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Zinc in PDB 5cnx: Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12

Protein crystallography data

The structure of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12, PDB code: 5cnx was solved by A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.202, 224.202, 74.636, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 24

Other elements in 5cnx:

The structure of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 also contains other interesting chemical elements:

Arsenic (As) 3 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 (pdb code 5cnx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12, PDB code: 5cnx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5cnx

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Zinc binding site 1 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


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 Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:44.1
occ:1.00
O1 A:CAC403 2.0 46.9 1.0
OE2 A:GLU335 2.1 40.4 1.0
OE2 A:GLU321 2.1 41.7 1.0
NE2 A:HIS292 2.2 41.5 1.0
OD2 A:ASP223 2.3 41.7 1.0
CD A:GLU321 2.8 42.9 1.0
OE1 A:GLU321 3.0 44.5 1.0
CD2 A:HIS292 3.1 41.7 1.0
CE1 A:HIS292 3.1 41.4 1.0
CD A:GLU335 3.1 41.1 1.0
CG A:ASP223 3.2 42.5 1.0
AS A:CAC403 3.2 55.7 1.0
ZN A:ZN402 3.2 37.6 1.0
OD1 A:ASP223 3.6 43.8 1.0
OE1 A:GLU335 3.6 40.1 1.0
C1 A:CAC403 3.6 49.6 1.0
OG1 A:THR319 3.6 34.2 1.0
O2 A:CAC403 3.9 62.0 1.0
CG2 A:THR319 3.9 33.7 1.0
CB A:THR319 4.1 34.4 1.0
CG A:GLU321 4.2 43.8 1.0
ND1 A:HIS292 4.2 41.8 1.0
CG A:HIS292 4.2 41.7 1.0
CB A:ASP223 4.3 42.5 1.0
CG A:GLU335 4.4 42.3 1.0
NE2 A:HIS299 4.8 50.5 1.0
C2 A:CAC403 4.9 55.3 1.0
CB A:GLU321 5.0 44.2 1.0

Zinc binding site 2 out of 6 in 5cnx

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Zinc binding site 2 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


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 Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:37.6
occ:1.00
OE1 A:GLU335 1.9 40.1 1.0
O1 A:CAC403 1.9 46.9 1.0
OD1 A:ASP212 2.1 38.9 1.0
OD1 A:ASP223 2.1 43.8 1.0
CD A:GLU335 2.7 41.1 1.0
CG A:ASP212 2.8 39.4 1.0
OD2 A:ASP212 2.8 39.1 1.0
OE2 A:GLU335 2.9 40.4 1.0
CG A:ASP223 3.0 42.5 1.0
ZN A:ZN401 3.2 44.1 1.0
OD2 A:ASP223 3.3 41.7 1.0
AS A:CAC403 3.3 55.7 1.0
OG1 A:THR225 3.6 43.1 1.0
OE1 A:GLU321 3.8 44.5 1.0
C2 A:CAC403 3.8 55.3 1.0
CZ A:PHE181 3.9 33.2 1.0
O2 A:CAC403 4.0 62.0 1.0
CG A:GLU335 4.1 42.3 1.0
CB A:ASP212 4.2 40.0 1.0
CB A:ASP223 4.3 42.5 1.0
O A:MET224 4.3 46.3 1.0
N A:MET224 4.4 45.3 1.0
C A:MET224 4.4 46.6 1.0
C A:ASP223 4.5 44.1 1.0
CD A:GLU321 4.5 42.9 1.0
CE1 A:PHE181 4.6 32.9 1.0
CE2 A:PHE181 4.6 32.7 1.0
CB A:GLU335 4.7 43.3 1.0
OE2 A:GLU321 4.7 41.7 1.0
CA A:ASP223 4.7 43.1 1.0
CA A:ASP212 4.7 40.5 1.0
N A:PHE213 4.8 37.3 1.0
N A:THR225 4.8 44.3 1.0
CA A:MET224 4.8 46.5 1.0
C1 A:CAC403 4.9 49.6 1.0
CB A:THR225 4.9 44.3 1.0
O A:ASP223 4.9 44.3 1.0
O A:PHE213 4.9 37.2 1.0
C A:ASP212 5.0 40.1 1.0

Zinc binding site 3 out of 6 in 5cnx

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Zinc binding site 3 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


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 Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:42.6
occ:1.00
OE2 B:GLU321 2.1 41.8 1.0
OE2 B:GLU335 2.1 41.4 1.0
O1 B:CAC403 2.1 59.6 1.0
NE2 B:HIS292 2.2 34.2 1.0
OD2 B:ASP223 2.2 38.3 1.0
CD B:GLU321 2.8 41.6 1.0
OE1 B:GLU321 3.0 42.0 1.0
CE1 B:HIS292 3.1 34.8 1.0
CG B:ASP223 3.1 38.4 1.0
CD2 B:HIS292 3.1 34.6 1.0
ZN B:ZN402 3.2 36.7 1.0
CD B:GLU335 3.2 40.8 1.0
AS B:CAC403 3.2 62.6 1.0
OD1 B:ASP223 3.6 37.9 1.0
OE1 B:GLU335 3.6 40.0 1.0
C1 B:CAC403 3.6 65.4 1.0
OG1 B:THR319 3.7 28.9 1.0
CG2 B:THR319 3.7 28.6 1.0
O2 B:CAC403 3.8 69.8 1.0
CB B:THR319 4.0 28.6 1.0
CG B:GLU321 4.1 41.4 1.0
ND1 B:HIS292 4.2 35.6 1.0
CG B:HIS292 4.2 35.5 1.0
CB B:ASP223 4.2 39.2 1.0
CG B:GLU335 4.4 41.0 1.0
NE2 B:HIS299 4.8 45.8 1.0
O B:HOH516 4.9 31.1 1.0
CB B:GLU321 5.0 40.4 1.0
C2 B:CAC403 5.0 56.7 1.0

Zinc binding site 4 out of 6 in 5cnx

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Zinc binding site 4 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:36.7
occ:1.00
O1 B:CAC403 1.9 59.6 1.0
OE1 B:GLU335 1.9 40.0 1.0
OD1 B:ASP223 2.0 37.9 1.0
OD1 B:ASP212 2.0 38.9 1.0
CG B:ASP212 2.7 38.7 1.0
OD2 B:ASP212 2.7 38.6 1.0
CD B:GLU335 2.7 40.8 1.0
CG B:ASP223 2.8 38.4 1.0
OE2 B:GLU335 2.8 41.4 1.0
OD2 B:ASP223 3.1 38.3 1.0
ZN B:ZN401 3.2 42.6 1.0
AS B:CAC403 3.3 62.6 1.0
OG1 B:THR225 3.5 37.0 1.0
OE1 B:GLU321 3.6 42.0 1.0
CZ B:PHE181 3.9 33.8 1.0
O2 B:CAC403 4.0 69.8 1.0
C2 B:CAC403 4.0 56.7 1.0
CG B:GLU335 4.2 41.0 1.0
CB B:ASP212 4.2 38.3 1.0
CB B:ASP223 4.2 39.2 1.0
O B:MET224 4.3 36.5 1.0
CD B:GLU321 4.4 41.6 1.0
N B:MET224 4.4 37.4 1.0
C B:MET224 4.5 36.6 1.0
C B:ASP223 4.5 38.8 1.0
OE2 B:GLU321 4.5 41.8 1.0
CE2 B:PHE181 4.5 33.6 1.0
CA B:ASP223 4.7 39.0 1.0
CE1 B:PHE181 4.7 34.4 1.0
CB B:GLU335 4.7 40.1 1.0
CA B:ASP212 4.8 38.1 1.0
N B:PHE213 4.8 35.2 1.0
N B:THR225 4.9 37.2 1.0
CA B:MET224 4.9 37.2 1.0
C1 B:CAC403 4.9 65.4 1.0
CB B:THR225 4.9 36.8 1.0
O B:PHE213 4.9 36.3 1.0

Zinc binding site 5 out of 6 in 5cnx

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Zinc binding site 5 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:49.8
occ:1.00
O1 C:CAC403 2.1 46.6 0.7
OD2 C:ASP223 2.1 44.4 1.0
NE2 C:HIS292 2.1 40.2 1.0
OE2 C:GLU321 2.1 50.3 1.0
OE2 C:GLU335 2.2 55.1 1.0
CD C:GLU321 2.9 50.2 1.0
CG C:ASP223 3.0 45.0 1.0
ZN C:ZN402 3.0 43.3 1.0
CE1 C:HIS292 3.1 41.1 1.0
OE1 C:GLU321 3.1 49.7 1.0
CD C:GLU335 3.1 54.8 1.0
CD2 C:HIS292 3.2 40.2 1.0
AS C:CAC403 3.2 51.0 0.7
OD1 C:ASP223 3.4 44.3 1.0
OE1 C:GLU335 3.5 53.8 1.0
C1 C:CAC403 3.6 47.2 0.7
O2 C:CAC403 3.8 45.5 0.7
CG2 C:THR319 3.9 49.0 1.0
OG1 C:THR319 3.9 47.9 1.0
CB C:THR319 4.1 49.1 1.0
CB C:ASP223 4.2 47.0 1.0
ND1 C:HIS292 4.2 41.8 1.0
CG C:GLU321 4.2 51.5 1.0
CG C:HIS292 4.3 41.3 1.0
CG C:GLU335 4.5 56.9 1.0
OD2 C:ASP212 4.9 40.5 1.0
NE2 C:HIS299 4.9 54.9 1.0
C2 C:CAC403 4.9 49.1 0.7
OD1 C:ASP212 5.0 41.9 1.0

Zinc binding site 6 out of 6 in 5cnx

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Zinc binding site 6 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:43.3
occ:1.00
O1 C:CAC403 1.9 46.6 0.7
OD1 C:ASP223 2.0 44.3 1.0
OD1 C:ASP212 2.0 41.9 1.0
OE1 C:GLU335 2.0 53.8 1.0
OD2 C:ASP212 2.5 40.5 1.0
CG C:ASP212 2.6 41.2 1.0
CG C:ASP223 2.8 45.0 1.0
CD C:GLU335 2.9 54.8 1.0
ZN C:ZN401 3.0 49.8 1.0
OE2 C:GLU335 3.1 55.1 1.0
OD2 C:ASP223 3.1 44.4 1.0
AS C:CAC403 3.4 51.0 0.7
OG1 C:THR225 3.6 45.7 1.0
OE1 C:GLU321 3.7 49.7 1.0
CZ C:PHE181 3.9 36.6 1.0
O2 C:CAC403 4.0 45.5 0.7
C2 C:CAC403 4.0 49.1 0.7
CB C:ASP212 4.1 40.4 1.0
CB C:ASP223 4.2 47.0 1.0
CG C:GLU335 4.3 56.9 1.0
N C:MET224 4.3 55.5 1.0
O C:MET224 4.3 53.5 1.0
CD C:GLU321 4.4 50.2 1.0
C C:ASP223 4.4 48.5 1.0
C C:MET224 4.5 55.0 1.0
OE2 C:GLU321 4.5 50.3 1.0
CE1 C:PHE181 4.6 37.6 1.0
CA C:ASP223 4.6 47.7 1.0
CE2 C:PHE181 4.7 34.8 1.0
CA C:ASP212 4.7 41.9 1.0
CB C:GLU335 4.7 56.1 1.0
N C:PHE213 4.8 46.7 1.0
CA C:MET224 4.9 56.7 1.0
O C:ASP223 4.9 50.1 1.0
C1 C:CAC403 4.9 47.2 0.7
N C:THR225 4.9 49.2 1.0
CB C:THR225 5.0 47.0 1.0
O C:PHE213 5.0 49.5 1.0
C C:ASP212 5.0 41.8 1.0

Reference:

V.N.Are, A.Kumar, V.D.Goyal, S.S.Gotad, B.Ghosh, R.Gadre, S.N.Jamdar, R.D.Makde. Structures and Activities of Widely Conserved Small Prokaryotic Aminopeptidases-P Clarify Classification of M24B Peptidases Proteins 2018.
ISSN: ESSN 1097-0134
PubMed: 30536999
DOI: 10.1002/PROT.25641
Page generated: Wed Dec 16 06:07:14 2020

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