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Cobalt in PDB 2wke: Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.

Enzymatic activity of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.

All present enzymatic activity of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate., PDB code: 2wke was solved by E.Sauvage, R.Herman, F.Kerff, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.06 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.981, 92.686, 107.133, 90.00, 95.03, 90.00
R / Rfree (%) 20.59 / 26.136

Cobalt Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. (pdb code 2wke). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 14 binding sites of Cobalt where determined in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate., PDB code: 2wke:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 14 in 2wke

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Cobalt binding site 1 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


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 the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co610

b:33.3
occ:1.00
 OE1 A:GLU251 2.0 17.2 1.0
NE2 A:HIS247 2.1 19.0 1.0
O A:GLU188 2.1 16.7 1.0
O A:HOH2169 2.3 22.6 1.0
CE1 A:HIS247 3.0 20.1 1.0
CD A:GLU251 3.0 18.2 1.0
CD2 A:HIS247 3.1 18.1 1.0
C A:GLU188 3.3 16.9 1.0
OE2 A:GLU251 3.3 19.5 1.0
CA A:GLY189 4.0 17.1 1.0
O A:ALA186 4.1 17.3 1.0
N A:GLY189 4.1 16.9 1.0
O A:HOH2087 4.1 26.6 1.0
ND1 A:HIS247 4.1 21.1 1.0
CG A:HIS247 4.2 18.4 1.0
CG A:GLU251 4.3 18.4 1.0
CA A:GLU188 4.3 17.3 1.0
CB A:GLU188 4.4 17.8 1.0
C A:GLY189 4.6 17.4 1.0
N A:GLU188 4.6 16.5 1.0
O A:HOH2103 4.8 42.5 1.0
N A:TYR190 4.9 17.8 1.0

Cobalt binding site 2 out of 14 in 2wke

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Cobalt binding site 2 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


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 the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co611

b:32.0
occ:1.00
 O A:HOH2170 2.2 18.8 1.0
ND1 A:HIS462 2.2 18.0 1.0
CG A:HIS462 3.2 18.9 1.0
CE1 A:HIS462 3.2 18.2 1.0
CB A:HIS462 3.4 19.8 1.0
CG2 A:VAL406 3.8 17.1 1.0
O A:HOH2152 4.3 27.0 1.0
NE2 A:HIS462 4.3 17.1 1.0
CD2 A:HIS462 4.3 17.0 1.0
CA A:HIS462 4.3 20.0 1.0
O A:ALA402 4.4 16.7 1.0
N A:GLN463 4.7 21.9 1.0
O A:GLN463 5.0 23.4 1.0

Cobalt binding site 3 out of 14 in 2wke

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Cobalt binding site 3 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


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 the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co612

b:66.1
occ:1.00
 O A:LEU63 2.1 21.4 1.0
ND1 A:HIS67 2.4 18.6 1.0
C A:LEU63 3.1 20.7 1.0
CG A:HIS67 3.3 19.5 1.0
CE1 A:HIS67 3.3 19.3 1.0
CB A:HIS67 3.6 19.0 1.0
CA A:LEU63 3.6 20.4 1.0
CA A:HIS67 4.2 19.6 1.0
CB A:LEU63 4.2 20.8 1.0
N A:GLY64 4.3 20.8 1.0
NE2 A:HIS67 4.5 18.2 1.0
CD2 A:HIS67 4.5 18.8 1.0
OD1 A:ASP66 4.6 26.4 1.0
O A:VAL62 4.7 21.1 1.0
N A:HIS67 4.7 20.4 1.0
CA A:GLY64 4.8 20.5 1.0
N A:LEU63 4.9 20.9 1.0
OE2 A:GLU313 4.9 21.5 1.0

Cobalt binding site 4 out of 14 in 2wke

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Cobalt binding site 4 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


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 the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co613

b:62.8
occ:1.00
 NE2 A:HIS158 2.3 20.7 1.0
OE2 A:GLU168 2.4 21.3 1.0
CD A:GLU168 3.1 22.3 1.0
O A:HOH2082 3.1 36.1 1.0
CE1 A:HIS158 3.3 19.9 1.0
OE1 A:GLU168 3.3 23.4 1.0
CD2 A:HIS158 3.3 19.7 1.0
CG A:GLU168 4.3 19.2 1.0
ND1 A:HIS158 4.4 19.9 1.0
CG A:HIS158 4.5 19.6 1.0
CD2 A:LEU235 4.7 19.8 1.0
CB A:GLU168 4.7 17.0 1.0

Cobalt binding site 5 out of 14 in 2wke

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Cobalt binding site 5 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co610

b:48.7
occ:1.00
 OE2 B:GLU251 2.1 25.0 1.0
NE2 B:HIS247 2.2 16.7 1.0
O B:GLU188 2.3 20.1 1.0
CD2 B:HIS247 3.2 18.5 1.0
CD B:GLU251 3.2 24.3 1.0
CE1 B:HIS247 3.3 18.7 1.0
C B:GLU188 3.4 20.0 1.0
OE1 B:GLU251 3.7 25.9 1.0
O B:ALA186 4.2 18.4 1.0
N B:GLY189 4.3 20.2 1.0
CA B:GLU188 4.3 20.3 1.0
CA B:GLY189 4.3 19.6 1.0
CG B:HIS247 4.3 17.8 1.0
CB B:GLU188 4.3 20.7 1.0
ND1 B:HIS247 4.4 18.3 1.0
CG B:GLU251 4.4 24.4 1.0
N B:GLU188 4.5 19.2 1.0
C B:GLY189 4.7 19.4 1.0
N B:TYR190 4.9 19.4 1.0

Cobalt binding site 6 out of 14 in 2wke

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Cobalt binding site 6 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co612

b:67.1
occ:1.00
 O B:LEU63 2.2 21.2 1.0
ND1 B:HIS67 2.5 18.4 1.0
C B:LEU63 3.2 20.9 1.0
CE1 B:HIS67 3.4 20.1 1.0
CG B:HIS67 3.5 19.5 1.0
CB B:HIS67 3.7 20.6 1.0
CA B:LEU63 3.7 20.1 1.0
CA B:HIS67 4.3 20.5 1.0
CB B:LEU63 4.3 19.7 1.0
N B:GLY64 4.4 20.6 1.0
NE2 B:HIS67 4.5 20.5 1.0
CD2 B:HIS67 4.6 19.2 1.0
OD1 B:ASP66 4.7 25.4 1.0
CA B:GLY64 4.8 20.6 1.0
N B:HIS67 4.8 20.4 1.0
O B:VAL62 4.9 21.3 1.0

Cobalt binding site 7 out of 14 in 2wke

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Cobalt binding site 7 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co613

b:97.3
occ:1.00
 NE2 B:HIS158 2.5 21.5 1.0
CD2 B:HIS158 3.0 20.8 1.0
CE1 B:HIS158 3.7 21.6 1.0
OE2 B:GLU168 3.9 26.2 1.0
CG B:HIS158 4.3 21.7 1.0
O B:HOH2063 4.4 43.6 1.0
CA B:GLY159 4.5 22.7 1.0
CD B:GLU168 4.5 23.3 1.0
OE1 B:GLU168 4.5 23.9 1.0
ND1 B:HIS158 4.6 21.6 1.0
N B:GLY159 4.9 22.1 1.0

Cobalt binding site 8 out of 14 in 2wke

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Cobalt binding site 8 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co610

b:47.2
occ:1.00
 OE1 C:GLU251 1.9 23.5 1.0
O C:GLU188 2.2 17.2 1.0
NE2 C:HIS247 2.2 15.9 1.0
CD C:GLU251 3.0 23.3 1.0
CE1 C:HIS247 3.1 15.8 1.0
CD2 C:HIS247 3.3 15.5 1.0
C C:GLU188 3.3 17.6 1.0
OE2 C:GLU251 3.5 25.2 1.0
N C:GLY189 4.2 17.5 1.0
CA C:GLY189 4.2 17.5 1.0
O C:ALA186 4.2 18.0 1.0
CG C:GLU251 4.3 21.7 1.0
ND1 C:HIS247 4.3 14.8 1.0
CA C:GLU188 4.3 17.9 1.0
CG C:HIS247 4.4 16.1 1.0
CB C:GLU188 4.4 18.2 1.0
O C:HOH2078 4.5 36.6 1.0
N C:GLU188 4.5 17.2 1.0
C C:GLY189 4.8 17.6 1.0
N C:TYR190 5.0 17.3 1.0

Cobalt binding site 9 out of 14 in 2wke

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Cobalt binding site 9 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co612

b:67.9
occ:1.00
 ND1 C:HIS67 2.2 15.8 1.0
O C:LEU63 2.5 11.5 1.0
CE1 C:HIS67 3.1 15.2 1.0
CG C:HIS67 3.3 14.4 1.0
C C:LEU63 3.5 11.9 1.0
CB C:HIS67 3.6 13.6 1.0
CA C:LEU63 3.9 11.2 1.0
CA C:HIS67 4.1 14.3 1.0
NE2 C:HIS67 4.3 15.1 1.0
CD2 C:HIS67 4.4 14.7 1.0
CB C:LEU63 4.5 10.9 1.0
O C:HOH2013 4.6 35.2 1.0
N C:GLY64 4.7 12.3 1.0
N C:HIS67 4.7 14.3 1.0
OE2 C:GLU313 4.8 29.6 1.0
O C:VAL62 5.0 11.8 1.0

Cobalt binding site 10 out of 14 in 2wke

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Cobalt binding site 10 out of 14 in the Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of the Actinomadura R39 Dd-Peptidase Inhibited By 6-Beta-Iodopenicillanate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co613

b:95.2
occ:1.00
 O C:HOH2148 2.1 37.1 1.0
OE2 C:GLU168 2.7 17.4 1.0
NE2 C:HIS158 3.2 17.8 1.0
CD C:GLU168 3.5 18.2 1.0
OE1 C:GLU168 3.6 18.9 1.0
CE1 C:HIS158 3.9 16.1 1.0
CD2 C:HIS158 4.3 17.3 1.0
CG C:GLU168 4.8 16.0 1.0

Reference:

E.Sauvage, A.Zervosen, G.Dive, R.Herman, A.Amoroso, B.Joris, E.Fonze, R.F.Pratt, A.Luxen, P.Charlier, F.Kerff. Structural Basis of the Inhibition of Class A Beta- Lactamases and Penicillin-Binding Proteins By 6- Beta-Iodopenicillanate. J.Am.Chem.Soc. V. 131 15262 2009.
ISSN: ISSN 0002-7863
PubMed: 19919161
DOI: 10.1021/JA9051526
Page generated: Sun Dec 13 10:39:07 2020

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