4 1.0
CB A:VAL22 3.6 60.3 1.0
CG1 A:VAL71 3.7 31.6 1.0
CB A:CYS23 3.7 47.6 1.0
CA A:CYS23 3.7 45.4 1.0
C A:ILE19 3.8 40.8 1.0
C A:VAL22 3.9 53.4 1.0
CA A:ILE19 4.1 31.4 1.0
CG2 A:VAL71 4.1 42.7 1.0
CB A:VAL71 4.2 35.0 1.0
CA A:VAL22 4.4 53.7 1.0
CD1 A:LEU26 4.4 34.7 1.0
CB A:ILE19 4.5 32.4 1.0
O A:VAL22 4.5 59.6 1.0
CG2 A:VAL22 4.9 51.0 1.0
N A:VAL22 5.0 50.7 1.0

Mercury binding site 2 out of 12 in 1jop

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Mercury binding site 2 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg202

b:56.5
occ:0.50
OD2 A:ASP70 2.0 33.1 1.0
NE2 A:HIS65 2.0 36.0 1.0
NE2 A:HIS130 2.3 49.6 1.0
O A:HOH219 2.7 56.7 1.0
CE1 A:HIS65 2.8 51.7 1.0
CG A:ASP70 3.0 28.7 1.0
CD2 A:HIS130 3.1 39.4 1.0
CD2 A:HIS65 3.2 50.0 1.0
OD1 A:ASP70 3.3 40.0 1.0
CE1 A:HIS130 3.4 42.5 1.0
OE1 A:GLU63 3.5 78.1 1.0
NZ A:LYS149 3.7 55.0 1.0
ND1 A:HIS65 4.0 35.3 1.0
NE2 A:GLN72 4.1 42.6 1.0
CD A:GLU63 4.1 56.2 1.0
CG A:HIS65 4.2 31.6 1.0
CG A:HIS130 4.3 33.6 1.0
CB A:ASP70 4.4 36.0 1.0
ND1 A:HIS130 4.4 32.1 1.0
OE2 A:GLU63 4.5 53.8 1.0
CB A:GLU63 4.9 35.2 1.0

Mercury binding site 3 out of 12 in 1jop

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Mercury binding site 3 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg203

b:62.5
occ:0.50
SG A:CYS105 1.8 55.5 1.0
N A:ASP107 2.2 36.4 1.0
N A:ALA106 2.6 52.6 1.0
O A:ASP107 2.7 32.0 1.0
CA A:ASP107 2.8 42.9 1.0
CB A:ASP107 2.9 56.6 1.0
C A:CYS105 3.0 47.6 1.0
CB A:CYS105 3.0 47.4 1.0
C A:ASP107 3.1 40.3 1.0
C A:ALA106 3.2 42.2 1.0
CA A:ALA106 3.4 52.4 1.0
CA A:CYS105 3.5 42.3 1.0
O A:CYS105 3.8 55.8 1.0
CG A:ASP107 3.9 86.2 1.0
CB A:ALA106 4.0 60.6 1.0
O A:HOH210 4.0 44.4 1.0
OD2 A:ASP107 4.2 0.0 1.0
N A:ILE108 4.3 48.1 1.0
O A:ALA106 4.3 42.8 1.0
N A:CYS105 4.8 29.2 1.0
OD1 A:ASP107 4.9 86.2 1.0

Mercury binding site 4 out of 12 in 1jop

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Mercury binding site 4 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg201

b:58.4
occ:0.50
SG B:CYS23 2.3 43.9 1.0
O B:HOH206 2.4 38.4 1.0
O B:ILE19 2.9 35.0 1.0
N B:CYS23 3.1 32.4 1.0
CB B:CYS23 3.4 46.1 1.0
CA B:CYS23 3.4 37.6 1.0
CG2 B:ILE19 3.5 30.1 1.0
CG1 B:VAL22 3.5 48.4 1.0
C B:VAL22 3.6 44.5 1.0
CB B:VAL22 3.7 42.5 1.0
C B:ILE19 3.8 39.4 1.0
CA B:ILE19 4.1 41.0 1.0
CG1 B:VAL71 4.2 39.3 1.0
CA B:VAL22 4.2 47.5 1.0
CD1 B:LEU26 4.2 32.0 1.0
O B:VAL22 4.2 51.7 1.0
CB B:ILE19 4.4 47.0 1.0
N B:VAL22 4.7 58.6 1.0
C B:CYS23 4.9 45.2 1.0
CB B:VAL71 4.9 42.6 1.0
N B:ALA20 4.9 27.5 1.0

Mercury binding site 5 out of 12 in 1jop

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Mercury binding site 5 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg202

b:57.7
occ:0.50
OD2 B:ASP70 1.9 35.0 1.0
NE2 B:HIS65 1.9 22.5 1.0
NE2 B:HIS130 2.0 48.4 1.0
CE1 B:HIS65 2.5 27.2 1.0
CD2 B:HIS130 2.8 21.4 1.0
O B:HOH213 2.8 61.2 1.0
CG B:ASP70 3.1 62.8 1.0
CE1 B:HIS130 3.2 46.1 1.0
CD2 B:HIS65 3.2 46.3 1.0
OE1 B:GLU63 3.3 60.1 1.0
CD B:GLU63 3.5 65.2 1.0
NZ B:LYS149 3.6 41.3 1.0
OD1 B:ASP70 3.7 45.0 1.0
CG B:GLU63 3.7 60.7 1.0
ND1 B:HIS65 3.7 29.3 1.0
CG B:HIS130 4.0 37.5 1.0
CG B:HIS65 4.1 18.9 1.0
OE2 B:GLU63 4.1 43.0 1.0
ND1 B:HIS130 4.2 49.5 1.0
NE2 B:GLN72 4.2 27.8 1.0
CB B:ASP70 4.2 34.1 1.0
CB B:GLU63 4.9 24.3 1.0
CE B:LYS149 5.0 42.0 1.0

Mercury binding site 6 out of 12 in 1jop

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Mercury binding site 6 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg203

b:72.6
occ:0.50
SG B:CYS105 1.7 76.3 1.0
N B:ASP107 1.9 38.4 1.0
CA B:ASP107 2.5 54.5 1.0
CB B:ASP107 2.6 75.7 1.0
O B:ASP107 2.8 55.4 1.0
N B:ALA106 2.8 57.8 1.0
CB B:CYS105 2.9 44.0 1.0
C B:ASP107 3.0 49.1 1.0
C B:CYS105 3.1 55.5 1.0
C B:ALA106 3.1 52.9 1.0
CA B:CYS105 3.4 46.2 1.0
CA B:ALA106 3.6 52.2 1.0
O B:CYS105 3.9 58.6 1.0
O B:ALA106 4.1 59.7 1.0
CG B:ASP107 4.1 0.6 1.0
N B:ILE108 4.3 52.0 1.0
CB B:ALA106 4.3 36.7 1.0
OD1 B:ASP107 4.8 0.3 1.0
N B:CYS105 4.8 43.4 1.0
OH B:TYR93 4.9 43.8 1.0
CE1 B:TYR93 4.9 38.0 1.0
CZ B:TYR93 5.0 51.0 1.0
OD2 B:ASP107 5.0 0.8 1.0

Mercury binding site 7 out of 12 in 1jop

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Mercury binding site 7 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg201

b:67.5
occ:0.50
SG C:CYS23 2.3 45.0 1.0
O C:HOH225 2.6 63.9 1.0
CB C:CYS23 3.3 37.7 1.0
CD2 C:LEU6 3.6 0.9 1.0
CD1 C:LEU6 3.8 0.5 1.0
CA C:CYS23 3.8 48.5 1.0
CG C:PHE121 3.8 22.6 1.0
CD2 C:PHE121 3.8 44.2 1.0
CG2 C:VAL73 4.1 47.9 1.0
CB C:PHE121 4.1 24.3 1.0
CG C:LEU6 4.2 93.3 1.0
CD1 C:LEU26 4.2 35.6 1.0
CD1 C:PHE121 4.3 50.8 1.0
CE2 C:PHE121 4.3 44.8 1.0
N C:CYS23 4.6 47.9 1.0
CE1 C:PHE121 4.8 29.8 1.0
CZ C:PHE121 4.8 50.7 1.0

Mercury binding site 8 out of 12 in 1jop

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Mercury binding site 8 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg202

b:62.6
occ:0.50
OD2 C:ASP70 1.8 29.8 1.0
NE2 C:HIS65 2.2 46.4 1.0
NE2 C:HIS130 2.3 58.3 1.0
O C:HOH205 2.6 45.1 1.0
CG C:ASP70 3.0 48.6 1.0
CE1 C:HIS65 3.1 27.0 1.0
CD2 C:HIS65 3.1 24.4 1.0
CD2 C:HIS130 3.2 30.9 1.0
CE1 C:HIS130 3.3 46.4 1.0
OD1 C:ASP70 3.6 44.0 1.0
NE2 C:GLN72 3.9 33.4 1.0
CD C:GLU63 3.9 79.1 1.0
OE1 C:GLU63 4.0 67.5 1.0
ND1 C:HIS65 4.1 31.1 1.0
CG C:HIS65 4.2 16.0 1.0
OE2 C:GLU63 4.2 85.4 1.0
CB C:ASP70 4.2 27.9 1.0
NZ C:LYS149 4.4 44.0 1.0
CG C:GLU63 4.4 52.4 1.0
ND1 C:HIS130 4.4 42.6 1.0
CG C:HIS130 4.4 45.1 1.0

Mercury binding site 9 out of 12 in 1jop

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Mercury binding site 9 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg203

b:0.7
occ:0.50
SG C:CYS105 2.2 66.5 1.0
CB C:CYS105 2.8 48.1 1.0
CB C:LYS92 3.0 0.8 1.0
O C:ASP107 3.1 57.2 1.0
CG C:LYS92 3.3 0.4 1.0
CE1 C:TYR93 3.5 36.5 1.0
O C:LYS92 3.6 89.7 1.0
CD1 C:TYR93 3.8 38.1 1.0
C C:LYS92 3.9 87.9 1.0
CD C:LYS92 3.9 89.1 1.0
CA C:LYS92 4.0 94.7 1.0
C C:ASP107 4.1 63.5 1.0
CZ C:TYR93 4.2 53.1 1.0
CA C:CYS105 4.3 56.9 1.0
CB C:ASP107 4.6 86.4 1.0
N C:ASP107 4.6 66.6 1.0
OH C:TYR93 4.7 41.4 1.0
CG C:TYR93 4.7 40.2 1.0
CA C:ASP107 4.7 71.5 1.0
N C:TYR93 4.7 67.7 1.0
OD1 C:ASP109 4.7 97.1 1.0
N C:LYS92 4.9 96.0 1.0
O C:ASN89 5.0 58.4 1.0
C C:CYS105 5.0 67.3 1.0

Mercury binding site 10 out of 12 in 1jop

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Mercury binding site 10 out of 12 in the Yhch Protein (HI0227)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Yhch Protein (HI0227) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg201

b:76.0
occ:0.50
CD2 D:LEU6 2.3 45.8 1.0
SG D:CYS23 2.4 60.0 1.0
CG D:LEU6 2.5 73.1 1.0
O D:HOH206 2.7 41.5 1.0
CD1 D:LEU6 2.7 28.7 1.0
CB D:CYS23 3.2 30.4 1.0
CA D:CYS23 3.5 41.2 1.0
CD1 D:PHE121 3.6 46.2 1.0
CG D:PHE121 3.6 22.0 1.0
CE1 D:PHE121 3.8 30.9 1.0
CD2 D:PHE121 3.9 33.3 1.0
CB D:LEU6 4.0 71.4 1.0
CB D:PHE121 4.1 33.2 1.0
CZ D:PHE121 4.1 37.6 1.0
CE2 D:PHE121 4.2 31.4 1.0
N D:CYS23 4.4 37.2 1.0
CD1 D:LEU26 4.5 45.3 1.0
C D:CYS23 4.7 55.0 1.0
CG2 D:VAL73 4.8 17.6 1.0
CA D:LEU6 4.9 69.8 1.0
O D:CYS23 4.9 63.4 1.0
CG1 D:VAL71 5.0 27.6 1.0

Reference:

A.Teplyakov, G.Obmolova, J.Toedt, M.Y.Galperin, G.L.Gilliland. Crystal Structure of the Bacterial Yhch Protein Indicates A Role in Sialic Acid Catabolism. J.Bacteriol. V. 187 5520 2005.
ISSN: ISSN 0021-9193
PubMed: 16077096
DOI: 10.1128/JB.187.16.5520-5527.2005
Page generated: Sun Dec 13 19:03:29 2020

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