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Magnesium in PDB 2vgk: Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin

Enzymatic activity of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin

All present enzymatic activity of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin, PDB code: 2vgk was solved by E.Sauvage, F.Kerff, R.Herman, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.71 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.140, 93.350, 109.100, 90.00, 94.98, 90.00
R / Rfree (%) 23 / 28.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin (pdb code 2vgk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin, PDB code: 2vgk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2vgk

Go back to Magnesium Binding Sites List in 2vgk
Magnesium binding site 1 out of 4 in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:13.0
occ:1.00
 O A:GLU188 2.1 24.7 1.0
NE2 A:HIS247 2.1 25.3 1.0
OE1 A:GLU251 2.3 29.8 1.0
CE1 A:HIS247 2.9 25.4 1.0
CD A:GLU251 3.2 29.7 1.0
CD2 A:HIS247 3.3 25.3 1.0
C A:GLU188 3.3 24.4 1.0
OE2 A:GLU251 3.4 29.9 1.0
O A:ALA186 4.0 23.5 1.0
ND1 A:HIS247 4.1 26.1 1.0
CA A:GLU188 4.2 24.0 1.0
CB A:GLU188 4.2 23.8 1.0
N A:GLY189 4.3 24.5 1.0
CG A:HIS247 4.3 26.0 1.0
CA A:GLY189 4.4 24.9 1.0
N A:GLU188 4.4 23.6 1.0
CG A:GLU251 4.5 29.7 1.0
O A:HOH2051 4.7 28.0 1.0
C A:GLY189 4.8 25.5 1.0

Magnesium binding site 2 out of 4 in 2vgk

Go back to Magnesium Binding Sites List in 2vgk
Magnesium binding site 2 out of 4 in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:13.4
occ:1.00
 ND1 A:HIS462 2.5 35.2 1.0
CG2 A:VAL406 3.1 25.9 1.0
CE1 A:HIS462 3.1 35.0 1.0
CG A:HIS462 3.7 35.0 1.0
CB A:HIS462 4.2 35.3 1.0
NE2 A:HIS462 4.3 35.0 1.0
CB A:VAL406 4.6 25.5 1.0
CD2 A:HIS462 4.6 35.2 1.0
O A:ALA402 4.8 24.9 1.0
O A:GLU404 4.8 23.8 1.0

Magnesium binding site 3 out of 4 in 2vgk

Go back to Magnesium Binding Sites List in 2vgk
Magnesium binding site 3 out of 4 in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg610

b:18.9
occ:1.00
 OE2 D:GLU251 2.1 28.2 1.0
O D:GLU188 2.2 25.8 1.0
NE2 D:HIS247 2.4 24.9 1.0
CD D:GLU251 3.0 27.6 1.0
CE1 D:HIS247 3.1 25.9 1.0
OE1 D:GLU251 3.3 27.8 1.0
C D:GLU188 3.4 25.6 1.0
CD2 D:HIS247 3.5 24.6 1.0
ND1 D:HIS247 4.2 24.3 1.0
CG D:GLU251 4.3 27.1 1.0
CA D:GLY189 4.3 25.0 1.0
N D:GLY189 4.3 25.4 1.0
CA D:GLU188 4.4 25.5 1.0
CG D:HIS247 4.4 23.7 1.0
CB D:GLU188 4.6 25.7 1.0
O D:ALA186 4.6 24.2 1.0
N D:GLU188 4.7 25.3 1.0
C D:GLY189 4.8 25.1 1.0

Magnesium binding site 4 out of 4 in 2vgk

Go back to Magnesium Binding Sites List in 2vgk
Magnesium binding site 4 out of 4 in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg611

b:2.0
occ:1.00
 ND1 D:HIS462 2.1 27.4 1.0
CE1 D:HIS462 2.9 27.7 1.0
CG D:HIS462 3.3 28.3 1.0
CB D:HIS462 3.7 29.7 1.0
CG2 D:VAL406 3.8 18.4 1.0
NE2 D:HIS462 4.1 27.1 1.0
CD2 D:HIS462 4.3 27.8 1.0
CA D:HIS462 4.4 30.1 1.0
O D:ALA402 4.6 19.0 1.0
O D:HOH2143 4.6 16.1 1.0
N D:GLN463 4.7 31.3 1.0
O D:GLN463 4.7 32.9 1.0

Reference:

E.Sauvage, A.J.Powell, J.Heilemann, H.R.Josephin, P.Charlier, C.Davies, R.F.Pratt. Crystal Structures of Complexes of Bacterial Dd-Peptidases with Peptidoglycan-Mimetic Ligands: the Substrate Specificity Puzzle. J.Mol.Biol. V. 381 383 2008.
ISSN: ISSN 0022-2836
PubMed: 18602645
DOI: 10.1016/J.JMB.2008.06.012
Page generated: Mon Dec 14 07:42:03 2020

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