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Mercury in PDB 5dsf: Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S

Enzymatic activity of Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S

All present enzymatic activity of Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S:
4.99.1.2;

Protein crystallography data

The structure of Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S, PDB code: 5dsf was solved by H.M.Wahba, L.Lecoq, M.Stevenson, A.Mansour, L.Cappadocia, J.Lafrance-Vanasse, K.J.Wilkinson, J.Sygusch, D.E.Wilcox, J.G.Omichinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.680, 88.349, 52.671, 90.00, 100.93, 90.00
R / Rfree (%) 16.5 / 20.8

Other elements in 5dsf:

The structure of Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S also contains other interesting chemical elements:

Bromine (Br) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S (pdb code 5dsf). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S, PDB code: 5dsf:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 5dsf

Go back to Mercury Binding Sites List in 5dsf
Mercury binding site 1 out of 2 in the Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S


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 Mercury-Bound Form of Merb Mutant D99S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg301

b:32.7
occ:0.80
SG A:CYS159 2.3 26.5 1.0
SG A:CYS96 2.6 21.6 1.0
O A:HOH488 2.7 30.2 1.0
HG A:SER99 2.7 28.1 1.0
HD2 A:PHE158 3.0 30.3 1.0
OG A:SER99 3.2 23.4 1.0
HE2 A:PHE158 3.3 31.0 1.0
CB A:CYS159 3.5 26.6 1.0
HA A:CYS159 3.5 32.1 1.0
HB3 A:CYS159 3.6 31.9 1.0
HB3 A:CYS96 3.7 18.0 1.0
CD2 A:PHE158 3.8 25.2 1.0
CE2 A:PHE158 3.9 25.9 1.0
CB A:CYS96 3.9 15.0 1.0
CA A:CYS159 4.0 26.7 1.0
HB2 A:TRP95 4.0 25.8 1.0
H A:SER99 4.2 20.9 1.0
HG22 A:VAL154 4.3 36.8 1.0
HB2 A:CYS159 4.3 31.9 1.0
H A:CYS159 4.3 32.7 1.0
HE3 A:TRP95 4.4 26.6 1.0
HB3 A:TRP95 4.4 25.8 1.0
N A:CYS159 4.5 27.3 1.0
HB2 A:CYS96 4.5 18.0 1.0
CB A:SER99 4.5 16.1 1.0
HB3 A:LEU98 4.6 24.8 1.0
H A:CYS96 4.7 21.4 1.0
CB A:TRP95 4.7 21.5 1.0
N A:CYS96 4.7 17.8 1.0
N A:SER99 4.8 17.4 1.0
HB2 A:SER99 4.8 19.3 1.0
HG21 A:VAL154 4.9 36.8 1.0
CA A:CYS96 4.9 16.1 1.0
HA A:SER99 4.9 25.0 1.0
HB3 A:PHE158 5.0 28.2 1.0

Mercury binding site 2 out of 2 in 5dsf

Go back to Mercury Binding Sites List in 5dsf
Mercury binding site 2 out of 2 in the Crystal Structure of the Mercury-Bound Form of Merb Mutant D99S


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 Mercury-Bound Form of Merb Mutant D99S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg301

b:26.7
occ:0.80
SG B:CYS159 2.4 24.6 1.0
O B:HOH495 2.4 20.4 1.0
SG B:CYS96 2.6 20.5 1.0
HG B:SER99 2.8 23.5 1.0
O B:HOH486 3.0 44.8 1.0
HD2 B:PHE158 3.1 26.7 1.0
HE2 B:PHE158 3.3 28.3 1.0
OG B:SER99 3.4 19.6 1.0
HA B:CYS159 3.4 29.9 1.0
CB B:CYS159 3.5 24.7 1.0
HB3 B:CYS159 3.5 29.7 1.0
HB3 B:CYS96 3.7 21.7 1.0
CD2 B:PHE158 3.8 22.3 1.0
HG22 B:VAL154 3.8 37.9 1.0
CB B:CYS96 3.8 18.1 1.0
CA B:CYS159 3.9 24.9 1.0
CE2 B:PHE158 3.9 23.6 1.0
HG21 B:VAL154 4.1 37.9 1.0
HB2 B:TRP95 4.2 22.3 1.0
H B:SER99 4.2 20.5 1.0
H B:CYS159 4.3 30.3 1.0
HB2 B:CYS159 4.3 29.7 1.0
N B:CYS159 4.4 25.2 1.0
HB3 B:LEU98 4.4 26.7 1.0
CG2 B:VAL154 4.4 31.6 1.0
HB2 B:CYS96 4.5 21.7 1.0
HE3 B:TRP95 4.5 29.2 1.0
HB3 B:TRP95 4.6 22.3 1.0
CB B:SER99 4.6 18.0 1.0
H B:CYS96 4.7 19.3 1.0
N B:CYS96 4.7 16.1 1.0
N B:SER99 4.8 17.1 1.0
CB B:TRP95 4.8 18.6 1.0
HB2 B:SER99 4.9 21.6 1.0
CA B:CYS96 4.9 18.6 1.0
HG23 B:VAL154 4.9 37.9 1.0
HA B:SER99 4.9 24.3 1.0
HB3 B:PHE158 5.0 29.7 1.0

Reference:

H.M.Wahba, L.Lecoq, M.Stevenson, A.Mansour, L.Cappadocia, J.Lafrance-Vanasse, K.J.Wilkinson, J.Sygusch, D.E.Wilcox, J.G.Omichinski. Structural and Biochemical Characterization of A Copper-Binding Mutant of the Organomercurial Lyase Merb: Insight Into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity. Biochemistry V. 55 1070 2016.
ISSN: ISSN 0006-2960
PubMed: 26820485
DOI: 10.1021/ACS.BIOCHEM.5B01298
Page generated: Sun Dec 13 19:12:31 2020

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