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Mercury in PDB 1nu9: Staphylocoagulase-Prethrombin-2 Complex

Enzymatic activity of Staphylocoagulase-Prethrombin-2 Complex

All present enzymatic activity of Staphylocoagulase-Prethrombin-2 Complex:
3.4.21.5;

Protein crystallography data

The structure of Staphylocoagulase-Prethrombin-2 Complex, PDB code: 1nu9 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) 19.98 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.160, 102.340, 135.540, 90.00, 129.91, 90.00
R / Rfree (%) 21 / 25.3

Mercury Binding Sites:

The binding sites of Mercury atom in the Staphylocoagulase-Prethrombin-2 Complex (pdb code 1nu9). 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-Prethrombin-2 Complex, PDB code: 1nu9:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 1nu9

Go back to Mercury Binding Sites List in 1nu9
Mercury binding site 1 out of 4 in the Staphylocoagulase-Prethrombin-2 Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Staphylocoagulase-Prethrombin-2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg999

b:53.2
occ:0.60
S2 A:0ZJ299 2.6 52.8 1.0
OD2 C:ASP106 2.9 48.3 1.0
C2 A:0ZJ299 3.2 42.1 1.0
HG C:HG996 3.4 53.8 0.4
CG C:ASP106 3.4 48.0 1.0
C1 A:0ZJ299 4.0 42.8 1.0
OD1 C:ASP106 4.0 51.8 1.0
O2 A:0ZJ299 4.1 40.1 1.0
CB C:ASP106 4.2 44.6 1.0
O A:HOH391 4.8 43.5 1.0

Mercury binding site 2 out of 4 in 1nu9

Go back to Mercury Binding Sites List in 1nu9
Mercury binding site 2 out of 4 in the Staphylocoagulase-Prethrombin-2 Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Staphylocoagulase-Prethrombin-2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg996

b:53.8
occ:0.40
S2 A:0ZJ299 2.3 52.8 1.0
O A:HOH391 2.8 43.5 1.0
O A:HOH378 3.0 41.4 1.0
OD1 C:ASP106 3.2 51.8 1.0
HG C:HG999 3.4 53.2 0.6
CG C:ASP106 3.8 48.0 1.0
C2 A:0ZJ299 3.8 42.1 1.0
OD2 C:ASP106 4.0 48.3 1.0
C1 A:0ZJ299 4.0 42.8 1.0
CA A:GLU217 4.1 33.5 1.0
N A:0ZJ299 4.1 39.9 1.0
CB A:GLU217 4.1 35.4 1.0
CG A:GLU217 4.3 37.8 1.0
N A:GLY219 4.3 35.3 1.0
C A:GLU217 4.6 34.3 1.0
O2 A:0ZJ299 4.7 40.1 1.0
O C:HOH2143 4.9 42.4 1.0
O A:HOH384 4.9 55.1 1.0
O A:GLY216 4.9 33.5 1.0
CB A:0ZJ299 4.9 40.3 1.0
CB C:ASP106 4.9 44.6 1.0
NH2 A:ARG221 5.0 42.6 1.0
CA A:0ZJ299 5.0 39.0 1.0

Mercury binding site 3 out of 4 in 1nu9

Go back to Mercury Binding Sites List in 1nu9
Mercury binding site 3 out of 4 in the Staphylocoagulase-Prethrombin-2 Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Staphylocoagulase-Prethrombin-2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Hg998

b:54.5
occ:0.60
S2 D:0ZJ299 2.5 49.4 1.0
C2 D:0ZJ299 3.1 44.5 1.0
HG F:HG997 3.3 55.2 0.4
OD1 F:ASP106 3.5 52.7 1.0
CG F:ASP106 3.5 48.8 1.0
OD2 F:ASP106 3.5 48.4 1.0
C1 D:0ZJ299 3.9 44.5 1.0
O2 D:0ZJ299 3.9 44.6 1.0
CB F:ASP106 4.2 45.6 1.0
N D:0ZJ299 5.0 41.6 1.0

Mercury binding site 4 out of 4 in 1nu9

Go back to Mercury Binding Sites List in 1nu9
Mercury binding site 4 out of 4 in the Staphylocoagulase-Prethrombin-2 Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Staphylocoagulase-Prethrombin-2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Hg997

b:55.2
occ:0.40
S2 D:0ZJ299 2.2 49.4 1.0
O D:HOH389 2.9 46.0 1.0
OD1 F:ASP106 2.9 52.7 1.0
O D:HOH384 3.3 43.8 1.0
HG F:HG998 3.3 54.5 0.6
C2 D:0ZJ299 3.7 44.5 1.0
C1 D:0ZJ299 3.9 44.5 1.0
CG F:ASP106 3.9 48.8 1.0
N D:0ZJ299 4.1 41.6 1.0
CA D:GLU217 4.1 36.8 1.0
OD2 F:ASP106 4.2 48.4 1.0
CG D:GLU217 4.2 40.0 1.0
CB D:GLU217 4.2 37.9 1.0
N D:GLY219 4.3 36.0 1.0
O2 D:0ZJ299 4.4 44.6 1.0
C D:GLU217 4.7 36.9 1.0
NH2 D:ARG221 4.7 39.5 1.0
O F:HOH2225 4.8 52.3 1.0
O D:GLY216 4.8 38.2 1.0
CB D:0ZJ299 4.8 42.0 1.0
CA D:0ZJ299 4.9 40.5 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 19:04:22 2020

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