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Mercury in PDB 3a0w: Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)

Enzymatic activity of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)

All present enzymatic activity of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic):
2.7.13.3;

Protein crystallography data

The structure of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic), PDB code: 3a0w was solved by S.Yamada, H.Sugimoto, M.Kobayashi, A.Ohno, H.Nakamura, Y.Shiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.092, 61.148, 90.287, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24

Mercury Binding Sites:

The binding sites of Mercury atom in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic) (pdb code 3a0w). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 7 binding sites of Mercury where determined in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic), PDB code: 3a0w:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7;

Mercury binding site 1 out of 7 in 3a0w

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Mercury binding site 1 out of 7 in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg801

b:29.8
occ:0.30
 HG A:EMC801 0.0 29.8 0.3
C1 A:EMC801 2.3 27.7 0.3
SG A:CYS634 2.5 24.5 0.5
CB A:CYS634 2.6 20.2 0.5
CB A:CYS634 2.9 20.5 0.5
C2 A:EMC801 3.2 28.9 0.3
N A:CYS634 3.3 20.0 1.0
O A:ILE672 3.5 14.1 1.0
CA A:CYS634 3.6 19.9 1.0
SG A:CYS634 3.7 24.4 0.5
CB A:LYS673 3.9 12.7 1.0
C A:PHE633 3.9 19.8 1.0
CA A:LYS673 4.2 12.0 1.0
OD1 A:ASP632 4.3 26.3 0.5
CG A:LYS673 4.3 17.6 1.0
C A:ILE672 4.3 12.9 1.0
CD A:LYS673 4.4 21.7 1.0
C A:CYS634 4.4 18.5 1.0
O A:CYS634 4.4 17.6 1.0
O A:PHE633 4.5 20.4 1.0
O A:ASP632 4.6 17.9 1.0
CA A:PHE633 4.6 18.8 1.0
N A:LYS673 4.6 11.5 1.0
CG A:ASP632 4.8 22.2 0.5
HG A:EMC801 4.8 44.8 0.3
C A:ASP632 4.9 18.9 1.0
N A:PHE633 4.9 18.8 1.0

Mercury binding site 2 out of 7 in 3a0w

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Mercury binding site 2 out of 7 in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg801

b:44.8
occ:0.30
 HG A:EMC801 0.0 44.8 0.3
C1 A:EMC801 2.4 43.5 0.3
SG A:CYS634 2.4 24.4 0.5
CB A:CYS634 2.8 20.5 0.5
CB A:CYS634 3.0 20.2 0.5
SG A:CYS634 3.2 24.5 0.5
C2 A:EMC801 3.3 43.6 0.3
OE2 A:GLU636 3.6 32.6 1.0
O A:HOH26 4.0 23.6 1.0
CA A:CYS634 4.1 19.9 1.0
CD A:GLU636 4.4 29.2 1.0
CG A:GLU636 4.4 23.0 1.0
N A:PHE635 4.7 17.3 1.0
C A:CYS634 4.7 18.5 1.0
HG A:EMC801 4.8 29.8 0.3
O A:PHE635 5.0 18.6 1.0

Mercury binding site 3 out of 7 in 3a0w

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Mercury binding site 3 out of 7 in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg802

b:25.2
occ:0.80
 HG A:EMC802 0.0 25.2 0.8
SG A:CYS721 2.3 18.4 1.0
C1 A:EMC802 2.4 25.0 0.8
C2 A:EMC802 3.1 23.3 0.8
O A:GLY717 3.1 20.4 1.0
N A:CYS721 3.2 14.0 1.0
CB A:CYS721 3.4 14.2 1.0
CA A:CYS721 3.4 13.7 1.0
CB A:ASN657 3.5 14.2 1.0
ND2 A:ASN657 3.6 19.6 1.0
CG A:ASN657 3.7 17.4 1.0
C A:ILE720 4.0 14.5 1.0
C A:GLY717 4.1 19.2 1.0
O A:GLN653 4.3 14.8 1.0
CB A:ILE720 4.3 14.6 1.0
CA A:VAL654 4.3 11.3 1.0
CG2 A:ILE720 4.3 14.3 1.0
OD1 A:ASN657 4.5 21.6 1.0
C A:GLN653 4.6 13.2 1.0
CA A:ILE720 4.6 13.8 1.0
O A:ILE720 4.7 14.1 1.0
N A:VAL654 4.7 12.1 1.0
CA A:GLY717 4.7 21.0 1.0
CG2 A:VAL654 4.8 13.4 1.0
CD1 A:ILE724 4.8 13.9 1.0
C A:CYS721 5.0 13.4 1.0

Mercury binding site 4 out of 7 in 3a0w

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Mercury binding site 4 out of 7 in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg803

b:99.9
occ:0.40
 HG A:EMT803 0.0 99.9 0.4
C1 A:EMT803 2.4 99.3 0.4
SD A:EMT803 2.6 98.8 0.4
OD2 A:EMT803 2.9 98.9 0.4
C2 A:EMT803 3.2 99.4 0.4
OG1 A:THR709 3.6 51.3 1.0
CE1 A:EMT803 3.6 98.7 0.4
CG A:EMT803 3.8 98.8 0.4
CZ A:EMT803 4.1 98.7 0.4
CB A:THR709 4.5 50.2 1.0
CD1 A:EMT803 4.6 98.5 0.4
CD1 A:LEU698 4.6 24.3 1.0
CG2 A:THR709 4.8 50.7 1.0

Mercury binding site 5 out of 7 in 3a0w

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Mercury binding site 5 out of 7 in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg801

b:24.5
occ:0.50
 HG B:EMC801 0.0 24.5 0.5
C1 B:EMC801 2.3 15.4 0.5
SG B:CYS634 2.4 24.0 0.5
SG B:CYS634 2.8 27.5 0.5
CB B:CYS634 2.8 19.4 0.5
CB B:CYS634 2.9 20.0 0.5
C2 B:EMC801 3.0 20.6 0.5
N B:CYS634 3.2 17.8 1.0
O B:ILE672 3.5 14.5 1.0
CA B:CYS634 3.5 19.4 1.0
HG B:EMC801 3.9 38.7 0.2
C B:PHE633 3.9 17.8 1.0
CB B:LYS673 3.9 12.6 1.0
CA B:LYS673 4.2 11.8 1.0
CG B:LYS673 4.3 14.2 1.0
C B:ILE672 4.3 12.9 1.0
C B:CYS634 4.3 17.4 1.0
O B:CYS634 4.4 15.4 1.0
CD B:LYS673 4.5 18.5 1.0
O B:PHE633 4.5 19.2 1.0
N B:LYS673 4.6 12.1 1.0
CA B:PHE633 4.6 16.9 1.0
O B:ASP632 4.8 15.6 1.0
N B:PHE633 5.0 17.1 1.0

Mercury binding site 6 out of 7 in 3a0w

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Mercury binding site 6 out of 7 in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg801

b:38.7
occ:0.20
 HG B:EMC801 0.0 38.7 0.2
C1 B:EMC801 2.4 37.9 0.2
SG B:CYS634 2.6 27.5 0.5
SG B:CYS634 2.9 24.0 0.5
C2 B:EMC801 3.2 38.2 0.2
CB B:CYS634 3.4 20.0 0.5
CB B:CYS634 3.4 19.4 0.5
OE2 B:GLU636 3.8 36.1 1.0
HG B:EMC801 3.9 24.5 0.5
NZ B:LYS673 4.8 29.6 1.0
CD B:GLU636 4.8 30.7 1.0
CA B:CYS634 4.9 19.4 1.0
CE B:LYS673 5.0 24.5 1.0

Mercury binding site 7 out of 7 in 3a0w

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Mercury binding site 7 out of 7 in the Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Catalytic Domain of Histidine Kinase Thka (TM1359) For Mad Phasing (Nucleotide Free Form 2, Orthorombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg802

b:29.2
occ:0.80
 HG B:EMC802 0.0 29.2 0.8
C1 B:EMC802 2.4 28.9 0.8
SG B:CYS721 2.5 20.1 1.0
O B:GLY717 3.1 29.2 1.0
C2 B:EMC802 3.2 30.6 0.8
N B:CYS721 3.2 19.6 1.0
CA B:CYS721 3.4 18.6 1.0
CB B:CYS721 3.4 18.8 1.0
CB B:ASN657 3.6 15.6 1.0
ND2 B:ASN657 3.6 21.6 1.0
CG B:ASN657 3.7 18.8 1.0
C B:ILE720 4.0 19.5 1.0
C B:GLY717 4.1 29.8 1.0
O B:GLN653 4.2 13.1 1.0
CA B:VAL654 4.2 11.4 1.0
CB B:ILE720 4.4 21.0 1.0
CG2 B:ILE720 4.5 20.5 1.0
C B:GLN653 4.5 12.6 1.0
CG2 B:VAL654 4.5 12.2 1.0
N B:VAL654 4.6 11.4 1.0
OD1 B:ASN657 4.6 25.3 1.0
O B:ILE720 4.7 19.1 1.0
CD1 B:ILE724 4.7 16.3 1.0
CA B:ILE720 4.7 21.0 1.0
CA B:GLY717 4.7 32.5 1.0
CB B:VAL654 4.9 12.3 1.0
O B:HOH38 4.9 25.1 1.0
C B:CYS721 4.9 18.6 1.0
N B:LEU718 5.0 28.1 1.0

Reference:

S.Yamada, H.Sugimoto, M.Kobayashi, A.Ohno, H.Nakamura, Y.Shiro. Structure of Pas-Linked Histidine Kinase and the Response Regulator Complex Structure V. 17 1333 2009.
ISSN: ISSN 0969-2126
PubMed: 19836334
DOI: 10.1016/J.STR.2009.07.016
Page generated: Sun Aug 11 03:11:27 2024

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