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Mercury in PDB 1kdg: Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase

Enzymatic activity of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase

All present enzymatic activity of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase:
1.1.99.18;

Protein crystallography data

The structure of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase, PDB code: 1kdg was solved by B.M.Hallberg, G.Henriksson, G.Pettersson, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.00 / 1.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 185.075, 185.075, 81.034, 90.00, 90.00, 120.00
R / Rfree (%) 13.3 / 16.9

Mercury Binding Sites:

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

Mercury binding site 1 out of 10 in 1kdg

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Mercury binding site 1 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:14.3
occ:0.50
 O A:ASN385 3.2 16.1 1.0
OD1 A:ASN317 3.3 14.4 1.0
O A:HOH2145 3.4 33.5 1.0
O A:HOH2143 3.5 32.8 1.0
CG A:ASN317 3.7 11.8 1.0
O A:HOH1090 3.9 17.4 1.0
C A:ASN385 4.0 14.7 1.0
O A:HOH2046 4.0 27.6 1.0
CA A:ASN385 4.0 14.3 1.0
O A:HOH1143 4.0 24.6 1.0
CB A:ASN317 4.1 12.0 1.0
ND2 A:ASN317 4.4 11.7 1.0
CB A:ASN385 4.4 13.6 1.0
N A:GLY319 4.5 12.0 1.0
OD1 A:ASN385 4.6 16.8 1.0
CA A:GLY319 4.8 12.7 1.0
CG A:ASN385 4.8 15.5 1.0
O A:HOH2065 4.9 17.8 1.0

Mercury binding site 2 out of 10 in 1kdg

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Mercury binding site 2 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg902

b:30.2
occ:0.25
 CD2 B:PHE288 3.4 8.6 1.0
O B:HOH3417 3.4 29.0 1.0
CE2 B:PHE288 3.5 8.8 1.0
CG B:PHE288 3.9 8.3 1.0
CZ B:PHE288 4.1 9.1 1.0
CD1 B:PHE288 4.4 9.3 1.0
CE1 B:PHE288 4.5 10.9 1.0
CB B:PHE288 4.6 9.6 1.0
O B:HOH3288 4.9 24.9 1.0

Mercury binding site 3 out of 10 in 1kdg

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Mercury binding site 3 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:26.4
occ:0.25
 O A:HOH2004 2.4 18.5 1.0
O A:THR265 3.4 11.3 1.0
O A:SER266 3.7 12.5 1.0
O A:HOH1269 3.9 17.3 1.0
C A:SER266 4.1 11.6 1.0
CA A:SER266 4.2 11.8 1.0
C A:THR265 4.4 10.9 1.0
N A:GLY268 4.5 9.5 1.0
CA A:GLY268 4.7 9.7 1.0
N A:SER266 4.9 11.3 1.0
N A:SER267 4.9 11.4 1.0

Mercury binding site 4 out of 10 in 1kdg

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Mercury binding site 4 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg904

b:25.5
occ:0.10
 SD A:EMT6907 3.8 20.4 1.0
HG A:HG906 3.9 20.4 0.1
HG A:EMT6907 4.0 24.5 0.5
HG A:HG905 4.8 24.0 0.1

Mercury binding site 5 out of 10 in 1kdg

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Mercury binding site 5 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg905

b:24.0
occ:0.10
 SD A:EMT6907 2.1 20.4 1.0
OD1 A:EMT6907 3.1 29.8 1.0
CE1 A:EMT6907 3.4 14.9 1.0
HG A:EMT6907 3.4 24.5 0.5
CG A:EMT6907 3.5 23.2 1.0
CZ A:EMT6907 3.8 18.6 1.0
OD2 A:EMT6907 4.0 25.5 1.0
CD1 A:EMT6907 4.5 17.5 1.0
HG A:HG904 4.8 25.5 0.1

Mercury binding site 6 out of 10 in 1kdg

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Mercury binding site 6 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg906

b:20.4
occ:0.10
 HG A:HG904 3.9 25.5 0.1
CD1 A:EMT6907 4.3 17.5 1.0
CD A:PRO700 4.5 12.0 1.0
CG A:PRO700 4.5 12.4 1.0

Mercury binding site 7 out of 10 in 1kdg

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Mercury binding site 7 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg6907

b:24.5
occ:0.50
 HG A:EMT6907 0.0 24.5 0.5
SD A:EMT6907 2.3 20.4 1.0
OD1 A:EMT6907 2.9 29.8 1.0
CE1 A:EMT6907 3.3 14.9 1.0
HG A:HG905 3.4 24.0 0.1
CG A:EMT6907 3.6 23.2 1.0
CZ A:EMT6907 3.8 18.6 1.0
CG A:PRO700 3.8 12.4 1.0
HG A:HG904 4.0 25.5 0.1
CD1 A:EMT6907 4.2 17.5 1.0
OD2 A:EMT6907 4.5 25.5 1.0
CB A:PRO700 4.7 13.2 1.0
CD A:PRO700 4.8 12.0 1.0
CE2 A:EMT6907 5.0 16.6 1.0

Mercury binding site 8 out of 10 in 1kdg

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Mercury binding site 8 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg901

b:25.9
occ:0.25
 OD1 B:ASN317 3.2 17.5 1.0
CG B:ASN317 3.6 15.7 1.0
O B:ASN385 3.6 20.7 1.0
OD1 B:ASN385 3.9 21.1 1.0
CB B:ASN317 3.9 14.6 1.0
O B:HOH3090 4.0 27.8 1.0
CA B:ASN385 4.1 17.7 1.0
O B:HOH3143 4.1 34.0 1.0
CB B:ASN385 4.2 18.5 1.0
N B:GLY319 4.2 16.3 1.0
C B:ASN385 4.3 18.0 1.0
CG B:ASN385 4.4 20.1 1.0
ND2 B:ASN317 4.5 16.8 1.0
N B:ASP318 4.6 14.9 1.0
CA B:GLY319 4.7 16.5 1.0

Mercury binding site 9 out of 10 in 1kdg

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Mercury binding site 9 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg902

b:35.6
occ:0.25
 O A:HOH1417 3.5 29.1 1.0
CD2 A:PHE288 3.5 8.7 1.0
CE2 A:PHE288 3.6 9.5 1.0
CG A:PHE288 3.9 9.2 1.0
CZ A:PHE288 4.1 8.4 1.0
CD1 A:PHE288 4.4 9.7 1.0
CE1 A:PHE288 4.5 9.8 1.0
CB A:PHE288 4.6 10.1 1.0
O A:HOH1288 4.9 25.8 1.0

Mercury binding site 10 out of 10 in 1kdg

Go back to Mercury Binding Sites List in 1kdg
Mercury binding site 10 out of 10 in the Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of the Flavin Domain of Cellobiose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg903

b:34.5
occ:0.25
 O B:HOH3069 2.7 28.3 1.0
O B:GLY754 2.8 22.8 1.0
O B:PRO755 3.2 25.8 1.0
C B:GLY754 3.6 22.5 1.0
O B:HOH3364 3.6 27.5 1.0
C B:PRO755 3.7 25.2 1.0
O B:HOH3386 3.8 42.0 1.0
O B:HOH4086 4.0 35.4 1.0
OXT B:PRO755 4.1 29.6 1.0
NZ B:LYS240 4.2 25.2 1.0
N B:PRO755 4.3 22.9 1.0
O B:HOH3337 4.3 30.8 1.0
CA B:PRO755 4.4 23.9 1.0
CA B:GLY754 4.4 21.6 1.0
N B:GLY754 4.5 21.5 1.0
O B:HOH3050 4.9 21.7 1.0

Reference:

B.M.Hallberg, G.Henriksson, G.Pettersson, C.Divne. Crystal Structure of the Flavoprotein Domain of the Extracellular Flavocytochrome Cellobiose Dehydrogenase J.Mol.Biol. V. 315 421 2002.
ISSN: ISSN 0022-2836
PubMed: 11786022
DOI: 10.1006/JMBI.2001.5246
Page generated: Sun Aug 11 00:20:14 2024

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