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Mercury in PDB 1qd9: Bacillus Subtilis Yabj

Protein crystallography data

The structure of Bacillus Subtilis Yabj, PDB code: 1qd9 was solved by J.L.Smith, S.Sinha, P.Rappu, S.C.Lange, P.Mantsala, H.Zalkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 53.350, 53.350, 204.960, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 19.7

Mercury Binding Sites:

The binding sites of Mercury atom in the Bacillus Subtilis Yabj (pdb code 1qd9). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Bacillus Subtilis Yabj, PDB code: 1qd9:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 1qd9

Go back to Mercury Binding Sites List in 1qd9
Mercury binding site 1 out of 6 in the Bacillus Subtilis Yabj


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Bacillus Subtilis Yabj within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg126

b:23.3
occ:0.60
HG A:HG126 0.0 23.3 0.6
SG A:CYS104 2.2 23.4 0.8
SD A:MET81 3.1 34.3 0.8
CB A:CYS104 3.2 17.9 1.0
CE A:MET81 3.2 13.7 0.8
CD1 A:PHE84 3.2 42.0 1.0
HG A:HG126 3.2 22.5 0.3
C A:CYS104 3.4 13.2 1.0
CE1 A:PHE84 3.4 33.2 1.0
CD1 A:ILE78 3.4 22.3 1.0
O A:CYS104 3.5 14.4 1.0
N A:VAL105 3.6 12.0 1.0
CG1 A:ILE78 3.8 12.8 1.0
CA A:CYS104 3.8 12.1 1.0
CA A:VAL105 4.0 11.2 1.0
C A:VAL105 4.2 12.4 1.0
CG A:PHE84 4.3 33.9 1.0
O A:VAL105 4.3 12.3 1.0
CZ A:PHE84 4.5 43.2 1.0
N A:GLU106 4.8 13.7 1.0
CB A:PHE84 4.9 29.2 1.0
CG2 A:ILE78 4.9 18.8 1.0
CG A:MET81 4.9 25.5 0.8
CB A:ILE78 5.0 17.1 1.0

Mercury binding site 2 out of 6 in 1qd9

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Mercury binding site 2 out of 6 in the Bacillus Subtilis Yabj


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Bacillus Subtilis Yabj within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg126

b:22.5
occ:0.26
HG A:HG126 0.0 22.5 0.3
SG A:CYS104 2.2 23.4 0.8
CB A:CYS104 3.2 17.9 1.0
HG A:HG126 3.2 23.3 0.6
CE1 A:PHE84 3.5 33.2 1.0
CZ A:PHE84 3.6 43.2 1.0
CD1 A:PHE84 3.7 42.0 1.0
CE2 A:PHE84 3.9 41.9 1.0
CG1 A:VAL76 4.0 14.1 1.0
CG A:PHE84 4.0 33.9 1.0
CD2 A:PHE84 4.1 41.2 1.0
CB A:VAL76 4.3 12.7 1.0
CZ A:ARG102 4.5 34.1 1.0
CA A:CYS104 4.6 12.1 1.0
NH1 A:ARG102 4.6 24.5 1.0
NH2 A:ARG102 4.6 26.4 1.0
CG1 A:VAL87 4.6 22.1 1.0
CG2 A:VAL76 4.8 13.6 1.0
NE A:ARG102 4.9 23.4 1.0
CG2 A:ILE78 4.9 18.8 1.0
O A:PHE84 4.9 19.4 1.0
CD1 A:ILE78 4.9 22.3 1.0

Mercury binding site 3 out of 6 in 1qd9

Go back to Mercury Binding Sites List in 1qd9
Mercury binding site 3 out of 6 in the Bacillus Subtilis Yabj


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Bacillus Subtilis Yabj within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg500

b:20.3
occ:0.73
HG B:EMC500 0.0 20.3 0.7
HG B:EMC500 1.2 32.0 0.1
C1 B:EMC500 1.9 27.1 0.1
C1 B:EMC500 2.1 19.8 0.7
C2 B:EMC500 2.1 27.1 0.1
SG B:CYS104 2.3 17.8 0.8
C2 B:EMC500 2.9 15.1 0.7
SG B:CYS104 3.0 36.5 0.2
CB B:CYS104 3.1 18.2 1.0
CE1 B:PHE84 3.3 18.7 1.0
CD1 B:PHE84 3.4 14.2 1.0
CG1 B:VAL76 3.9 10.5 1.0
CZ B:PHE84 4.1 24.3 1.0
CB B:VAL76 4.2 9.7 1.0
CG B:PHE84 4.3 17.1 1.0
CA B:CYS104 4.4 14.1 1.0
CD1 B:ILE78 4.5 27.0 1.0
CG2 B:VAL76 4.7 17.2 1.0
NE B:ARG102 4.9 16.0 1.0
CZ B:ARG102 4.9 20.5 1.0
CE2 B:PHE84 4.9 20.3 1.0
CD2 B:PHE84 5.0 17.3 1.0

Mercury binding site 4 out of 6 in 1qd9

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Mercury binding site 4 out of 6 in the Bacillus Subtilis Yabj


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Bacillus Subtilis Yabj within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg500

b:32.0
occ:0.15
HG B:EMC500 0.0 32.0 0.1
HG B:EMC500 1.2 20.3 0.7
C1 B:EMC500 2.0 19.8 0.7
C1 B:EMC500 2.1 27.1 0.1
SG B:CYS104 2.4 36.5 0.2
C2 B:EMC500 2.4 15.1 0.7
C2 B:EMC500 2.9 27.1 0.1
SG B:CYS104 3.0 17.8 0.8
CB B:CYS104 3.1 18.2 1.0
CE1 B:PHE84 3.6 18.7 1.0
NE B:ARG102 3.7 16.0 1.0
CZ B:ARG102 3.8 20.5 1.0
CB B:VAL76 4.0 9.7 1.0
CG1 B:VAL76 4.1 10.5 1.0
CD B:ARG102 4.1 15.2 1.0
NH2 B:ARG102 4.1 23.2 1.0
CZ B:PHE84 4.1 24.3 1.0
CD1 B:PHE84 4.1 14.2 1.0
NH1 B:ARG102 4.1 16.4 1.0
CG2 B:VAL76 4.2 17.2 1.0
CA B:CYS104 4.4 14.1 1.0
O B:HOH540 4.6 22.3 1.0
O B:HOH635 4.6 34.3 1.0
CG B:ARG102 4.8 14.7 1.0
CE2 B:PHE84 5.0 20.3 1.0

Mercury binding site 5 out of 6 in 1qd9

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Mercury binding site 5 out of 6 in the Bacillus Subtilis Yabj


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Bacillus Subtilis Yabj within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg501

b:27.0
occ:0.68
HG C:EMC501 0.0 27.0 0.7
HG C:EMC501 2.0 46.4 0.2
C1 C:EMC501 2.1 24.4 0.7
C2 C:EMC501 2.3 22.6 0.2
SG C:CYS104 2.3 22.0 0.8
C1 C:EMC501 2.7 28.4 0.2
C2 C:EMC501 2.9 15.8 0.7
CE1 C:PHE84 3.1 30.8 1.0
CB C:CYS104 3.2 20.2 1.0
SG C:CYS104 3.2 30.1 0.2
CD1 C:PHE84 3.3 28.7 1.0
CZ C:PHE84 3.8 19.8 1.0
CG1 C:VAL76 4.0 14.8 1.0
CG C:PHE84 4.1 25.7 1.0
CB C:VAL76 4.3 14.8 1.0
CD1 C:ILE78 4.4 25.1 1.0
CA C:CYS104 4.5 14.7 1.0
CE2 C:PHE84 4.6 26.5 1.0
CD2 C:PHE84 4.7 24.0 1.0
CG2 C:VAL76 4.7 18.1 1.0
CG2 C:ILE78 5.0 26.5 1.0
CA C:PHE84 5.0 17.9 1.0

Mercury binding site 6 out of 6 in 1qd9

Go back to Mercury Binding Sites List in 1qd9
Mercury binding site 6 out of 6 in the Bacillus Subtilis Yabj


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Bacillus Subtilis Yabj within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg501

b:46.4
occ:0.18
HG C:EMC501 0.0 46.4 0.2
HG C:EMC501 2.0 27.0 0.7
C1 C:EMC501 2.1 28.4 0.2
C2 C:EMC501 2.1 15.8 0.7
C1 C:EMC501 2.3 24.4 0.7
SG C:CYS104 2.4 30.1 0.2
C2 C:EMC501 2.8 22.6 0.2
NE C:ARG102 3.4 19.1 1.0
CB C:CYS104 3.4 20.2 1.0
CD C:ARG102 3.5 14.1 1.0
CZ C:ARG102 3.5 29.7 1.0
SG C:CYS104 3.6 22.0 0.8
CG2 C:VAL76 3.6 18.1 1.0
NH1 C:ARG102 3.7 15.4 1.0
CB C:VAL76 3.8 14.8 1.0
CG1 C:VAL76 4.1 14.8 1.0
NH2 C:ARG102 4.1 26.3 1.0
CE1 C:PHE84 4.2 30.8 1.0
CG C:ARG102 4.2 20.2 1.0
CZ C:PHE84 4.4 19.8 1.0
O C:HOH579 4.4 32.2 1.0
CA C:CYS104 4.6 14.7 1.0
CD1 C:PHE84 4.8 28.7 1.0
OD1 C:ASN88 4.9 17.7 1.0
O C:SER103 5.0 14.8 1.0

Reference:

S.Sinha, P.Rappu, S.C.Lange, P.Mantsala, H.Zalkin, J.L.Smith. Crystal Structure of Bacillus Subtilis Yabj, A Purine Regulatory Protein and Member of the Highly Conserved Yjgf Family. Proc.Natl.Acad.Sci.Usa V. 96 13074 1999.
ISSN: ISSN 0027-8424
PubMed: 10557275
DOI: 10.1073/PNAS.96.23.13074
Page generated: Sun Dec 13 19:04:47 2020

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