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Zinc in PDB 3o9p: The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa

Protein crystallography data

The structure of The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa, PDB code: 3o9p was solved by A.Maqbool, V.M.Levdikov, E.V.Blagova, A.J.Wilkinson, G.H.Thomas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.27 / 2.07
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 165.074, 165.074, 38.167, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa (pdb code 3o9p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa, PDB code: 3o9p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3o9p

Go back to Zinc Binding Sites List in 3o9p
Zinc binding site 1 out of 4 in the The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn517

b:28.5
occ:1.00
O A:HOH694 1.8 20.4 1.0
NE2 A:HIS142 2.1 27.1 1.0
CD2 A:HIS142 2.9 24.3 1.0
CE1 A:HIS142 3.2 26.9 1.0
OD1 A:ASP78 3.7 41.3 1.0
O A:HOH751 3.9 44.5 1.0
CG A:HIS142 4.2 25.5 1.0
ND1 A:HIS142 4.3 25.9 1.0
CG A:ASP78 4.7 34.8 1.0

Zinc binding site 2 out of 4 in 3o9p

Go back to Zinc Binding Sites List in 3o9p
Zinc binding site 2 out of 4 in the The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn518

b:38.6
occ:1.00
O A:HOH752 2.0 37.3 1.0
NE2 A:HIS208 2.1 30.9 1.0
CE1 A:HIS208 3.1 31.9 1.0
CD2 A:HIS208 3.1 29.4 1.0
ND1 A:HIS208 4.2 31.6 1.0
CG A:HIS208 4.2 30.7 1.0
O A:ALA83 4.3 24.3 1.0
OG1 A:THR207 4.7 28.2 1.0
C A:ASP84 4.9 25.6 1.0
N A:GLY85 4.9 24.6 1.0

Zinc binding site 3 out of 4 in 3o9p

Go back to Zinc Binding Sites List in 3o9p
Zinc binding site 3 out of 4 in the The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn519

b:53.5
occ:1.00
OD1 A:ASP318 2.0 37.6 1.0
NE2 A:HIS314 2.2 44.9 1.0
O A:HOH654 2.3 41.0 1.0
O A:HOH649 2.4 39.1 1.0
CE1 A:HIS314 3.0 43.3 1.0
CG A:ASP318 3.0 31.6 1.0
O A:HOH549 3.2 28.7 1.0
CD2 A:HIS314 3.3 42.1 1.0
OD2 A:ASP318 3.3 37.4 1.0
O A:HOH762 3.5 60.4 1.0
O A:HOH619 3.7 32.0 1.0
CG A:PRO325 3.7 44.8 1.0
ND1 A:HIS314 4.2 45.2 1.0
CG A:HIS314 4.3 38.6 1.0
CB A:ASP318 4.3 29.9 1.0
CB A:PRO325 4.5 46.0 1.0
CA A:ASP318 4.9 28.2 1.0
CD A:PRO325 4.9 44.6 1.0
OE1 A:GLU331 5.0 72.0 1.0

Zinc binding site 4 out of 4 in 3o9p

Go back to Zinc Binding Sites List in 3o9p
Zinc binding site 4 out of 4 in the The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the Escherichia Coli Murein Tripeptide Binding Protein Mppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn520

b:45.9
occ:1.00
O A:HOH858 1.8 32.8 1.0
NE2 A:HIS515 2.2 29.4 1.0
O A:HOH795 2.4 50.0 1.0
O A:HOH521 2.5 44.6 1.0
CE1 A:HIS515 3.1 29.3 1.0
CD2 A:HIS515 3.2 28.4 1.0
NE1 A:TRP492 3.9 33.7 1.0
CE2 A:TRP492 4.1 33.1 1.0
O A:HOH825 4.2 35.4 1.0
CZ2 A:TRP492 4.2 36.0 1.0
ND1 A:HIS515 4.3 27.1 1.0
CG A:HIS515 4.3 29.3 1.0
OD1 A:ASP241 4.5 34.7 1.0
CD1 A:TRP492 4.6 32.8 1.0

Reference:

A.Maqbool, V.M.Levdikov, E.V.Blagova, M.Herve, R.S.Horler, A.J.Wilkinson, G.H.Thomas. Compensating Stereochemical Changes Allow Murein Tripeptide to Be Accommodated in A Conventional Peptide-Binding Protein. J.Biol.Chem. V. 286 31512 2011.
ISSN: ISSN 0021-9258
PubMed: 21705338
DOI: 10.1074/JBC.M111.267179
Page generated: Wed Dec 16 04:40:07 2020

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