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Magnesium in PDB 3ebi: Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog

Protein crystallography data

The structure of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog, PDB code: 3ebi was solved by S.Mcgowan, C.J.Porter, A.M.Buckle, J.C.Whisstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.61 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.852, 108.633, 118.325, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.1

Other elements in 3ebi:

The structure of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog (pdb code 3ebi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog, PDB code: 3ebi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3ebi

Go back to Magnesium Binding Sites List in 3ebi
Magnesium binding site 1 out of 4 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg10

b:54.8
occ:1.00
O A:HOH1473 1.9 38.0 1.0
O A:HOH1543 2.0 39.1 1.0
O A:HOH1542 2.2 35.2 1.0
O A:HOH103 2.4 21.6 1.0
O A:HOH100 2.5 33.0 1.0
O A:HOH159 3.9 22.9 1.0
OD1 A:ASP438 4.2 20.9 1.0
CB A:ALA434 4.2 12.4 1.0
OH A:TYR399 4.4 17.7 1.0
OE1 A:GLU437 4.4 15.6 1.0
OD2 A:ASP438 4.4 24.3 1.0
CG A:ASP438 4.7 22.2 1.0
CA A:ALA434 4.8 14.6 1.0

Magnesium binding site 2 out of 4 in 3ebi

Go back to Magnesium Binding Sites List in 3ebi
Magnesium binding site 2 out of 4 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:44.6
occ:1.00
O A:HOH26 2.1 32.3 1.0
O A:HOH1536 2.1 21.9 1.0
O A:HOH1214 2.2 23.6 1.0
O A:GLY250 2.3 19.3 1.0
O A:HOH1099 2.4 30.4 1.0
C A:GLY250 3.4 16.9 1.0
CA A:GLY250 4.1 17.3 1.0
ND1 A:HIS297 4.1 19.8 1.0
O A:HOH111 4.2 37.7 1.0
O A:HOH1193 4.2 19.2 1.0
O A:HOH1471 4.4 17.1 1.0
O A:ILE295 4.5 16.9 1.0
N A:LEU251 4.5 18.5 1.0
CA A:ILE296 4.7 14.6 1.0
CA A:LEU251 4.8 17.8 1.0
CE1 A:HIS297 4.8 22.0 1.0
N A:HIS297 4.9 14.2 1.0

Magnesium binding site 3 out of 4 in 3ebi

Go back to Magnesium Binding Sites List in 3ebi
Magnesium binding site 3 out of 4 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8

b:40.3
occ:1.00
O A:HOH1539 2.1 33.1 1.0
O A:HOH1177 2.2 28.5 1.0
O A:HOH1540 2.2 38.8 1.0
O A:HOH1537 2.2 30.5 1.0
O A:HOH1538 2.6 35.8 1.0
O A:HOH1430 3.6 44.9 1.0
O A:HOH1224 4.2 35.7 1.0
O A:HOH112 4.3 34.0 1.0
OG A:SER542 4.3 18.5 1.0
CG2 A:THR492 4.3 7.1 1.0
OE2 A:GLU526 4.3 21.7 1.0
OE1 A:GLU526 4.4 18.3 1.0
OD1 A:ASN527 4.4 22.6 1.0
O A:THR539 4.6 12.3 1.0
CD2 A:HIS543 4.7 5.8 0.5
CB A:HIS543 4.8 8.0 0.5
CD A:GLU526 4.8 18.9 1.0

Magnesium binding site 4 out of 4 in 3ebi

Go back to Magnesium Binding Sites List in 3ebi
Magnesium binding site 4 out of 4 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg9

b:46.3
occ:1.00
O A:HOH1541 2.0 36.0 1.0
OE2 A:GLU957 3.2 24.1 1.0
CD A:GLU957 3.9 18.2 1.0
ND2 A:ASN992 4.0 16.3 1.0
CG A:GLU957 4.1 18.5 1.0
O A:HOH190 4.3 15.1 1.0
OD2 A:ASP995 4.3 20.3 1.0
O A:HOH1418 4.3 24.9 1.0
OE1 A:GLU957 4.9 19.8 1.0
CB A:GLU957 5.0 18.2 1.0
CE A:LYS311 5.0 21.1 1.0
CG A:ASN992 5.0 14.2 1.0

Reference:

S.Mcgowan, C.J.Porter, J.Lowther, C.M.Stack, S.J.Golding, T.S.Skinner-Adams, K.R.Trenholme, F.Teuscher, S.M.Donnelly, J.Grembecka, A.Mucha, P.Kafarski, R.Degori, A.M.Buckle, D.L.Gardiner, J.C.Whisstock, J.P.Dalton. Structural Basis For the Inhibition of the Essential Plasmodium Falciparum M1 Neutral Aminopeptidase Proc.Natl.Acad.Sci.Usa V. 106 2537 2009.
ISSN: ISSN 0027-8424
PubMed: 19196988
DOI: 10.1073/PNAS.0807398106
Page generated: Mon Dec 14 08:06:04 2020

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