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Zinc in PDB 5mrv: Crystal Structure of Human Carboxypeptidase O in Complex with Nvci

Protein crystallography data

The structure of Crystal Structure of Human Carboxypeptidase O in Complex with Nvci, PDB code: 5mrv was solved by J.Garcia-Pardo, M.C.Garcia-Guerrero, R.Fernandez-Alvarez, P.Lyons, F.X.Aviles, J.Lorenzo, D.Reverter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.95 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.114, 72.144, 90.187, 90.00, 94.66, 90.00
R / Rfree (%) 18.5 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Carboxypeptidase O in Complex with Nvci (pdb code 5mrv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Carboxypeptidase O in Complex with Nvci, PDB code: 5mrv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5mrv

Go back to Zinc Binding Sites List in 5mrv
Zinc binding site 1 out of 2 in the Crystal Structure of Human Carboxypeptidase O in Complex with Nvci


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 Human Carboxypeptidase O in Complex with Nvci within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:20.7
occ:1.00
ND1 A:HIS216 2.0 18.9 1.0
OE2 A:GLU91 2.1 19.1 1.0
ND1 A:HIS88 2.1 13.5 1.0
O C:ALA53 2.3 22.9 1.0
OE1 A:GLU91 2.4 19.0 1.0
OXT C:ALA53 2.6 23.7 1.0
CD A:GLU91 2.6 16.1 1.0
C C:ALA53 2.7 24.7 1.0
CE1 A:HIS216 2.9 21.8 1.0
CE1 A:HIS88 3.0 17.7 1.0
CG A:HIS88 3.1 20.1 1.0
CG A:HIS216 3.1 18.1 1.0
CB A:HIS88 3.5 17.6 1.0
CB A:HIS216 3.6 17.9 1.0
NE2 A:HIS216 4.1 22.5 1.0
CG A:GLU91 4.1 16.4 1.0
CA C:ALA53 4.1 23.0 1.0
O A:SER217 4.2 19.7 1.0
NE2 A:HIS88 4.2 16.6 1.0
CD2 A:HIS216 4.2 21.2 1.0
O C:HOH110 4.2 22.3 1.0
CD2 A:HIS88 4.2 15.8 1.0
O A:HOH605 4.3 21.5 1.0
NH2 A:ARG146 4.4 21.0 1.0
OE2 A:GLU290 4.4 26.3 1.0
CA A:HIS216 4.5 16.6 1.0
N A:SER217 4.7 17.6 1.0
CA A:HIS88 4.8 17.5 1.0
CG2 A:ILE87 4.9 17.6 1.0
N A:HIS88 5.0 17.8 1.0
CB C:ALA53 5.0 21.3 1.0

Zinc binding site 2 out of 2 in 5mrv

Go back to Zinc Binding Sites List in 5mrv
Zinc binding site 2 out of 2 in the Crystal Structure of Human Carboxypeptidase O in Complex with Nvci


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 Human Carboxypeptidase O in Complex with Nvci within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:28.6
occ:1.00
ND1 B:HIS88 2.1 24.4 1.0
OE1 B:GLU91 2.2 22.1 1.0
ND1 B:HIS216 2.2 22.1 1.0
OE2 B:GLU91 2.4 22.7 1.0
CD B:GLU91 2.6 22.1 1.0
CE1 B:HIS88 3.0 25.6 1.0
CG B:HIS88 3.1 24.4 1.0
CG B:HIS216 3.2 22.0 1.0
CE1 B:HIS216 3.2 24.9 1.0
CB B:HIS216 3.4 20.0 1.0
CB B:HIS88 3.4 20.4 1.0
O B:SER217 4.1 20.4 1.0
CG B:GLU91 4.2 18.0 1.0
O B:HOH663 4.2 26.1 1.0
NE2 B:HIS88 4.2 25.9 1.0
CD2 B:HIS88 4.2 26.7 1.0
CA B:HIS216 4.3 18.4 1.0
NE2 B:HIS216 4.3 25.6 1.0
CD2 B:HIS216 4.3 22.4 1.0
O B:HOH641 4.4 37.8 1.0
O B:HOH566 4.5 33.3 1.0
N B:SER217 4.5 19.7 1.0
OE2 B:GLU290 4.5 32.8 1.0
O B:HOH507 4.7 43.3 1.0
OE1 B:GLU290 4.7 29.1 1.0
CA B:HIS88 4.8 18.6 1.0
NH2 B:ARG146 4.9 48.0 1.0
N B:HIS88 4.9 19.3 1.0
CB B:GLU91 4.9 17.3 1.0
CG2 B:ILE87 4.9 25.4 1.0
C B:HIS216 5.0 16.8 1.0

Reference:

M.C.Garcia-Guerrero, J.Garcia-Pardo, E.Berenguer, R.Fernandez-Alvarez, G.B.Barfi, P.J.Lyons, F.X.Aviles, R.Huber, J.Lorenzo, D.Reverter. Crystal Structure and Mechanism of Human Carboxypeptidase O: Insights Into Its Specific Activity For Acidic Residues. Proc. Natl. Acad. Sci. V. 115 E3932 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29636417
DOI: 10.1073/PNAS.1803685115
Page generated: Wed Dec 16 06:33:36 2020

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