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Zinc in PDB 5lrj: Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin C Complex

Enzymatic activity of Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin C Complex

All present enzymatic activity of Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin C Complex:
3.4.17.2;

Protein crystallography data

The structure of Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin C Complex, PDB code: 5lrj was solved by H.Schreuder, A.Liesum, P.Loenze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.12 / 2.20
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 124.960, 124.960, 48.120, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin C Complex (pdb code 5lrj). 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 the Porcine Carboxypeptidase B - Anabaenopeptin C Complex, PDB code: 5lrj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5lrj

Go back to Zinc Binding Sites List in 5lrj
Zinc binding site 1 out of 3 in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin C Complex


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 the Porcine Carboxypeptidase B - Anabaenopeptin C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:20.8
occ:1.00
ND1 A:HIS69 2.2 12.4 1.0
O F:HOH103 2.2 33.5 1.0
ND1 A:HIS196 2.3 13.1 1.0
OE1 A:GLU72 2.3 14.1 1.0
OE2 A:GLU72 2.3 14.4 1.0
CD A:GLU72 2.6 14.2 1.0
O26 F:73P1 2.9 39.9 1.0
CE1 A:HIS69 3.0 12.1 1.0
CG A:HIS196 3.2 14.2 1.0
CG A:HIS69 3.2 11.6 1.0
CE1 A:HIS196 3.3 13.6 1.0
CB A:HIS196 3.3 14.2 1.0
C25 F:73P1 3.6 39.8 1.0
CB A:HIS69 3.6 11.2 1.0
O A:HOH651 3.9 17.2 1.0
O A:SER197 3.9 18.9 1.0
CG A:GLU72 4.2 13.7 1.0
NE2 A:HIS69 4.2 12.9 1.0
N23 F:73P1 4.2 38.9 1.0
CA A:HIS196 4.3 15.7 1.0
OE2 A:GLU270 4.3 21.9 1.0
CD2 A:HIS69 4.3 12.7 1.0
C12 F:73P1 4.3 37.1 1.0
N F:DLY2 4.3 40.5 1.0
CD2 A:HIS196 4.4 13.9 1.0
O22 F:73P1 4.4 36.5 1.0
NE2 A:HIS196 4.4 13.5 1.0
O F:HOH104 4.4 21.6 1.0
N A:SER197 4.5 16.8 1.0
CA F:DLY2 4.5 41.5 1.0
NH1 A:ARG127 4.5 12.7 1.0
C20 F:73P1 4.7 37.0 1.0
OE1 A:GLU270 4.8 21.7 1.0
N A:HIS69 4.9 12.3 1.0
CA A:HIS69 4.9 11.9 1.0
C A:HIS196 4.9 16.4 1.0
C A:SER197 4.9 18.2 1.0
CD A:GLU270 4.9 21.3 1.0
CB A:GLU72 5.0 13.4 1.0

Zinc binding site 2 out of 3 in 5lrj

Go back to Zinc Binding Sites List in 5lrj
Zinc binding site 2 out of 3 in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin C Complex


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 the Porcine Carboxypeptidase B - Anabaenopeptin C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:16.8
occ:1.00
O G:HOH102 2.1 29.4 1.0
ND1 B:HIS69 2.2 9.8 1.0
OE2 B:GLU72 2.2 11.0 1.0
ND1 B:HIS196 2.2 9.2 1.0
OE1 B:GLU72 2.4 10.3 1.0
CD B:GLU72 2.6 10.3 1.0
CE1 B:HIS69 3.1 8.5 1.0
CG B:HIS196 3.2 10.8 1.0
CG B:HIS69 3.2 9.3 1.0
CE1 B:HIS196 3.2 7.9 1.0
O26 G:73P1 3.2 36.6 1.0
CB B:HIS196 3.4 9.9 1.0
CB B:HIS69 3.6 9.9 1.0
C25 G:73P1 3.8 36.3 1.0
O B:SER197 3.9 17.2 1.0
O B:HOH642 4.0 10.8 1.0
CG B:GLU72 4.1 9.7 1.0
NE2 B:HIS69 4.2 9.9 1.0
OE2 B:GLU270 4.3 14.2 1.0
CD2 B:HIS69 4.3 9.6 1.0
CA B:HIS196 4.3 11.7 1.0
CD2 B:HIS196 4.3 9.6 1.0
NE2 B:HIS196 4.3 9.2 1.0
N B:SER197 4.5 13.6 1.0
C12 G:73P1 4.5 34.5 1.0
N23 G:73P1 4.5 35.5 1.0
N G:DLY2 4.5 36.3 1.0
NH1 B:ARG127 4.6 8.8 1.0
CA G:DLY2 4.6 36.0 1.0
O B:HOH587 4.6 20.2 1.0
OE1 B:GLU270 4.9 14.8 1.0
CA B:HIS69 4.9 9.8 1.0
O21 G:73P1 4.9 31.7 1.0
C20 G:73P1 4.9 33.7 1.0
C B:SER197 4.9 16.2 1.0
C B:HIS196 5.0 13.2 1.0
N B:HIS69 5.0 9.7 1.0
CB B:GLU72 5.0 11.1 1.0

Zinc binding site 3 out of 3 in 5lrj

Go back to Zinc Binding Sites List in 5lrj
Zinc binding site 3 out of 3 in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin C Complex


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 the Porcine Carboxypeptidase B - Anabaenopeptin C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:24.7
occ:1.00
O H:HOH102 2.2 40.5 1.0
ND1 C:HIS196 2.2 21.3 1.0
ND1 C:HIS69 2.3 22.7 1.0
OE2 C:GLU72 2.3 20.0 1.0
OE1 C:GLU72 2.4 19.8 1.0
CD C:GLU72 2.7 19.6 1.0
CG C:HIS196 3.1 22.2 1.0
CE1 C:HIS69 3.2 21.6 1.0
CE1 C:HIS196 3.2 21.5 1.0
CG C:HIS69 3.3 21.2 1.0
CB C:HIS196 3.3 22.1 1.0
O26 H:73P1 3.4 53.8 1.0
CB C:HIS69 3.6 20.8 1.0
C25 H:73P1 3.8 54.1 1.0
O C:SER197 3.8 25.0 1.0
O C:HOH584 4.0 29.5 1.0
CG C:GLU72 4.2 18.6 1.0
O C:HOH548 4.2 26.8 1.0
CA C:HIS196 4.2 22.4 1.0
CD2 C:HIS196 4.3 22.2 1.0
NE2 C:HIS196 4.3 22.0 1.0
NE2 C:HIS69 4.3 20.7 1.0
N23 H:73P1 4.3 53.0 1.0
N C:SER197 4.4 24.0 1.0
CD2 C:HIS69 4.4 21.3 1.0
N H:DLY2 4.4 55.5 1.0
C12 H:73P1 4.5 52.0 1.0
OE2 C:GLU270 4.5 28.4 1.0
NH1 C:ARG127 4.6 22.4 1.0
CA H:DLY2 4.6 57.0 1.0
OE1 C:GLU270 4.7 29.5 1.0
C C:HIS196 4.9 23.8 1.0
C C:SER197 4.9 26.1 1.0
CA C:HIS69 4.9 20.0 1.0
CB C:GLU72 5.0 18.4 1.0
N C:HIS69 5.0 20.1 1.0
C20 H:73P1 5.0 51.5 1.0

Reference:

H.Schreuder, A.Liesum, P.Lonze, H.Stump, H.Hoffmann, M.Schiell, M.Kurz, L.Toti, A.Bauer, C.Kallus, C.Klemke-Jahn, J.Czech, D.Kramer, H.Enke, T.H.Niedermeyer, V.Morrison, V.Kumar, M.Bronstrup. Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins As Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (Tafia). Sci Rep V. 6 32958 2016.
ISSN: ESSN 2045-2322
PubMed: 27604544
DOI: 10.1038/SREP32958
Page generated: Wed Dec 16 06:30:30 2020

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