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Zinc in PDB 1kwm: Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi)

Enzymatic activity of Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi)

All present enzymatic activity of Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi):
3.4.17.2;

Protein crystallography data

The structure of Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi), PDB code: 1kwm was solved by P.J.B.Pereira, S.Segura-Martin, C.Ferrer-Orta, J.Vendrell, F.-X.Aviles, M.Coll, F.-X.Gomis-Rueth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.40 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.959, 83.558, 127.447, 90.00, 99.12, 90.00
R / Rfree (%) 13.6 / 18.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) (pdb code 1kwm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi), PDB code: 1kwm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1kwm

Go back to Zinc Binding Sites List in 1kwm
Zinc binding site 1 out of 2 in the Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:45.3
occ:1.00
ND1 A:HIS69 2.0 16.3 0.5
ND1 A:HIS196 2.3 16.2 1.0
OE1 A:GLU72 2.3 14.1 1.0
O A:HOH1352 2.4 45.6 1.0
OE2 A:GLU72 2.5 14.8 1.0
CD A:GLU72 2.8 12.6 1.0
CE1 A:HIS69 2.9 17.2 0.5
CG A:HIS69 3.1 15.5 0.5
CG A:HIS196 3.2 13.9 1.0
CE1 A:HIS196 3.3 17.1 1.0
CB A:HIS196 3.4 12.0 1.0
CB A:HIS69 3.5 15.0 0.5
OD1 A:ASN144 3.5 17.5 0.4
CB A:HIS69 3.6 14.9 0.5
ND1 A:HIS69 3.6 17.2 0.5
CG A:HIS69 3.6 16.0 0.5
O A:HOH953 3.6 20.8 1.0
O A:HOH1286 3.6 48.3 1.0
NE2 A:HIS69 4.1 17.0 0.5
O A:HOH1211 4.1 34.4 1.0
CD2 A:HIS69 4.2 15.8 0.5
CG A:GLU72 4.2 12.1 1.0
CA A:HIS196 4.3 9.3 1.0
CE1 A:HIS69 4.3 17.1 0.5
CD2 A:HIS69 4.3 16.1 0.5
O A:SER197 4.3 11.3 1.0
CD2 A:HIS196 4.4 14.7 1.0
NE2 A:HIS196 4.4 16.3 1.0
OE2 A:GLU270 4.4 45.3 1.0
CG A:ASN144 4.5 17.0 0.4
N A:SER197 4.6 10.6 1.0
N A:HIS69 4.6 15.0 1.0
ND2 A:ASN144 4.7 17.3 0.4
CA A:HIS69 4.7 13.7 1.0
NE2 A:HIS69 4.7 16.9 0.5
O A:HOH914 4.8 15.6 1.0
CB A:GLU72 5.0 12.4 1.0

Zinc binding site 2 out of 2 in 1kwm

Go back to Zinc Binding Sites List in 1kwm
Zinc binding site 2 out of 2 in the Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:53.5
occ:1.00
ND1 B:HIS69 2.1 18.4 0.3
OE1 B:GLU72 2.3 14.2 1.0
ND1 B:HIS196 2.3 17.8 1.0
OE2 B:GLU72 2.5 17.1 1.0
O B:HOH761 2.6 42.0 1.0
CD B:GLU72 2.7 14.2 1.0
CE1 B:HIS69 3.0 19.7 0.3
CG B:HIS69 3.1 17.4 0.3
CG B:HIS196 3.1 15.8 1.0
CB B:HIS196 3.2 14.9 1.0
OD1 B:ASN144 3.4 19.8 0.6
CE1 B:HIS196 3.4 19.4 1.0
O B:HOH762 3.5 39.3 1.0
CB B:HIS69 3.5 16.1 0.3
CB B:HIS69 3.6 15.8 0.7
CG B:HIS69 3.6 18.0 0.7
ND1 B:HIS69 3.6 19.2 0.7
O B:HOH460 3.7 27.2 1.0
NE2 B:HIS69 4.1 19.1 0.3
O B:HOH616 4.2 37.5 1.0
O B:HOH681 4.2 33.1 1.0
CD2 B:HIS69 4.2 18.3 0.3
CA B:HIS196 4.2 13.1 1.0
CG B:GLU72 4.2 15.3 1.0
O B:SER197 4.3 14.3 1.0
CG B:ASN144 4.3 18.5 0.6
CE1 B:HIS69 4.3 18.1 0.7
CD2 B:HIS69 4.3 18.4 0.7
CD2 B:HIS196 4.3 18.4 1.0
ND2 B:ASN144 4.4 20.0 0.6
N B:SER197 4.4 12.6 1.0
NE2 B:HIS196 4.4 19.4 1.0
N B:HIS69 4.5 15.4 1.0
OE1 B:GLU270 4.6 36.0 1.0
CA B:HIS69 4.7 14.4 1.0
NE2 B:HIS69 4.7 18.1 0.7
O B:HOH428 4.8 20.5 1.0
C B:HIS196 4.9 13.5 1.0
CB B:GLU72 5.0 15.5 1.0

Reference:

P.J.Barbosa Pereira, S.Segura-Martin, B.Oliva, C.Ferrer-Orta, F.X.Aviles, M.Coll, F.X.Gomis-Ruth, J.Vendrell. Human Procarboxypeptidase B: Three-Dimensional Structure and Implications For Thrombin-Activatable Fibrinolysis Inhibitor (Tafi). J.Mol.Biol. V. 321 537 2002.
ISSN: ISSN 0022-2836
PubMed: 12162965
DOI: 10.1016/S0022-2836(02)00648-4
Page generated: Wed Dec 16 02:55:40 2020

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