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Mercury in PDB 2hk7: Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution

Enzymatic activity of Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution:
1.1.1.25;

Protein crystallography data

The structure of Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution, PDB code: 2hk7 was solved by J.H.Gan, P.Prabakaran, Y.J.Gu, M.Andrykovitch, Y.Li, H.H.Liu, H.Yan, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.42 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.181, 74.928, 190.046, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.2

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution (pdb code 2hk7). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution, PDB code: 2hk7:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 2hk7

Go back to Mercury Binding Sites List in 2hk7
Mercury binding site 1 out of 6 in the Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution


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 Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg270

b:74.4
occ:0.50
 O A:HOH322 2.5 51.7 1.0
O A:HOH321 2.6 51.8 1.0
NE2 A:HIS18 2.7 58.8 1.0
O B:HOH289 3.3 31.3 1.0
CD2 A:HIS18 3.6 54.0 1.0
CE1 A:HIS18 3.6 60.3 1.0
O A:HOH323 4.4 50.5 1.0
ND1 A:HIS18 4.7 52.5 1.0
CG A:HIS18 4.7 53.7 1.0
O A:HOH307 5.0 47.8 1.0

Mercury binding site 2 out of 6 in 2hk7

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Mercury binding site 2 out of 6 in the Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution


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 Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg271

b:75.9
occ:0.50
 SD A:MET1 2.8 43.9 1.0
O A:MET1 2.8 39.4 1.0
CA A:MET1 2.8 37.5 1.0
C A:MET1 3.2 32.8 1.0
CE A:MET1 3.2 45.6 1.0
CB A:MET1 3.5 41.8 1.0
CG A:MET1 3.6 44.2 1.0
N A:MET1 3.9 36.7 1.0
ND2 A:ASN3 4.3 28.5 1.0
N A:ILE2 4.5 29.6 1.0

Mercury binding site 3 out of 6 in 2hk7

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Mercury binding site 3 out of 6 in the Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution


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 Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg272

b:67.6
occ:0.25
 SG A:CYS253 2.7 65.2 1.0
CB A:ALA32 3.8 46.4 1.0
CA A:ALA32 4.1 45.1 1.0
O A:GLU254 4.2 66.8 1.0
CG2 A:VAL255 4.4 43.5 1.0
CB A:CYS253 4.5 66.7 1.0
C A:GLU254 4.9 63.2 1.0
CD2 A:TYR31 4.9 26.1 1.0
N A:ALA32 5.0 42.5 1.0

Mercury binding site 4 out of 6 in 2hk7

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Mercury binding site 4 out of 6 in the Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution


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 Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg270

b:79.3
occ:0.50
 NE2 B:HIS18 2.3 81.2 1.0
CE1 B:HIS18 3.0 80.1 1.0
CD2 B:HIS18 3.3 76.8 1.0
ND1 B:HIS18 4.0 77.0 1.0
CG B:HIS18 4.2 71.7 1.0

Mercury binding site 5 out of 6 in 2hk7

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Mercury binding site 5 out of 6 in the Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution


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 Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg271

b:75.9
occ:0.50
 O B:MET1 2.5 51.4 1.0
SD B:MET1 2.6 87.0 1.0
CB B:MET1 2.9 55.9 1.0
CA B:MET1 2.9 47.3 1.0
C B:MET1 3.1 43.9 1.0
CG B:MET1 3.2 70.2 1.0
O B:HOH304 3.5 22.3 1.0
N B:MET1 4.3 44.0 1.0
CE B:MET1 4.4 79.1 1.0
N B:ILE2 4.4 32.5 1.0
O B:HOH305 4.8 11.2 1.0
OD1 B:ASN35 4.8 25.2 1.0

Mercury binding site 6 out of 6 in 2hk7

Go back to Mercury Binding Sites List in 2hk7
Mercury binding site 6 out of 6 in the Crystal Structure of Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution


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 Shikimate Dehydrogenase From Aquifex Aeolicus in Complex with Mercury at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg272

b:65.9
occ:0.15
 SG B:CYS253 3.0 75.8 1.0
CB B:CYS253 3.1 69.6 1.0
CB B:ALA32 4.4 43.4 1.0
O B:ASN251 4.4 42.5 1.0
CA B:CYS253 4.5 65.8 1.0
CD2 B:LEU34 4.6 46.8 1.0
O B:ALA32 4.8 48.8 1.0
CB B:ASN251 5.0 37.0 1.0

Reference:

J.Gan, Y.Wu, P.Prabakaran, Y.Gu, Y.Li, M.Andrykovitch, H.Liu, Y.Gong, H.Yan, X.Ji. Structural and Biochemical Analyses of Shikimate Dehydrogenase Aroe From Aquifex Aeolicus: Implications For the Catalytic Mechanism. Biochemistry V. 46 9513 2007.
ISSN: ISSN 0006-2960
PubMed: 17649975
DOI: 10.1021/BI602601E
Page generated: Sun Aug 11 02:36:51 2024

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