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Mercury in PDB 1gcb: GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol)

Protein crystallography data

The structure of GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol), PDB code: 1gcb was solved by L.Joshua-Tor, H.E.Xu, S.A.Johnston, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 151.150, 151.150, 89.880, 90.00, 90.00, 120.00
R / Rfree (%) 20.9 / 27.4

Mercury Binding Sites:

The binding sites of Mercury atom in the GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol) (pdb code 1gcb). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol), PDB code: 1gcb:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 1gcb

Go back to Mercury Binding Sites List in 1gcb
Mercury binding site 1 out of 4 in the GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:33.2
occ:0.81
SG A:CYS415 2.5 31.6 1.0
CB A:CYS415 3.2 20.7 1.0
CE1 A:PHE411 3.6 35.0 1.0
C A:CYS415 3.6 20.4 1.0
O A:HOH584 3.7 34.2 1.0
O A:CYS415 3.7 21.5 1.0
O A:PHE411 3.7 23.4 1.0
N A:GLN417 3.8 24.4 1.0
CZ A:PHE411 3.9 35.0 1.0
CD1 A:PHE411 3.9 32.2 1.0
N A:PHE416 3.9 19.7 1.0
CA A:CYS415 4.0 19.4 1.0
O A:GLN417 4.2 19.5 1.0
CG2 A:ILE418 4.2 24.2 1.0
C A:PHE416 4.3 24.4 1.0
CE2 A:PHE411 4.4 31.9 1.0
C A:GLN417 4.4 19.7 1.0
CG A:PHE411 4.4 28.5 1.0
CA A:PHE416 4.4 22.7 1.0
CA A:GLN417 4.5 22.4 1.0
CD2 A:PHE411 4.7 30.5 1.0
C A:PHE411 4.7 21.9 1.0

Mercury binding site 2 out of 4 in 1gcb

Go back to Mercury Binding Sites List in 1gcb
Mercury binding site 2 out of 4 in the GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg902

b:29.5
occ:0.35
SG A:CYS376 2.2 31.6 1.0
CG2 A:VAL378 2.3 43.1 1.0
HG A:HG903 2.6 18.2 0.1
N A:VAL378 3.1 37.1 1.0
OG1 A:THR55 3.2 42.0 1.0
CB A:VAL378 3.5 44.5 1.0
CB A:CYS376 3.6 22.7 1.0
CA A:VAL378 3.7 42.7 1.0
C A:HIS377 3.7 30.6 1.0
N A:HIS377 3.7 24.1 1.0
CG2 A:THR55 3.8 31.4 1.0
C A:CYS376 3.9 23.7 1.0
CA A:HIS377 4.0 27.1 1.0
CG1 A:VAL312 4.0 23.6 1.0
CB A:THR55 4.1 32.4 1.0
OD1 A:ASN54 4.1 37.2 1.0
CG2 A:VAL312 4.2 26.9 1.0
O A:CYS376 4.2 25.4 1.0
CA A:CYS376 4.4 22.9 1.0
O A:HIS377 4.5 33.1 1.0
CB A:PRO385 4.5 33.7 1.0
CB A:VAL312 4.7 26.6 1.0
CG1 A:VAL378 4.7 44.3 1.0
CA A:PRO385 4.8 35.8 1.0

Mercury binding site 3 out of 4 in 1gcb

Go back to Mercury Binding Sites List in 1gcb
Mercury binding site 3 out of 4 in the GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:18.2
occ:0.10
CG2 A:VAL312 2.5 26.9 1.0
SG A:CYS376 2.6 31.6 1.0
HG A:HG902 2.6 29.5 0.3
CB A:PRO385 3.0 33.7 1.0
CB A:CYS376 3.3 22.7 1.0
CB A:VAL312 3.6 26.6 1.0
CG A:PRO385 3.8 37.6 1.0
CG1 A:VAL312 4.0 23.6 1.0
CG2 A:VAL378 4.1 43.1 1.0
CA A:PRO385 4.1 35.8 1.0
CE2 A:TYR388 4.1 18.8 1.0
CA A:VAL312 4.1 23.7 1.0
CD A:PRO385 4.3 41.4 1.0
OH A:TYR388 4.5 23.4 1.0
CZ A:TYR388 4.5 22.5 1.0
N A:VAL312 4.5 22.5 1.0
N A:PRO385 4.7 40.6 1.0
CA A:CYS376 4.7 22.9 1.0
N A:HIS377 4.7 24.1 1.0
O A:SER308 4.8 25.4 1.0
CD2 A:TYR388 4.8 20.8 1.0
C A:CYS376 4.9 23.7 1.0
OG1 A:THR55 4.9 42.0 1.0
N A:VAL378 5.0 37.1 1.0

Mercury binding site 4 out of 4 in 1gcb

Go back to Mercury Binding Sites List in 1gcb
Mercury binding site 4 out of 4 in the GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of GAL6, Yeast Bleomycin Hydrolase Dna-Binding Protease (Thiol) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg904

b:64.7
occ:0.31
SG A:CYS73 2.1 25.0 1.0
C A:ALA453 3.0 39.9 1.0
CB A:CYS73 3.5 20.0 1.0
O A:ALA453 3.5 36.2 1.0
O A:GLY71 3.6 14.1 1.0
C A:GLY71 3.8 15.4 1.0
O A:THR368 3.8 17.2 1.0
CA A:GLY71 3.8 14.9 1.0
N A:CYS73 4.0 20.7 1.0
CA A:ALA453 4.2 41.2 1.0
ND1 A:HIS369 4.3 20.8 1.0
CA A:CYS73 4.3 17.9 1.0
NE2 A:GLN67 4.4 18.5 1.0
CA A:HIS369 4.5 15.5 1.0
N A:ARG72 4.5 14.4 1.0
C A:THR368 4.8 16.2 1.0
N A:TRP74 4.9 14.6 1.0
CB A:ALA453 4.9 38.4 1.0
O A:HOH737 5.0 46.4 1.0

Reference:

L.Joshua-Tor, H.E.Xu, S.A.Johnston, D.C.Rees. Crystal Structure of A Conserved Protease That Binds Dna: the Bleomycin Hydrolase, GAL6. Science V. 269 945 1995.
ISSN: ISSN 0036-8075
PubMed: 7638617
Page generated: Wed Oct 28 18:39:29 2020

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