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Zinc in PDB 3d67: Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa)

Enzymatic activity of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa)

All present enzymatic activity of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa):
3.4.17.20;

Protein crystallography data

The structure of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa), PDB code: 3d67 was solved by T.H.C.Brondijk, E.G.Huizinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.09 / 3.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.050, 161.050, 138.990, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa) (pdb code 3d67). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa), PDB code: 3d67:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3d67

Go back to Zinc Binding Sites List in 3d67
Zinc binding site 1 out of 3 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:0.7
occ:1.00
 O13 A:GEM660 1.7 0.9 1.0
OE1 A:GLU162 2.0 0.9 1.0
OE2 A:GLU162 2.0 0.4 1.0
ND1 A:HIS288 2.1 0.7 1.0
ND1 A:HIS159 2.1 0.4 1.0
CD A:GLU162 2.3 0.7 1.0
C11 A:GEM660 2.5 0.6 1.0
O12 A:GEM660 2.8 0.1 1.0
CE1 A:HIS159 2.9 0.0 1.0
CE1 A:HIS288 2.9 0.6 1.0
CG A:HIS288 3.0 0.7 1.0
CG A:HIS159 3.2 0.9 1.0
CB A:HIS288 3.4 0.0 1.0
CB A:HIS159 3.7 0.3 1.0
CG A:GLU162 3.8 1.0 1.0
C10 A:GEM660 3.9 0.2 1.0
NH1 A:ARG217 3.9 0.3 1.0
NE2 A:HIS288 4.0 0.9 1.0
NE2 A:HIS159 4.1 0.3 1.0
CD2 A:HIS288 4.1 0.4 1.0
CD2 A:HIS159 4.2 0.5 1.0
CA A:HIS288 4.3 0.3 1.0
O14 A:GEM660 4.5 0.4 1.0
S7 A:GEM660 4.5 0.9 1.0
N A:SER289 4.5 1.0 1.0
C8 A:GEM660 4.6 0.7 1.0
CB A:GLU162 4.7 0.4 1.0
C9 A:GEM660 4.8 0.9 1.0
CZ A:ARG217 4.9 0.1 1.0
O A:SER289 4.9 0.8 1.0
N A:HIS159 5.0 0.2 1.0
C A:HIS288 5.0 0.6 1.0

Zinc binding site 2 out of 3 in 3d67

Go back to Zinc Binding Sites List in 3d67
Zinc binding site 2 out of 3 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:0.7
occ:1.00
 OE1 B:GLU162 2.0 0.0 1.0
OE2 B:GLU162 2.0 0.7 1.0
O13 B:GEM660 2.1 0.3 1.0
ND1 B:HIS159 2.1 0.1 1.0
ND1 B:HIS288 2.1 0.6 1.0
CD B:GLU162 2.3 0.6 1.0
O12 B:GEM660 2.6 0.8 1.0
C11 B:GEM660 2.6 0.6 1.0
CE1 B:HIS159 2.8 0.4 1.0
CE1 B:HIS288 2.9 0.1 1.0
CG B:HIS288 3.2 0.3 1.0
CG B:HIS159 3.2 0.2 1.0
CB B:HIS288 3.6 0.7 1.0
CB B:HIS159 3.7 0.4 1.0
CG B:GLU162 3.9 0.6 1.0
NE2 B:HIS159 4.0 0.6 1.0
C10 B:GEM660 4.1 0.2 1.0
NE2 B:HIS288 4.1 0.5 1.0
NH1 B:ARG217 4.2 0.9 1.0
CD2 B:HIS159 4.2 0.4 1.0
CD2 B:HIS288 4.3 0.6 1.0
S7 B:GEM660 4.4 0.1 1.0
O14 B:GEM660 4.4 0.4 1.0
CA B:HIS288 4.4 0.5 1.0
N B:SER289 4.4 0.3 1.0
C8 B:GEM660 4.7 0.1 1.0
CB B:GLU162 4.7 0.5 1.0
N B:HIS159 4.8 0.3 1.0
O B:SER289 4.8 0.6 1.0
CA B:HIS159 4.9 0.3 1.0
C9 B:GEM660 4.9 0.7 1.0
C B:HIS288 5.0 0.6 1.0

Zinc binding site 3 out of 3 in 3d67

Go back to Zinc Binding Sites List in 3d67
Zinc binding site 3 out of 3 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) in Complex with 2-Guanidino-Ethyl-Mercaptosuccinic Acid (Gemsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:0.2
occ:1.00
 OE2 C:GLU162 2.0 0.2 1.0
OE1 C:GLU162 2.0 0.6 1.0
ND1 C:HIS159 2.1 0.7 1.0
ND1 C:HIS288 2.1 0.8 1.0
O13 C:GEM660 2.1 0.5 1.0
CD C:GLU162 2.3 0.7 1.0
O12 C:GEM660 2.6 0.3 1.0
C11 C:GEM660 2.7 0.9 1.0
CE1 C:HIS288 2.9 0.4 1.0
CE1 C:HIS159 3.0 0.4 1.0
CG C:HIS159 3.1 0.2 1.0
CG C:HIS288 3.2 0.4 1.0
CB C:HIS159 3.5 0.8 1.0
CB C:HIS288 3.6 0.2 1.0
CG C:GLU162 3.8 0.8 1.0
NH1 C:ARG217 3.9 0.9 1.0
NE2 C:HIS288 4.1 0.6 1.0
NE2 C:HIS159 4.1 0.8 1.0
C10 C:GEM660 4.2 0.1 1.0
CD2 C:HIS288 4.2 0.8 1.0
CD2 C:HIS159 4.2 1.0 1.0
CA C:HIS288 4.4 0.3 1.0
N C:SER289 4.5 0.4 1.0
CB C:GLU162 4.8 0.0 1.0
CA C:HIS159 4.8 0.9 1.0
N C:HIS159 4.8 0.8 1.0
O15 C:GEM660 4.9 0.2 1.0
C8 C:GEM660 4.9 0.8 1.0
S7 C:GEM660 4.9 0.5 1.0
CZ C:ARG217 5.0 0.8 1.0
OE2 C:GLU363 5.0 0.3 1.0
C C:HIS288 5.0 0.3 1.0

Reference:

P.F.Marx, T.H.Brondijk, T.Plug, R.A.Romijn, W.Hemrika, J.C.M.Meijers, E.G.Huizinga. Crystal Structures of Tafi Elucidate the Inactivation Mechanism of Activated Tafi: A Novel Mechanism For Enzyme Autoregulation Blood V. 112 2803 2008.
ISSN: ISSN 0006-4971
PubMed: 18559974
DOI: 10.1182/BLOOD-2008-03-146001
Page generated: Thu Oct 24 12:04:05 2024

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