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Mercury in PDB 3wmz: Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative

Enzymatic activity of Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative

All present enzymatic activity of Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative:
3.2.1.55;

Protein crystallography data

The structure of Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative, PDB code: 3wmz was solved by Z.Fujimoto, T.Maehara, H.Ichinose, M.Michikawa, K.Harazono, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.64 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.285, 97.285, 103.480, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 19.8

Other elements in 3wmz:

The structure of Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative (pdb code 3wmz). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 3 binding sites of Mercury where determined in the Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative, PDB code: 3wmz:
Jump to Mercury binding site number: 1; 2; 3;

Mercury binding site 1 out of 3 in 3wmz

Go back to Mercury Binding Sites List in 3wmz
Mercury binding site 1 out of 3 in the Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative


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 Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg503

b:45.2
occ:0.50
HG A:EMC503 0.0 45.2 0.5
NE2 A:HIS212 2.1 26.8 1.0
C1 A:EMC503 2.4 41.2 0.5
CE1 A:HIS212 2.9 26.9 1.0
O A:THR233 3.0 28.0 1.0
C2 A:EMC503 3.2 39.4 0.9
CD2 A:HIS212 3.2 26.4 1.0
O A:HOH662 3.3 35.6 1.0
CD1 A:TRP235 3.8 23.9 1.0
O A:HOH744 3.8 47.8 1.0
NE1 A:TRP235 3.8 23.0 1.0
ND1 A:HIS212 4.1 26.3 1.0
C A:THR233 4.2 27.4 1.0
CA A:ASN234 4.2 26.1 0.3
CA A:ASN234 4.2 27.1 0.7
CG A:HIS212 4.2 26.5 1.0
N A:TRP235 4.3 24.7 1.0
O A:HOH771 4.4 50.3 1.0
CG A:TRP235 4.5 22.9 1.0
CE2 A:TRP235 4.6 22.7 1.0
N A:ASN234 4.7 27.0 1.0
C A:ASN234 4.7 25.6 1.0

Mercury binding site 2 out of 3 in 3wmz

Go back to Mercury Binding Sites List in 3wmz
Mercury binding site 2 out of 3 in the Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative


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 Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg504

b:41.4
occ:0.10
HG A:EMC504 0.0 41.4 0.1
C1 A:EMC504 2.4 40.9 0.1
C2 A:EMC504 3.2 40.8 0.1
OD1 A:ASN209 4.5 50.1 1.0

Mercury binding site 3 out of 3 in 3wmz

Go back to Mercury Binding Sites List in 3wmz
Mercury binding site 3 out of 3 in the Crystal Structure of Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative


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 Streptomyces Coelicolor Alpha-L- Arabinofuranosidase Ethylmercury Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg505

b:38.6
occ:0.10
HG A:EMC505 0.0 38.6 0.1
O1 A:TRS502 0.9 33.9 0.9
C1 A:TRS502 2.0 32.9 0.9
C1 A:EMC505 2.4 38.1 0.1
OD2 A:ASP309 2.4 21.6 1.0
C A:TRS502 2.5 32.6 0.9
N A:TRS502 2.6 30.8 0.9
C2 A:TRS502 2.8 33.7 0.9
CD A:GLU361 2.9 26.6 1.0
OE2 A:GLU361 3.0 26.6 1.0
CG A:ASP309 3.2 21.4 1.0
OD1 A:ASP309 3.2 22.8 1.0
C2 A:EMC505 3.2 38.2 0.1
OE1 A:GLU361 3.2 26.1 1.0
O A:HOH704 3.4 22.9 1.0
O2 A:TRS502 3.4 32.2 0.9
ND1 A:HIS427 3.4 23.5 1.0
CG A:GLU361 3.5 24.5 1.0
O A:HOH616 3.6 24.1 1.0
CB A:GLU361 3.9 23.1 1.0
C3 A:TRS502 4.0 32.9 0.9
CE1 A:HIS427 4.1 24.6 1.0
N A:GLY362 4.5 19.7 1.0
CG A:HIS427 4.5 23.9 1.0
OD1 A:ASP202 4.5 22.1 1.0
O3 A:TRS502 4.6 31.6 0.9
CB A:ASP309 4.6 20.7 1.0
CB A:HIS427 4.7 22.4 1.0
CD1 A:ILE308 4.8 28.7 1.0
OH A:TYR461 5.0 32.5 1.0
CA A:GLY362 5.0 19.7 1.0
O A:HOH677 5.0 37.4 1.0

Reference:

T.Maehara, Z.Fujimoto, H.Ichinose, M.Michikawa, K.Harazono, S.Kaneko. Crystal Structure and Characterization of the Glycoside Hydrolase Family 62 Alpha-L-Arabinofuranosidase From Streptomyces Coelicolor J.Biol.Chem. V. 289 7962 2014.
ISSN: ISSN 0021-9258
PubMed: 24482228
DOI: 10.1074/JBC.M113.540542
Page generated: Sun Dec 13 19:10:35 2020

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