Zinc in PDB 5zeq: Carboxypeptidase B in Complex with DD28

Enzymatic activity of Carboxypeptidase B in Complex with DD28

All present enzymatic activity of Carboxypeptidase B in Complex with DD28:
3.4.17.2;

Protein crystallography data

The structure of Carboxypeptidase B in Complex with DD28, PDB code: 5zeq was solved by T.Itoh, N.Yoshimoto, K.Yamamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.71 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.860, 78.860, 100.040, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 20.4

Other elements in 5zeq:

The structure of Carboxypeptidase B in Complex with DD28 also contains other interesting chemical elements:

Arsenic (As) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Carboxypeptidase B in Complex with DD28 (pdb code 5zeq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Carboxypeptidase B in Complex with DD28, PDB code: 5zeq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5zeq

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Zinc binding site 1 out of 7 in the Carboxypeptidase B in Complex with DD28


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Carboxypeptidase B in Complex with DD28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:14.3
occ:1.00
 OE1 A:GLU291 2.0 12.2 1.0
OE2 A:GLU85 2.1 16.2 1.0
OE2 A:GLU291 2.3 13.2 1.0
CD A:GLU291 2.5 13.0 1.0
CD A:GLU85 3.0 15.5 1.0
OE1 A:GLU85 3.3 18.1 1.0
NH2 A:ARG84 3.9 17.6 1.0
CG A:GLU291 4.0 13.1 1.0
NE1 A:TRP81 4.3 12.1 1.0
CG A:GLU85 4.4 14.2 1.0
O A:HOH531 4.4 11.9 1.0
O A:HOH774 4.5 26.1 1.0
CB A:GLU291 5.0 12.8 1.0
CZ2 A:TRP81 5.0 12.3 1.0

Zinc binding site 2 out of 7 in 5zeq

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Zinc binding site 2 out of 7 in the Carboxypeptidase B in Complex with DD28


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Carboxypeptidase B in Complex with DD28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:23.6
occ:1.00
 NE2 A:HIS307 2.2 19.2 1.0
CE1 A:HIS307 3.0 19.2 1.0
CD2 A:HIS307 3.3 19.6 1.0
O A:HOH538 3.8 22.0 1.0
ND1 A:HIS307 4.2 19.6 1.0
CG A:HIS307 4.3 18.4 1.0
CE2 A:TYR303 4.5 13.5 1.0
O A:HOH541 4.8 33.3 1.0

Zinc binding site 3 out of 7 in 5zeq

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Zinc binding site 3 out of 7 in the Carboxypeptidase B in Complex with DD28


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Carboxypeptidase B in Complex with DD28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:82.7
occ:1.00
 NE2 A:HIS95 2.5 35.0 1.0
CD2 A:HIS95 3.3 31.8 1.0
CE1 A:HIS95 3.5 38.0 1.0
O A:HOH639 4.2 36.0 1.0
CG A:HIS95 4.5 28.8 1.0
ND1 A:HIS95 4.6 36.6 1.0
OG A:SER94 4.6 22.7 1.0

Zinc binding site 4 out of 7 in 5zeq

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Zinc binding site 4 out of 7 in the Carboxypeptidase B in Complex with DD28


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Carboxypeptidase B in Complex with DD28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:13.4
occ:1.00
 ND1 A:HIS196 2.0 11.7 1.0
OE1 A:GLU72 2.1 10.8 1.0
ND1 A:HIS69 2.1 13.3 1.0
OE2 A:GLU72 2.2 11.5 1.0
SE1 A:9B3406 2.4 28.5 1.0
CD A:GLU72 2.5 11.3 1.0
CE1 A:HIS196 2.9 10.8 1.0
CG A:HIS196 3.0 10.4 1.0
CE1 A:HIS69 3.1 13.0 1.0
CG A:HIS69 3.1 13.2 1.0
CB A:HIS196 3.3 10.0 1.0
CB A:HIS69 3.5 11.7 1.0
C9 A:9B3406 3.7 21.9 1.0
ZN A:ZN405 3.8 32.1 0.7
O A:SER197 3.9 11.5 1.0
O A:HOH727 4.0 11.1 1.0
CG A:GLU72 4.0 10.8 1.0
NE2 A:HIS196 4.0 10.7 1.0
CD2 A:HIS196 4.1 10.3 1.0
NE2 A:HIS69 4.2 12.2 1.0
C7 A:9B3406 4.2 21.2 1.0
CD2 A:HIS69 4.2 12.4 1.0
CA A:HIS196 4.3 9.8 1.0
NH1 A:ARG127 4.3 17.1 1.0
C8 A:9B3406 4.4 21.6 1.0
N A:SER197 4.5 10.3 1.0
O1 A:9B3406 4.5 16.5 1.0
O A:HOH598 4.6 20.4 1.0
CA A:HIS69 4.8 11.9 1.0
OE1 A:GLU270 4.8 16.0 1.0
CB A:GLU72 4.8 10.1 1.0
N A:HIS69 4.9 12.3 1.0
C A:SER197 5.0 11.0 1.0
C A:HIS196 5.0 9.2 1.0

Zinc binding site 5 out of 7 in 5zeq

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Zinc binding site 5 out of 7 in the Carboxypeptidase B in Complex with DD28


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Carboxypeptidase B in Complex with DD28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:32.1
occ:0.70
 O1 A:CAC407 2.2 20.8 0.6
O A:SER197 2.2 11.5 1.0
OE2 A:GLU270 2.3 30.8 1.0
SE1 A:9B3406 2.4 28.5 1.0
OE1 A:GLU270 2.6 16.0 1.0
C A:SER197 2.7 11.0 1.0
CD A:GLU270 2.8 19.1 1.0
C9 A:9B3406 3.0 21.9 1.0
N A:TYR198 3.0 11.1 1.0
O2 A:CAC407 3.2 20.6 0.6
AS A:CAC407 3.2 22.8 0.6
O A:TYR198 3.6 13.4 1.0
OE2 A:GLU72 3.7 11.5 1.0
ZN A:ZN404 3.8 13.4 1.0
CA A:SER197 3.9 10.7 1.0
CD A:GLU72 4.0 11.3 1.0
N A:SER197 4.0 10.3 1.0
OE1 A:GLU72 4.2 10.8 1.0
CG A:GLU270 4.3 17.4 1.0
CA A:TYR198 4.3 11.4 1.0
CB A:HIS196 4.3 10.0 1.0
C A:TYR198 4.4 11.9 1.0
CE1 A:PHE279 4.5 14.4 1.0
C2 A:CAC407 4.5 19.5 0.6
C7 A:9B3406 4.6 21.2 1.0
C1 A:CAC407 4.7 19.9 0.6
CG A:GLU72 4.9 10.8 1.0
C A:HIS196 4.9 9.2 1.0
ND1 A:HIS196 4.9 11.7 1.0
CZ A:PHE279 4.9 15.8 1.0
O A:HOH598 5.0 20.4 1.0

Zinc binding site 6 out of 7 in 5zeq

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Zinc binding site 6 out of 7 in the Carboxypeptidase B in Complex with DD28


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Carboxypeptidase B in Complex with DD28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:63.5
occ:0.50
 ZN A:ZN409 1.3 45.4 0.5
OG A:SER207 2.6 14.4 1.0
OD1 A:ASP256 2.7 13.0 1.0
OD2 A:ASP255 2.8 31.1 1.0
OD1 A:ASP255 2.9 23.1 1.0
N2 A:9B3406 3.0 34.1 1.0
N1 A:9B3406 3.1 27.1 1.0
CG A:ASP255 3.2 19.5 1.0
CB A:SER207 3.3 14.2 1.0
C3 A:9B3406 3.4 28.8 1.0
CG A:ASP256 3.4 13.5 1.0
N A:SER207 3.5 11.9 1.0
OD2 A:ASP256 3.6 16.0 1.0
O A:TYR204 3.8 12.8 1.0
CA A:SER207 4.0 14.2 1.0
CA A:PRO205 4.1 13.6 1.0
C4 A:9B3406 4.1 30.3 1.0
C A:TYR206 4.2 12.9 1.0
C A:TYR204 4.2 13.2 1.0
N A:PRO205 4.3 13.2 1.0
N A:ASP256 4.5 11.9 1.0
CA A:TYR206 4.5 12.8 1.0
CA A:GLY243 4.5 12.9 1.0
CB A:ASP256 4.6 13.1 1.0
CB A:ASP255 4.6 17.0 1.0
C2 A:9B3406 4.6 27.0 1.0
N A:GLY243 4.7 13.2 1.0
CA A:ASP256 4.9 12.2 1.0
O A:HOH644 4.9 13.1 1.0
O A:HOH623 4.9 22.7 1.0
O A:TYR206 4.9 12.9 1.0
CG A:PRO205 4.9 13.2 1.0
CB A:PRO205 5.0 12.5 1.0
OG1 A:THR268 5.0 12.7 1.0

Zinc binding site 7 out of 7 in 5zeq

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Zinc binding site 7 out of 7 in the Carboxypeptidase B in Complex with DD28


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Carboxypeptidase B in Complex with DD28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:45.4
occ:0.50
 ZN A:ZN408 1.3 63.5 0.5
OD2 A:ASP255 1.9 31.1 1.0
N2 A:9B3406 2.0 34.1 1.0
OD1 A:ASP255 2.3 23.1 1.0
CG A:ASP255 2.4 19.5 1.0
C3 A:9B3406 2.8 28.8 1.0
N1 A:9B3406 3.0 27.1 1.0
C4 A:9B3406 3.2 30.3 1.0
OG A:SER207 3.2 14.4 1.0
OD1 A:ASP256 3.7 13.0 1.0
OG1 A:THR268 3.7 12.7 1.0
CB A:ASP255 3.9 17.0 1.0
O A:HOH702 4.0 19.6 1.0
CB A:SER207 4.1 14.2 1.0
C2 A:9B3406 4.2 27.0 1.0
CG A:ASP256 4.3 13.5 1.0
O A:TYR204 4.5 12.8 1.0
C5 A:9B3406 4.5 29.1 1.0
N A:ASP256 4.5 11.9 1.0
OD2 A:ASP256 4.6 16.0 1.0
CB A:THR268 4.6 12.9 1.0
C A:TYR204 4.7 13.2 1.0
N A:SER207 4.7 11.9 1.0
CA A:ASP255 4.8 14.1 1.0
C1 A:9B3406 4.8 28.7 1.0
O A:HOH623 4.9 22.7 1.0
N A:PRO205 4.9 13.2 1.0
C A:ASP255 4.9 13.2 1.0
CB A:LEU203 5.0 14.8 1.0

Reference:

T.Itoh, N.Yoshimoto, Y.Hirano, K.Yamamoto. Structural Basis For the Selective Inhibition of Activated Thrombin-Activatable Fibrinolysis Inhibitor (Tafia) By A Selenium-Containing Inhibitor with Chloro-Aminopyridine As A Basic Group Bioorg. Med. Chem. Lett. V. 28 2256 2018.
ISSN: ESSN 1464-3405
PubMed: 29859906
DOI: 10.1016/J.BMCL.2018.05.042
Page generated: Wed Dec 16 11:26:17 2020

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