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Mercury in PDB 3ldi: Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding

Protein crystallography data

The structure of Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding, PDB code: 3ldi was solved by I.S.Yang, T.G.Kim, B.S.Park, K.H.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.77 / 2.20
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 119.080, 119.080, 110.794, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 23.4

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding (pdb code 3ldi). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 5 binding sites of Mercury where determined in the Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding, PDB code: 3ldi:
Jump to Mercury binding site number: 1; 2; 3; 4; 5;

Mercury binding site 1 out of 5 in 3ldi

Go back to Mercury Binding Sites List in 3ldi
Mercury binding site 1 out of 5 in the Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding


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 Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg63

b:29.3
occ:0.50
O A:CYS30 2.8 17.4 1.0
C A:CYS30 4.0 17.6 1.0
CD1 A:LEU29 4.1 27.7 1.0
CA A:GLN31 4.3 16.4 1.0
CG A:LEU29 4.4 26.0 1.0
CG A:GLN31 4.5 16.7 1.0
N A:GLN31 4.6 16.8 1.0
O E:HOH71 4.7 31.6 1.0
O E:HOH102 4.8 22.5 1.0
CB A:GLN31 4.9 16.4 1.0

Mercury binding site 2 out of 5 in 3ldi

Go back to Mercury Binding Sites List in 3ldi
Mercury binding site 2 out of 5 in the Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding


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 Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg64

b:38.7
occ:0.50
O B:CYS30 2.8 14.5 1.0
O B:HOH92 3.9 21.1 1.0
C B:CYS30 4.0 14.6 1.0
CD1 B:LEU29 4.0 18.6 1.0
CA B:GLN31 4.2 14.3 1.0
CG B:GLN31 4.3 13.8 1.0
N B:GLN31 4.5 14.2 1.0
CD2 B:LEU29 4.5 17.7 1.0
CB B:GLN31 4.7 14.1 1.0
CG B:LEU29 4.8 18.1 1.0

Mercury binding site 3 out of 5 in 3ldi

Go back to Mercury Binding Sites List in 3ldi
Mercury binding site 3 out of 5 in the Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding


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 Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg62

b:31.8
occ:0.50
O B:HOH84 2.8 21.8 1.0
O C:CYS30 2.9 22.5 1.0
C C:CYS30 4.1 22.6 1.0
CA C:GLN31 4.3 21.1 1.0
CG C:GLN31 4.4 21.2 1.0
CD1 C:LEU29 4.5 30.5 1.0
O C:HOH90 4.6 26.3 1.0
N C:GLN31 4.7 21.8 1.0
CD2 C:LEU29 4.8 29.6 1.0
CB C:GLN31 4.9 21.2 1.0

Mercury binding site 4 out of 5 in 3ldi

Go back to Mercury Binding Sites List in 3ldi
Mercury binding site 4 out of 5 in the Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding


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 Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg63

b:31.4
occ:0.50
O D:CYS30 2.9 17.7 1.0
CD1 D:LEU29 3.6 25.5 1.0
C D:CYS30 4.0 17.6 1.0
CA D:GLN31 4.2 17.1 1.0
CG D:GLN31 4.2 17.9 1.0
O C:HOH76 4.4 27.5 1.0
N D:GLN31 4.6 17.1 1.0
CB D:GLN31 4.7 17.1 1.0
O C:HOH65 4.8 25.9 1.0
CG D:LEU29 5.0 23.4 1.0

Mercury binding site 5 out of 5 in 3ldi

Go back to Mercury Binding Sites List in 3ldi
Mercury binding site 5 out of 5 in the Crystal Structure of Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding


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 Aprotinin in Complex with Sucrose Octasulfate: Unusual Interactions and Implication For Heparin Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg63

b:12.7
occ:0.50
O E:CYS30 2.8 15.9 1.0
O E:HOH100 3.0 27.3 1.0
C E:CYS30 4.0 16.1 1.0
CA E:GLN31 4.1 15.2 1.0
CG E:GLN31 4.3 15.8 1.0
N E:GLN31 4.5 15.6 1.0
CB E:GLN31 4.7 15.0 1.0

Reference:

I.S.Yang, T.G.Kim, B.S.Park, K.J.Cho, J.-H.Lee, Y.Park, K.H.Kim. Crystal Structures of Aprotinin and Its Complex with Sucrose Octasulfate Reveal Multiple Modes of Interactions with Implications For Heparin Binding Biochem.Biophys.Res.Commun. V. 397 429 2010.
ISSN: ISSN 0006-291X
PubMed: 20529698
DOI: 10.1016/J.BBRC.2010.05.113
Page generated: Sun Dec 13 19:09:58 2020

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