Zinc in PDB 1kwm: 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;

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

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 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 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

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