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Mercury in PDB 1nu7: Staphylocoagulase-Thrombin Complex

Enzymatic activity of Staphylocoagulase-Thrombin Complex

All present enzymatic activity of Staphylocoagulase-Thrombin Complex:
3.4.21.5;

Protein crystallography data

The structure of Staphylocoagulase-Thrombin Complex, PDB code: 1nu7 was solved by R.Friedrich, W.Bode, P.Fuentes-Prior, P.Panizzi, P.E.Bock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.99 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 180.170, 102.000, 135.300, 90.00, 130.08, 90.00
R / Rfree (%) 20.9 / 24.9

Mercury Binding Sites:

The binding sites of Mercury atom in the Staphylocoagulase-Thrombin Complex (pdb code 1nu7). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Staphylocoagulase-Thrombin Complex, PDB code: 1nu7:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 1nu7

Go back to Mercury Binding Sites List in 1nu7
Mercury binding site 1 out of 4 in the Staphylocoagulase-Thrombin Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Staphylocoagulase-Thrombin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1003

b:82.3
occ:0.40
S2 B:0ZJ299 2.4 56.1 1.0
OD2 D:ASP106 3.4 49.7 1.0
OD1 D:ASP106 3.5 52.4 1.0
HG D:HG1004 3.6 55.0 0.4
CG D:ASP106 3.7 50.0 1.0
CA B:GLU217 3.9 36.1 1.0
CB B:GLU217 3.9 38.4 1.0
C2 B:0ZJ299 4.1 46.2 1.0
CG B:GLU217 4.2 43.1 1.0
N B:GLY219 4.3 37.8 1.0
N B:0ZJ299 4.3 41.5 1.0
C1 B:0ZJ299 4.4 45.2 1.0
C B:GLU217 4.5 36.8 1.0
NH2 B:ARG221 4.5 37.1 1.0
OE2 B:GLU217 4.7 48.2 1.0
O D:HOH2216 4.8 47.3 1.0
O B:GLY216 5.0 35.4 1.0
CD B:GLU217 5.0 45.5 1.0

Mercury binding site 2 out of 4 in 1nu7

Go back to Mercury Binding Sites List in 1nu7
Mercury binding site 2 out of 4 in the Staphylocoagulase-Thrombin Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Staphylocoagulase-Thrombin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1004

b:55.0
occ:0.40
S2 B:0ZJ299 2.5 56.1 1.0
OD2 D:ASP106 2.9 49.7 1.0
C2 B:0ZJ299 3.1 46.2 1.0
HG D:HG1003 3.6 82.3 0.4
CG D:ASP106 3.7 50.0 1.0
C1 B:0ZJ299 3.9 45.2 1.0
O2 B:0ZJ299 4.1 43.3 1.0
CB D:ASP106 4.2 44.8 1.0
OD1 D:ASP106 4.5 52.4 1.0
N B:0ZJ299 4.9 41.5 1.0

Mercury binding site 3 out of 4 in 1nu7

Go back to Mercury Binding Sites List in 1nu7
Mercury binding site 3 out of 4 in the Staphylocoagulase-Thrombin Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Staphylocoagulase-Thrombin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Hg1001

b:82.3
occ:0.50
S2 F:0ZJ299 2.4 58.4 1.0
OD1 H:ASP106 3.1 51.1 1.0
HG H:HG1002 3.4 68.4 0.5
C2 F:0ZJ299 3.9 47.7 1.0
C1 F:0ZJ299 4.0 45.8 1.0
CG H:ASP106 4.0 48.3 1.0
CA F:GLU217 4.1 39.0 1.0
N F:0ZJ299 4.1 42.6 1.0
CB F:GLU217 4.1 40.7 1.0
CG F:GLU217 4.2 44.7 1.0
N F:GLY219 4.3 39.5 1.0
O H:HOH2195 4.4 39.7 1.0
OD2 H:ASP106 4.5 47.7 1.0
O2 F:0ZJ299 4.5 44.2 1.0
NH2 F:ARG221 4.5 40.2 1.0
C F:GLU217 4.6 39.5 1.0
CB F:0ZJ299 4.8 41.5 1.0
O F:GLY216 4.9 36.6 1.0
CA F:0ZJ299 4.9 40.5 1.0

Mercury binding site 4 out of 4 in 1nu7

Go back to Mercury Binding Sites List in 1nu7
Mercury binding site 4 out of 4 in the Staphylocoagulase-Thrombin Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Staphylocoagulase-Thrombin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Hg1002

b:68.4
occ:0.50
S2 F:0ZJ299 2.7 58.4 1.0
C2 F:0ZJ299 3.3 47.7 1.0
OD2 H:ASP106 3.4 47.7 1.0
HG H:HG1001 3.4 82.3 0.5
CG H:ASP106 3.4 48.3 1.0
OD1 H:ASP106 3.5 51.1 1.0
O2 F:0ZJ299 3.9 44.2 1.0
C1 F:0ZJ299 3.9 45.8 1.0
CB H:ASP106 4.1 45.8 1.0
N F:0ZJ299 5.0 42.6 1.0

Reference:

R.Friedrich, P.Panizzi, P.Fuentes-Prior, K.Richter, I.Verhamme, P.J.Anderson, S.Kawabata, R.Huber, W.Bode, P.E.Bock. Staphylocoagulase Is A Prototype For the Mechanism of Cofactor-Induced Zymogen Activation Nature V. 425 535 2003.
ISSN: ISSN 0028-0836
PubMed: 14523451
DOI: 10.1038/NATURE01962
Page generated: Sun Dec 13 19:04:21 2020

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