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Cobalt in PDB 2xk1: Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor

Enzymatic activity of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor

All present enzymatic activity of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor, PDB code: 2xk1 was solved by E.Sauvage, R.Herman, F.Kerff, M.Rocaboy, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.53 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.898, 92.348, 143.829, 90.00, 92.25, 90.00
R / Rfree (%) 21.7 / 26.4

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor (pdb code 2xk1). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor, PDB code: 2xk1:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2xk1

Go back to Cobalt Binding Sites List in 2xk1
Cobalt binding site 1 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co610

b:58.9
occ:1.00
 O A:GLU188 2.2 40.9 1.0
OE1 A:GLU251 2.2 32.9 1.0
NE2 A:HIS247 2.3 41.8 1.0
OE2 A:GLU251 2.8 35.0 1.0
CD A:GLU251 2.8 35.8 1.0
CE1 A:HIS247 3.1 42.3 1.0
C A:GLU188 3.3 40.9 1.0
CD2 A:HIS247 3.4 38.7 1.0
CA A:GLU188 4.1 41.0 1.0
CB A:GLU188 4.2 41.6 1.0
N A:GLY189 4.3 41.1 1.0
ND1 A:HIS247 4.3 42.4 1.0
CG A:GLU251 4.3 37.1 1.0
CA A:GLY189 4.4 40.9 1.0
CG A:HIS247 4.4 38.5 1.0
N A:GLU188 4.4 39.8 1.0
O A:ALA186 4.5 38.5 1.0
C A:GLY189 4.7 39.6 1.0

Cobalt binding site 2 out of 4 in 2xk1

Go back to Cobalt Binding Sites List in 2xk1
Cobalt binding site 2 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co611

b:48.4
occ:1.00
 ND1 A:HIS462 2.1 77.4 1.0
CE1 A:HIS462 3.0 77.4 1.0
CG A:HIS462 3.1 77.0 1.0
CB A:HIS462 3.5 77.0 1.0
CG2 A:VAL406 3.6 61.1 1.0
NE2 A:HIS462 4.1 77.1 1.0
CA A:HIS462 4.2 79.2 1.0
CD2 A:HIS462 4.2 76.8 1.0
O A:ALA402 4.2 62.6 1.0
N A:GLN463 4.8 80.3 1.0
CB A:VAL406 4.9 59.3 1.0

Cobalt binding site 3 out of 4 in 2xk1

Go back to Cobalt Binding Sites List in 2xk1
Cobalt binding site 3 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co610

b:95.6
occ:1.00
 OE1 D:GLU251 1.6 87.4 1.0
O D:GLU188 2.1 85.7 1.0
NE2 D:HIS247 2.5 84.1 1.0
CD D:GLU251 2.7 88.1 1.0
CD2 D:HIS247 3.1 83.6 1.0
OE2 D:GLU251 3.2 87.8 1.0
C D:GLU188 3.2 85.2 1.0
CE1 D:HIS247 3.7 85.3 1.0
CA D:GLU188 3.8 84.0 1.0
N D:GLU188 3.8 82.7 1.0
CB D:GLU188 3.9 84.7 1.0
CG D:GLU251 4.0 89.7 1.0
O D:ALA186 4.1 81.3 1.0
N D:GLY189 4.3 85.9 1.0
CG D:HIS247 4.3 84.3 1.0
CD2 D:LEU248 4.6 83.6 1.0
ND1 D:HIS247 4.6 85.4 1.0
C D:ALA187 4.7 81.7 1.0
CA D:GLY189 4.7 87.4 1.0
C D:ALA186 4.8 80.8 1.0

Cobalt binding site 4 out of 4 in 2xk1

Go back to Cobalt Binding Sites List in 2xk1
Cobalt binding site 4 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Boronate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co611

b:0.6
occ:1.00
 ND1 D:HIS462 2.3 0.5 1.0
CG D:HIS462 3.3 0.4 1.0
CE1 D:HIS462 3.3 0.7 1.0
CG2 D:VAL406 3.3 90.7 1.0
CB D:HIS462 3.5 0.2 1.0
CA D:HIS462 4.2 0.6 1.0
NE2 D:HIS462 4.4 1.0 1.0
CD2 D:HIS462 4.4 0.3 1.0
N D:GLN463 4.6 0.2 1.0
CB D:VAL406 4.7 89.0 1.0
O D:GLN463 4.7 0.9 1.0
C D:HIS462 4.9 0.1 1.0
CG1 D:VAL406 4.9 89.9 1.0
O D:ALA402 5.0 91.7 1.0

Reference:

E.C.Y.Woon, A.Zervosen, E.Sauvage, K.J.Simmons, M.Ivec, S.R.Inglis, C.W.G.Fishwick, S.Gobec, P.Charlier, A.Luxen, C.J.Schofield. Structure Guided Development of Potent Reversibly Binding Penicillin Binding Protein Inhibitors Acs Med.Chem.Lett. V. 2 219 2011.
ISSN: ISSN 1948-5875
PubMed: 24900305
DOI: 10.1021/ML100260X
Page generated: Tue Jul 30 15:34:57 2024

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