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Mercury in PDB 1o9l: Succinate:Coenzyme-A Transferase (Pig Heart)

Enzymatic activity of Succinate:Coenzyme-A Transferase (Pig Heart)

All present enzymatic activity of Succinate:Coenzyme-A Transferase (Pig Heart):
2.8.3.5;

Protein crystallography data

The structure of Succinate:Coenzyme-A Transferase (Pig Heart), PDB code: 1o9l was solved by E.P.Mitchell, A.J.Lloyd, G.Lewis, P.Shoolingin-Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 2.4
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.800, 133.800, 101.900, 90.00, 104.40, 90.00
R / Rfree (%) 24 / 27

Mercury Binding Sites:

The binding sites of Mercury atom in the Succinate:Coenzyme-A Transferase (Pig Heart) (pdb code 1o9l). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 9 binding sites of Mercury where determined in the Succinate:Coenzyme-A Transferase (Pig Heart), PDB code: 1o9l:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Mercury binding site 1 out of 9 in 1o9l

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Mercury binding site 1 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg9003

b:25.1
occ:0.41
 HG A:EMC9003 0.0 25.1 0.4
C1 A:EMC9003 2.0 23.2 0.4
SG A:CYS465 2.4 16.8 1.0
C2 A:EMC9003 2.8 23.6 0.4
CB A:CYS465 3.2 34.5 1.0
CA A:CYS465 3.3 40.8 1.0
O A:GLN464 3.6 47.6 1.0
O A:LYS463 3.8 47.2 1.0
O A:VAL430 3.8 35.9 1.0
N A:CYS465 4.0 43.5 1.0
C A:GLN464 4.1 46.6 1.0
O A:SER432 4.5 46.4 1.0
C A:CYS465 4.6 43.8 1.0
O A:SER431 4.6 42.7 1.0
CA A:ALA433 4.7 46.5 1.0
C A:SER432 4.7 45.5 1.0
O A:CYS465 4.7 45.3 1.0
N A:ALA433 4.8 46.1 1.0
C A:SER431 4.9 41.8 1.0
CB A:ALA433 4.9 45.9 1.0
C A:LYS463 5.0 47.4 1.0

Mercury binding site 2 out of 9 in 1o9l

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Mercury binding site 2 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg9007

b:8.3
occ:0.27
 HG A:EMT9007 0.0 8.3 0.3
C1 A:EMT9007 2.0 5.8 0.3
SD A:EMT9007 2.4 13.1 0.3
C2 A:EMT9007 2.8 7.0 0.3
CE1 A:EMT9007 3.2 12.2 0.3
O A:VAL133 3.2 38.6 1.0
CG A:LEU135 3.5 33.1 1.0
O A:PRO171 3.6 35.4 1.0
CD1 A:LEU135 3.6 35.3 1.0
OD1 A:EMT9007 3.7 11.4 0.3
CD1 A:EMT9007 3.8 11.8 0.3
N A:LEU135 3.9 34.4 1.0
CB A:LEU135 4.0 33.5 1.0
CZ A:EMT9007 4.1 11.9 0.3
C A:VAL133 4.1 36.8 1.0
CG2 A:VAL133 4.2 34.3 1.0
CG1 A:VAL133 4.3 36.9 1.0
OH A:TYR126 4.3 32.4 1.0
CG A:EMT9007 4.4 12.2 0.3
C A:PRO171 4.5 37.3 1.0
CA A:LEU135 4.6 33.6 1.0
CB A:VAL133 4.7 36.3 1.0
CA A:GLU134 4.8 35.5 1.0
CA A:ILE172 4.8 34.2 1.0
C A:GLU134 4.8 35.5 1.0
CD2 A:LEU135 4.8 33.4 1.0
CZ A:TYR126 4.8 31.5 1.0
N A:GLU134 4.8 36.0 1.0
CE1 A:TYR126 4.9 30.2 1.0

Mercury binding site 3 out of 9 in 1o9l

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Mercury binding site 3 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg9004

b:44.4
occ:0.76
 HG B:EMC9004 0.0 44.4 0.8
C1 B:EMC9004 2.0 42.6 0.8
SG B:CYS465 2.4 42.1 1.0
N B:CYS465 2.6 52.8 1.0
C2 B:EMC9004 2.8 45.0 0.8
CB B:CYS465 3.1 48.2 1.0
CA B:CYS465 3.4 51.0 1.0
O B:HOH2077 3.9 24.6 1.0
OD2 B:EMT9008 3.9 44.9 0.7
O B:HOH2085 4.2 46.5 1.0
CG B:EMT9008 4.2 45.3 0.7
CE2 B:EMT9008 4.2 43.3 0.7
CZ B:EMT9008 4.4 42.5 0.7
C B:CYS465 4.7 52.4 1.0
OD1 B:EMT9008 4.9 47.7 0.7
N B:VAL466 5.0 52.6 1.0
CD2 B:EMT9008 5.0 42.3 0.7

Mercury binding site 4 out of 9 in 1o9l

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Mercury binding site 4 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg9008

b:37.5
occ:0.65
 HG B:EMT9008 0.0 37.5 0.7
C1 B:EMT9008 2.0 38.2 0.7
OD1 B:EMT9008 2.3 47.7 0.7
SD B:EMT9008 2.4 32.6 0.7
C2 B:EMT9008 2.9 37.0 0.7
CG B:EMT9008 3.0 45.3 0.7
CE1 B:EMT9008 3.2 40.1 0.7
CZ B:EMT9008 3.4 42.5 0.7
O B:HOH2086 3.9 51.0 1.0
OD2 B:EMT9008 4.0 44.9 0.7
CG2 B:VAL466 4.3 52.2 1.0
CD1 B:EMT9008 4.3 41.7 0.7
CE2 B:EMT9008 4.7 43.3 0.7
O B:HOH2085 4.7 46.5 1.0
O B:HOH2002 5.0 50.4 1.0

Mercury binding site 5 out of 9 in 1o9l

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Mercury binding site 5 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg9005

b:5.8
occ:0.73
 HG C:EMC9005 0.0 5.8 0.7
C1 C:EMC9005 2.0 2.9 0.7
SG C:CYS465 2.4 15.4 1.0
O C:HOH2133 2.7 49.9 1.0
C2 C:EMC9005 2.8 2.9 0.7
CB C:CYS465 2.9 24.7 1.0
O C:HOH2013 4.3 48.2 1.0
CA C:CYS465 4.4 36.6 1.0
N C:CYS465 4.9 40.3 1.0

Mercury binding site 6 out of 9 in 1o9l

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Mercury binding site 6 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg9006

b:70.0
occ:0.37
 HG C:EMC9006 0.0 70.0 0.4
C1 C:EMC9006 2.0 65.6 0.4
SG C:CYS504 2.4 69.4 1.0
C2 C:EMC9006 2.8 65.8 0.4
CB C:CYS504 3.1 74.8 1.0
N C:CYS504 3.6 75.8 1.0
CD1 C:LEU484 3.7 65.1 1.0
CA C:CYS504 4.0 75.1 1.0
CG2 C:THR502 4.0 76.9 1.0
N C:GLY503 4.5 75.9 1.0
C C:GLY503 4.7 75.5 1.0
C C:CYS504 4.9 75.8 1.0
CA C:GLY503 4.9 75.2 1.0
O C:CYS504 4.9 75.6 1.0
CG C:LEU484 5.0 66.1 1.0

Mercury binding site 7 out of 9 in 1o9l

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Mercury binding site 7 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg9000

b:48.3
occ:0.55
 HG D:EMC9000 0.0 48.3 0.6
C1 D:EMC9000 2.0 47.5 0.6
O D:ASP505 2.1 53.9 1.0
SG D:CYS504 2.4 48.8 1.0
C2 D:EMC9000 2.8 46.3 0.6
CB D:LEU484 3.2 43.5 1.0
C D:ASP505 3.2 53.2 1.0
CD1 D:LEU484 3.2 44.1 1.0
CG D:LEU484 3.4 43.1 1.0
CB D:CYS504 3.5 51.2 1.0
N D:LEU484 3.6 44.7 1.0
CA D:PHE506 3.7 48.9 1.0
CB D:LYS406 3.7 36.2 1.0
N D:PHE506 3.9 51.3 1.0
CB D:PHE506 3.9 46.2 1.0
CA D:LEU484 3.9 44.0 1.0
N D:ASP505 3.9 54.2 1.0
CA D:ASP505 4.3 54.1 1.0
O D:LEU484 4.4 43.0 1.0
C D:CYS504 4.5 53.4 1.0
CA D:LYS406 4.5 34.9 1.0
C D:LEU484 4.6 43.5 1.0
CD D:LYS406 4.6 41.9 1.0
CA D:CYS504 4.6 53.4 1.0
C D:GLY483 4.7 45.5 1.0
CG D:LYS406 4.8 39.7 1.0
CD2 D:LEU484 4.9 41.8 1.0
CB D:ASP505 4.9 56.3 1.0
C D:PHE506 5.0 47.5 1.0
CA D:GLY483 5.0 46.7 1.0

Mercury binding site 8 out of 9 in 1o9l

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Mercury binding site 8 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg9001

b:11.7
occ:0.71
 HG D:EMC9001 0.0 11.7 0.7
C1 D:EMC9001 1.9 2.9 0.7
SG D:CYS465 2.3 28.3 1.0
C2 D:EMC9001 2.6 2.9 0.7
CG2 D:VAL430 2.8 32.0 1.0
O D:VAL430 3.2 30.4 1.0
O D:HOH2058 3.2 26.7 1.0
CB D:CYS465 3.2 22.9 1.0
CA D:GLY462 3.2 28.2 1.0
CB D:VAL430 3.5 32.9 1.0
C D:GLY462 3.6 29.2 1.0
N D:LYS463 3.7 30.7 1.0
C D:VAL430 3.7 32.2 1.0
O D:HOH2057 4.1 23.6 1.0
CA D:CYS465 4.2 25.5 1.0
CA D:VAL430 4.3 31.9 1.0
N D:GLY462 4.3 25.5 1.0
O D:LYS463 4.4 30.7 1.0
N D:SER431 4.5 31.8 1.0
O D:GLY462 4.5 28.1 1.0
N D:CYS465 4.6 26.4 1.0
O D:THR461 4.6 24.2 1.0
C D:LYS463 4.7 31.4 1.0
CA D:SER431 4.7 30.8 1.0
CA D:LYS463 4.8 32.5 1.0
CG1 D:VAL430 4.8 30.6 1.0
C D:THR461 4.8 24.6 1.0

Mercury binding site 9 out of 9 in 1o9l

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Mercury binding site 9 out of 9 in the Succinate:Coenzyme-A Transferase (Pig Heart)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Succinate:Coenzyme-A Transferase (Pig Heart) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg9002

b:25.8
occ:0.44
 HG D:EMC9002 0.0 25.8 0.4
C1 D:EMC9002 2.0 25.7 0.4
SG D:CYS456 2.4 23.1 1.0
N D:CYS456 2.7 35.4 1.0
C2 D:EMC9002 2.9 27.3 0.4
O D:CYS456 3.0 30.3 1.0
CB D:CYS456 3.2 29.8 1.0
CA D:CYS456 3.3 32.6 1.0
C D:LYS455 3.5 39.3 1.0
C D:CYS456 3.6 31.4 1.0
CA D:LYS455 3.8 41.1 1.0
CB D:LYS455 3.8 43.4 1.0
O D:LYS455 4.5 40.4 1.0
OD2 D:ASP409 4.5 40.8 1.0
N D:THR457 4.9 30.7 1.0
CD2 D:LEU460 4.9 32.8 1.0

Reference:

E.P.Mitchell, A.J.Lloyd, G.Lewis, P.Shoolingin-Jordan. Succinate:Coenzyme-A Transferase Deficiency: A Structural View of Pathogenic Mutations To Be Published.
Page generated: Sun Aug 11 00:43:54 2024

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