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Zinc in PDB 3mn8: Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short

Protein crystallography data

The structure of Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short, PDB code: 3mn8 was solved by S.Tanco, J.L.Arolas, T.Guevara, J.Lorenzo, F.X.Aviles, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.020, 135.700, 141.710, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 28.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short (pdb code 3mn8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short, PDB code: 3mn8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3mn8

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Zinc binding site 1 out of 4 in the Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn999

b:42.6
occ:1.00
OE1 A:GLU104 2.0 61.5 1.0
OE2 A:GLU104 2.0 66.2 1.0
O13 A:GEM601 2.1 33.3 1.0
ND1 A:HIS217 2.1 29.2 1.0
ND1 A:HIS101 2.1 49.9 1.0
CD A:GLU104 2.3 53.7 1.0
O12 A:GEM601 2.6 39.2 1.0
C11 A:GEM601 2.6 54.2 1.0
CE1 A:HIS101 2.9 53.9 1.0
CG A:HIS217 3.0 35.8 1.0
CG A:HIS101 3.1 39.5 1.0
CE1 A:HIS217 3.2 33.3 1.0
CB A:HIS217 3.2 32.3 1.0
CB A:HIS101 3.6 19.9 1.0
CG A:GLU104 3.8 44.7 1.0
NE2 A:HIS101 3.9 52.2 1.0
NH1 A:ARG165 4.0 34.3 1.0
CD2 A:HIS101 4.0 52.5 1.0
CA A:HIS217 4.1 29.1 1.0
C10 A:GEM601 4.1 45.9 1.0
CD2 A:HIS217 4.2 31.4 1.0
NE2 A:HIS217 4.3 27.2 1.0
N A:GLY218 4.4 33.2 1.0
O A:GLY218 4.4 51.1 1.0
CB A:GLU104 4.5 26.4 1.0
O14 A:GEM601 4.7 32.9 1.0
C9 A:GEM601 4.7 64.4 1.0
OE1 A:GLU305 4.8 38.2 1.0
C A:HIS217 4.8 33.0 1.0
CZ A:ARG165 4.8 33.9 1.0
C8 A:GEM601 4.9 57.0 1.0
CA A:HIS101 4.9 29.6 1.0
N A:HIS101 4.9 37.7 1.0
OE2 A:GLU305 5.0 46.8 1.0

Zinc binding site 2 out of 4 in 3mn8

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Zinc binding site 2 out of 4 in the Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn999

b:38.8
occ:1.00
OE1 B:GLU104 2.0 64.9 1.0
OE2 B:GLU104 2.0 59.5 1.0
O13 B:GEM601 2.1 24.9 1.0
ND1 B:HIS101 2.1 46.7 1.0
ND1 B:HIS217 2.2 28.0 1.0
CD B:GLU104 2.3 55.1 1.0
O12 B:GEM601 2.6 32.9 1.0
C11 B:GEM601 2.6 34.9 1.0
CE1 B:HIS101 2.9 47.4 1.0
CG B:HIS101 3.0 37.2 1.0
CG B:HIS217 3.1 28.5 1.0
CE1 B:HIS217 3.2 29.9 1.0
CB B:HIS217 3.4 20.9 1.0
CB B:HIS101 3.5 19.1 1.0
NH1 B:ARG165 3.7 35.7 1.0
CG B:GLU104 3.8 52.7 1.0
NE2 B:HIS101 3.9 51.6 1.0
CD2 B:HIS101 3.9 52.1 1.0
C10 B:GEM601 4.1 23.5 1.0
CA B:HIS217 4.2 30.8 1.0
CD2 B:HIS217 4.3 30.1 1.0
NE2 B:HIS217 4.3 31.9 1.0
O14 B:GEM601 4.3 31.9 1.0
O B:GLY218 4.4 34.1 1.0
N B:GLY218 4.4 30.9 1.0
C9 B:GEM601 4.5 40.9 1.0
CB B:GLU104 4.6 25.1 1.0
CZ B:ARG165 4.7 36.9 1.0
C8 B:GEM601 4.8 23.3 1.0
OE1 B:GLU305 4.8 40.1 1.0
S7 B:GEM601 4.8 36.4 1.0
O15 B:GEM601 4.9 47.5 1.0
CA B:HIS101 4.9 30.9 1.0
C B:HIS217 4.9 35.6 1.0

Zinc binding site 3 out of 4 in 3mn8

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Zinc binding site 3 out of 4 in the Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn999

b:42.4
occ:1.00
OE1 C:GLU104 2.0 69.1 1.0
OE2 C:GLU104 2.1 69.0 1.0
O13 C:GEM601 2.1 38.1 1.0
ND1 C:HIS101 2.1 47.9 1.0
ND1 C:HIS217 2.2 34.4 1.0
CD C:GLU104 2.3 62.3 1.0
O12 C:GEM601 2.6 59.0 1.0
C11 C:GEM601 2.7 46.6 1.0
CE1 C:HIS101 2.9 54.1 1.0
CG C:HIS101 3.0 42.3 1.0
CE1 C:HIS217 3.1 42.2 1.0
CG C:HIS217 3.1 28.2 1.0
CB C:HIS217 3.4 35.6 1.0
CB C:HIS101 3.5 25.6 1.0
CG C:GLU104 3.8 47.4 1.0
NE2 C:HIS101 3.9 56.8 1.0
NH1 C:ARG165 3.9 38.0 1.0
CD2 C:HIS101 4.0 56.6 1.0
O14 C:GEM601 4.1 41.8 1.0
C10 C:GEM601 4.2 36.2 1.0
CA C:HIS217 4.2 27.9 1.0
NE2 C:HIS217 4.2 34.5 1.0
CD2 C:HIS217 4.3 36.2 1.0
O C:HOH1003 4.3 44.7 1.0
N C:GLY218 4.4 39.3 1.0
O C:GLY218 4.5 38.6 1.0
CB C:GLU104 4.6 20.1 1.0
C9 C:GEM601 4.6 36.0 1.0
O1 C:GOL804 4.6 52.2 1.0
CZ C:ARG165 4.7 37.6 1.0
C8 C:GEM601 4.8 38.1 1.0
CA C:HIS101 4.8 28.1 1.0
N C:HIS101 4.9 40.6 1.0
C C:HIS217 4.9 27.9 1.0
OE1 C:GLU305 4.9 50.2 1.0
S7 C:GEM601 5.0 44.1 1.0
NH2 C:ARG165 5.0 29.6 1.0

Zinc binding site 4 out of 4 in 3mn8

Go back to Zinc Binding Sites List in 3mn8
Zinc binding site 4 out of 4 in the Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Drosophila Melanogaster Carboxypeptidase D Isoform 1B Short within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn999

b:33.8
occ:1.00
OE1 D:GLU104 2.0 54.7 1.0
OE2 D:GLU104 2.0 69.6 1.0
O13 D:GEM601 2.1 27.8 1.0
ND1 D:HIS217 2.1 33.4 1.0
ND1 D:HIS101 2.2 40.5 1.0
CD D:GLU104 2.3 53.8 1.0
O12 D:GEM601 2.6 41.0 1.0
C11 D:GEM601 2.6 38.3 1.0
CE1 D:HIS101 2.9 45.2 1.0
CG D:HIS217 3.0 30.8 1.0
CG D:HIS101 3.1 39.4 1.0
CB D:HIS217 3.2 30.7 1.0
CE1 D:HIS217 3.2 34.5 1.0
CB D:HIS101 3.6 20.7 1.0
O D:HOH1034 3.7 15.2 1.0
CG D:GLU104 3.8 41.6 1.0
NE2 D:HIS101 4.0 52.6 1.0
CA D:HIS217 4.0 36.0 1.0
NH1 D:ARG165 4.1 24.0 1.0
CD2 D:HIS101 4.1 51.5 1.0
C10 D:GEM601 4.1 28.1 1.0
CD2 D:HIS217 4.2 35.2 1.0
NE2 D:HIS217 4.3 32.6 1.0
N D:GLY218 4.3 39.7 1.0
O D:GLY218 4.4 32.0 1.0
CB D:GLU104 4.5 31.3 1.0
C D:HIS217 4.7 37.1 1.0
OE1 D:GLU305 4.7 39.0 1.0
C9 D:GEM601 4.8 27.8 1.0
C8 D:GEM601 4.8 42.0 1.0
O14 D:GEM601 4.9 41.9 1.0
CA D:HIS101 4.9 31.0 1.0
N D:HIS101 4.9 39.5 1.0
CZ D:ARG165 4.9 36.4 1.0
OE2 D:GLU305 5.0 36.3 1.0

Reference:

S.Tanco, J.L.Arolas, T.Guevara, J.Lorenzo, F.X.Aviles, F.X.Gomis-Ruth. Structure-Function Analysis of the Short Splicing Variant Carboxypeptidase Encoded By Drosophila Melanogaster Silver. J.Mol.Biol. V. 401 465 2010.
ISSN: ISSN 0022-2836
PubMed: 20600119
DOI: 10.1016/J.JMB.2010.06.035
Page generated: Wed Dec 16 04:35:42 2020

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