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Ruthenium in PDB 5vle: Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase

Enzymatic activity of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase

All present enzymatic activity of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase, PDB code: 5vle was solved by E.M.Lewandowski, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 0.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.745, 106.418, 47.611, 90.00, 102.38, 90.00
R / Rfree (%) n/a / n/a

Other elements in 5vle:

The structure of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase also contains other interesting chemical elements:

Potassium (K) 2 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase (pdb code 5vle). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 7 binding sites of Ruthenium where determined in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase, PDB code: 5vle:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6; 7;

Ruthenium binding site 1 out of 7 in 5vle

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Ruthenium binding site 1 out of 7 in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru901

b:10.2
occ:0.86
 RU A:JSD901 0.0 10.2 0.9
C13 A:JSD901 2.1 19.4 0.9
C18 A:JSD901 2.1 10.2 0.9
C17 A:JSD901 2.1 10.9 0.9
C12 A:JSD901 2.1 18.1 0.9
C19 A:JSD901 2.1 10.5 0.9
C14 A:JSD901 2.1 18.9 0.9
C16 A:JSD901 2.2 11.9 0.9
C20 A:JSD901 2.2 12.4 0.9
C11 A:JSD901 2.2 17.2 0.9
C15 A:JSD901 2.2 16.7 0.9
C24 A:JSD901 3.1 13.0 0.9
C25 A:JSD901 3.8 12.7 0.9
O28 A:JSD901 3.9 12.4 0.9
HB2 A:PRO167 4.0 10.6 1.0
O A:HOH1073 4.5 29.5 1.0
O A:HOH1309 4.6 38.2 1.0
O A:HOH1302 4.8 33.3 1.0
HB2 A:ASN170 4.8 8.5 1.0
HG2 A:PRO167 4.9 11.7 1.0
CB A:PRO167 4.9 8.9 1.0
O A:PRO167 4.9 6.9 1.0
HG23 A:THR171 5.0 11.2 1.0

Ruthenium binding site 2 out of 7 in 5vle

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Ruthenium binding site 2 out of 7 in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru902

b:9.8
occ:0.32
 RU A:JSC902 0.0 9.8 0.3
C18 A:JSC902 2.2 10.1 0.3
C11 A:JSC902 2.2 12.2 0.3
C19 A:JSC902 2.2 9.9 0.3
C20 A:JSC902 2.2 8.7 0.3
C13 A:JSC902 2.2 13.7 0.3
C14 A:JSC902 2.2 11.9 0.3
C15 A:JSC902 2.2 10.7 0.3
C17 A:JSC902 2.2 10.5 0.3
C12 A:JSC902 2.2 13.4 0.3
C16 A:JSC902 2.2 10.8 0.3
C24 A:JSC902 3.2 12.0 0.3
O28 A:JSC902 3.7 20.0 0.3
HD2 A:LYS82 3.8 12.3 1.0
C25 A:JSC902 4.0 11.2 0.3
O A:HOH1086 4.3 44.6 1.0
O A:HOH1075 4.7 13.4 1.0
O29 A:JSC902 4.7 11.4 0.3
CD A:LYS82 4.8 10.3 1.0
O38 A:JSC902 4.9 11.7 0.3

Ruthenium binding site 3 out of 7 in 5vle

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Ruthenium binding site 3 out of 7 in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru903

b:8.4
occ:0.38
 RU A:JSD903 0.0 8.4 0.4
O29 A:JSE904 1.8 11.2 0.2
C18 A:JSD903 2.1 6.9 0.4
C13 A:JSD903 2.1 10.1 0.4
C17 A:JSD903 2.1 7.5 0.4
C14 A:JSD903 2.1 10.0 0.4
C12 A:JSD903 2.1 11.5 0.4
C19 A:JSD903 2.2 7.3 0.4
C15 A:JSD903 2.2 10.2 0.4
C16 A:JSD903 2.2 8.3 0.4
C11 A:JSD903 2.2 12.0 0.4
C20 A:JSD903 2.2 8.1 0.4
C27 A:JSE904 2.5 7.3 0.2
O67 A:JSE904 2.6 10.3 0.2
C32 A:JSE904 2.7 7.2 0.2
O28 A:JSE904 2.9 8.7 0.2
N30 A:JSE904 3.0 7.2 0.2
C24 A:JSE904 3.1 8.0 0.2
OD1 A:ASN54 3.1 11.3 0.4
C31 A:JSE904 3.1 7.8 0.2
HD21 A:ASN54 3.2 13.9 0.4
C24 A:JSD903 3.2 6.8 0.4
O38 A:JSE904 3.2 9.4 0.2
C26 A:JSE904 3.4 9.7 0.2
C25 A:JSE904 3.4 8.5 0.2
HH21 A:ARG191 3.7 30.0 0.5
O28 A:JSD903 3.7 7.7 0.4
ND2 A:ASN54 3.8 11.6 0.4
CG A:ASN54 3.8 10.1 0.4
C18 A:JSE904 3.9 8.2 0.2
C25 A:JSD903 4.0 7.3 0.4
NH2 A:ARG191 4.1 25.0 0.5
HH22 A:ARG191 4.1 30.0 0.5
HD12 A:ILE49 4.2 16.1 1.0
HD2 A:ARG191 4.2 17.1 0.5
HE22 A:GLN56 4.3 13.9 0.5
HG2 A:GLN188 4.5 16.7 0.6
C19 A:JSE904 4.5 9.2 0.2
HD2 A:ARG191 4.6 13.6 0.5
HB3 A:ASN54 4.6 10.4 0.6
HD22 A:ASN54 4.6 13.9 0.4
C34 A:JSE904 4.6 7.2 0.2
HG22 A:ILE49 4.7 15.9 1.0
C17 A:JSE904 4.7 8.3 0.2
NE2 A:GLN56 4.8 11.6 0.5
HG3 A:GLN188 4.8 7.0 0.4
HG23 A:ILE49 4.9 15.9 1.0
CZ A:ARG191 4.9 11.4 0.5
NH2 A:ARG191 4.9 15.5 0.5
HE21 A:GLN56 4.9 13.9 0.5
HD11 A:ILE49 4.9 16.1 1.0
CZ A:ARG191 4.9 18.1 0.5
CD1 A:ILE49 5.0 10.7 1.0
HH21 A:ARG191 5.0 18.6 0.5

Ruthenium binding site 4 out of 7 in 5vle

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Ruthenium binding site 4 out of 7 in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru904

b:7.9
occ:0.19
 RU A:JSE904 0.0 7.9 0.2
HH12 A:ARG191 1.3 16.0 0.5
NH1 A:ARG191 2.2 13.3 0.5
C17 A:JSE904 2.2 8.3 0.2
C11 A:JSE904 2.2 9.2 0.2
C15 A:JSE904 2.2 10.3 0.2
C12 A:JSE904 2.2 9.7 0.2
C19 A:JSE904 2.2 9.2 0.2
C20 A:JSE904 2.2 10.0 0.2
C18 A:JSE904 2.2 8.2 0.2
C14 A:JSE904 2.2 10.0 0.2
C16 A:JSE904 2.2 9.5 0.2
C13 A:JSE904 2.2 10.6 0.2
HH22 A:ARG191 2.4 18.6 0.5
HH11 A:ARG191 2.8 16.0 0.5
CZ A:ARG191 2.9 11.4 0.5
NH2 A:ARG191 3.0 15.5 0.5
C24 A:JSE904 3.2 8.0 0.2
HH21 A:ARG191 3.8 18.6 0.5
O28 A:JSE904 3.9 8.7 0.2
C25 A:JSE904 3.9 8.5 0.2
NE A:ARG191 4.2 10.6 0.5
HD21 A:ASN54 4.5 16.6 0.6
HE A:ARG191 4.5 12.7 0.5
C20 A:JSD903 4.6 8.1 0.4
HH11 A:ARG191 4.7 15.1 0.5
HE A:ARG191 4.7 21.3 0.5
NH1 A:ARG191 4.9 12.5 0.5
ND2 A:ASN54 5.0 13.8 0.6
NE A:ARG191 5.0 17.8 0.5

Ruthenium binding site 5 out of 7 in 5vle

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Ruthenium binding site 5 out of 7 in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru906

b:8.5
occ:0.23
 CG A:PCA25 2.8 14.9 0.3
CB A:PCA25 3.1 13.8 0.5
HB3 A:SER27 3.9 15.8 1.0
O A:HOH1275 4.0 14.8 0.5
O A:PCA25 4.1 17.2 0.6
CD A:PCA25 4.2 14.8 0.5
CA A:PCA25 4.2 13.3 0.6
C A:PCA25 4.3 13.8 0.5
H A:SER27 4.5 13.8 1.0
OE1 A:GLN30 4.6 18.3 1.0
N A:SER27 4.6 11.5 1.0
HA B:ASP176 4.7 11.7 1.0
N A:THR26 4.7 12.4 1.0
N A:PCA25 4.7 13.2 0.5
CB A:SER27 4.8 13.2 1.0
HB2 B:ASP176 4.8 11.7 1.0
HA A:SER27 4.8 14.5 1.0
C A:THR26 4.9 10.8 1.0
CA A:SER27 5.0 12.1 1.0
OE A:PCA25 5.0 25.5 0.7

Ruthenium binding site 6 out of 7 in 5vle

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Ruthenium binding site 6 out of 7 in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 6 of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru301

b:10.3
occ:0.87
 RU B:JSD301 0.0 10.3 0.9
C18 B:JSD301 2.1 11.0 0.9
C13 B:JSD301 2.1 17.0 0.9
C17 B:JSD301 2.1 11.0 0.9
C19 B:JSD301 2.1 11.5 0.9
C12 B:JSD301 2.1 17.0 0.9
C14 B:JSD301 2.1 15.4 0.9
C15 B:JSD301 2.2 14.4 0.9
C20 B:JSD301 2.2 12.3 0.9
C11 B:JSD301 2.2 15.2 0.9
C16 B:JSD301 2.2 11.8 0.9
C24 B:JSD301 3.2 12.5 0.9
C25 B:JSD301 3.8 13.5 0.9
HB2 B:PRO167 3.9 11.4 1.0
O28 B:JSD301 3.9 14.8 0.9
O B:HOH689 4.3 29.6 1.0
O B:HOH414 4.4 35.8 1.0
O B:HOH731 4.5 56.5 1.0
O B:HOH659 4.8 39.4 1.0
HG2 B:PRO167 4.8 11.7 1.0
CB B:PRO167 4.8 9.5 1.0
HB2 B:ASN170 4.8 9.8 1.0
O B:PRO167 4.9 7.9 1.0

Ruthenium binding site 7 out of 7 in 5vle

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Ruthenium binding site 7 out of 7 in the Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 7 of Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru302

b:12.1
occ:0.65
 RU B:JSE302 0.0 12.1 0.7
C12 B:JSE302 2.1 21.6 0.7
C11 B:JSE302 2.1 13.3 0.7
C13 B:JSE302 2.2 12.6 0.7
C17 B:JSE302 2.2 27.1 0.7
C16 B:JSE302 2.2 27.1 0.7
C15 B:JSE302 2.2 10.7 0.7
C20 B:JSE302 2.2 24.8 0.7
C14 B:JSE302 2.2 10.9 0.7
C18 B:JSE302 2.2 25.4 0.7
C19 B:JSE302 2.2 24.3 0.7
HE1 B:TYR129 4.1 8.9 1.0
HB3 B:ALA124 4.2 13.6 1.0
HB2 B:ALA124 4.5 13.6 1.0
HG21 B:ILE108 4.6 13.5 1.0
HG2 B:GLU121 4.6 12.6 1.0
CE1 B:TYR129 4.7 7.4 1.0
CB B:ALA124 4.8 9.0 1.0
HA B:GLU121 4.9 9.3 1.0
HD13 B:ILE108 4.9 15.1 1.0

Reference:

E.M.Lewandowski, K.G.Lethbridge, R.Sanishvili, J.Skiba, K.Kowalski, Y.Chen. Mechanisms of Proton Relay and Product Release By Class A Beta-Lactamase at Ultrahigh Resolution. Febs J. V. 285 87 2018.
ISSN: ISSN 1742-4658
PubMed: 29095570
DOI: 10.1111/FEBS.14315
Page generated: Thu Oct 10 13:03:29 2024

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