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Zinc in PDB 4eyf: Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin

Enzymatic activity of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin

All present enzymatic activity of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin, PDB code: 4eyf was solved by N.C.J.Strynadka, D.T.King, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.70 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.030, 79.490, 134.210, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin (pdb code 4eyf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin, PDB code: 4eyf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4eyf

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Zinc binding site 1 out of 6 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:6.4
occ:1.00
 ND1 A:HIS122 2.0 2.6 1.0
O A:HOH401 2.0 6.4 1.0
NE2 A:HIS189 2.0 6.5 1.0
NE2 A:HIS120 2.2 7.7 1.0
O4 A:PNK301 2.5 8.8 1.0
CE1 A:HIS122 2.9 9.5 1.0
CD2 A:HIS189 2.9 5.7 1.0
CG A:HIS122 3.0 5.8 1.0
CE1 A:HIS189 3.0 7.4 1.0
CE1 A:HIS120 3.1 5.0 1.0
CD2 A:HIS120 3.2 6.6 1.0
C2 A:PNK301 3.2 11.7 1.0
CB A:HIS122 3.4 5.0 1.0
C1 A:PNK301 3.8 7.5 1.0
NE2 A:HIS122 4.0 4.3 1.0
O3 A:PNK301 4.1 10.3 1.0
N1 A:PNK301 4.1 4.8 1.0
ND1 A:HIS189 4.1 6.9 1.0
CG A:HIS189 4.1 5.1 1.0
CD2 A:HIS122 4.1 7.2 1.0
CG2 A:THR190 4.2 5.5 1.0
ND1 A:HIS120 4.2 3.8 1.0
OD1 A:ASP124 4.3 5.0 1.0
CG A:HIS120 4.3 4.8 1.0
SG A:CYS208 4.4 6.0 1.0
CB A:CYS208 4.4 2.1 1.0
C4 A:PNK301 4.6 8.1 1.0
ZN A:ZN303 4.6 5.8 1.0
O A:HOH491 4.8 9.8 1.0
CA A:HIS122 4.9 4.2 1.0
C5 A:PNK301 4.9 7.3 1.0

Zinc binding site 2 out of 6 in 4eyf

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Zinc binding site 2 out of 6 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:5.8
occ:1.00
 NE2 A:HIS250 2.0 4.0 1.0
OD2 A:ASP124 2.1 4.8 1.0
O2 A:PNK301 2.2 4.1 1.0
N1 A:PNK301 2.2 4.8 1.0
SG A:CYS208 2.4 6.0 1.0
C9 A:PNK301 3.0 4.3 1.0
CE1 A:HIS250 3.0 6.2 1.0
C5 A:PNK301 3.0 7.3 1.0
CD2 A:HIS250 3.0 7.0 1.0
O A:HOH401 3.1 6.4 1.0
C4 A:PNK301 3.3 8.1 1.0
CG A:ASP124 3.3 4.3 1.0
CB A:CYS208 3.5 2.1 1.0
C13 A:PNK301 3.6 8.7 1.0
OD1 A:ASP124 3.8 5.0 1.0
C6 A:PNK301 3.8 7.5 1.0
ND1 A:HIS250 4.1 4.9 1.0
CB A:SER249 4.1 5.2 1.0
CG A:HIS250 4.2 7.1 1.0
O1 A:PNK301 4.2 8.4 1.0
C1 A:PNK301 4.2 7.5 1.0
O4 A:PNK301 4.4 8.8 1.0
CA A:CYS208 4.5 4.1 1.0
S1 A:PNK301 4.5 9.3 1.0
CB A:ASP124 4.5 4.3 1.0
OG A:SER249 4.6 4.2 1.0
ZN A:ZN302 4.6 6.4 1.0
C2 A:PNK301 4.8 11.7 1.0
CE1 A:HIS189 4.9 7.4 1.0
NE2 A:HIS189 4.9 6.5 1.0

Zinc binding site 3 out of 6 in 4eyf

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Zinc binding site 3 out of 6 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:38.6
occ:0.80
 OE2 A:GLU152 2.2 21.5 1.0
OD2 A:ASP223 2.3 14.7 1.0
O A:HOH475 2.5 25.4 1.0
OE1 A:GLU152 2.8 19.4 1.0
CD A:GLU152 2.8 22.2 1.0
CG A:ASP223 3.0 17.2 1.0
OD1 A:ASP223 3.1 23.7 1.0
NE2 A:HIS122 4.0 4.3 1.0
O A:HOH406 4.3 10.6 1.0
CG A:GLU152 4.3 13.5 1.0
CB A:ASP223 4.5 13.1 1.0
O A:HOH492 4.5 21.6 1.0
CD2 A:HIS122 4.6 7.2 1.0
O A:HOH535 4.9 18.8 1.0

Zinc binding site 4 out of 6 in 4eyf

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Zinc binding site 4 out of 6 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:6.2
occ:1.00
 NE2 B:HIS250 2.0 4.3 1.0
OD2 B:ASP124 2.1 6.7 1.0
O1 B:PNK301 2.1 6.4 1.0
N1 B:PNK301 2.2 4.6 1.0
SG B:CYS208 2.3 6.3 1.0
CD2 B:HIS250 2.9 7.6 1.0
C9 B:PNK301 3.0 5.7 1.0
CE1 B:HIS250 3.0 4.8 1.0
C5 B:PNK301 3.0 3.4 1.0
O B:HOH401 3.1 4.6 1.0
CG B:ASP124 3.3 3.4 1.0
C4 B:PNK301 3.3 7.3 1.0
CB B:CYS208 3.4 6.3 1.0
C13 B:PNK301 3.5 10.9 1.0
OD1 B:ASP124 3.8 4.6 1.0
C6 B:PNK301 3.8 7.2 1.0
CG B:HIS250 4.1 5.6 1.0
ND1 B:HIS250 4.1 6.7 1.0
CB B:SER249 4.1 4.7 1.0
O2 B:PNK301 4.2 7.9 1.0
C1 B:PNK301 4.3 4.5 1.0
O3 B:PNK301 4.4 10.2 1.0
CA B:CYS208 4.5 5.1 1.0
CB B:ASP124 4.5 4.2 1.0
S1 B:PNK301 4.5 9.8 1.0
OG B:SER249 4.5 3.2 1.0
ZN B:ZN303 4.6 6.0 1.0
CE1 B:HIS189 4.8 5.8 1.0
NE2 B:HIS189 4.8 5.2 1.0
C2 B:PNK301 4.8 8.8 1.0

Zinc binding site 5 out of 6 in 4eyf

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Zinc binding site 5 out of 6 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:6.0
occ:1.00
 O B:HOH401 1.9 4.6 1.0
ND1 B:HIS122 2.0 2.0 1.0
NE2 B:HIS189 2.0 5.2 1.0
NE2 B:HIS120 2.2 3.7 1.0
O3 B:PNK301 2.4 10.2 1.0
CE1 B:HIS122 3.0 5.5 1.0
CD2 B:HIS189 3.0 3.8 1.0
CG B:HIS122 3.0 3.4 1.0
CE1 B:HIS189 3.1 5.8 1.0
CD2 B:HIS120 3.1 5.1 1.0
CE1 B:HIS120 3.1 5.2 1.0
C2 B:PNK301 3.3 8.8 1.0
CB B:HIS122 3.4 6.0 1.0
C1 B:PNK301 3.8 4.5 1.0
N1 B:PNK301 4.0 4.6 1.0
NE2 B:HIS122 4.1 4.9 1.0
CD2 B:HIS122 4.1 5.2 1.0
CG B:HIS189 4.1 5.3 1.0
ND1 B:HIS189 4.2 3.5 1.0
O4 B:PNK301 4.2 8.3 1.0
OD1 B:ASP124 4.2 4.6 1.0
CG2 B:THR190 4.3 4.1 1.0
ND1 B:HIS120 4.3 7.0 1.0
CG B:HIS120 4.3 7.0 1.0
SG B:CYS208 4.4 6.3 1.0
CB B:CYS208 4.5 6.3 1.0
C4 B:PNK301 4.5 7.3 1.0
ZN B:ZN302 4.6 6.2 1.0
CA B:HIS122 4.8 4.4 1.0
C5 B:PNK301 4.9 3.4 1.0
O B:HOH427 4.9 10.4 1.0
OD2 B:ASP124 5.0 6.7 1.0
N2 B:PNK301 5.0 9.5 1.0

Zinc binding site 6 out of 6 in 4eyf

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Zinc binding site 6 out of 6 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Benzylpenicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:11.7
occ:0.80
 O B:HOH488 1.9 18.0 1.0
OD2 B:ASP223 2.1 8.5 1.0
OE2 B:GLU152 2.1 13.3 1.0
OE1 B:GLU152 2.7 7.8 1.0
CD B:GLU152 2.7 9.8 1.0
CG B:ASP223 2.8 8.2 1.0
OD1 B:ASP223 2.9 11.3 1.0
O B:HOH412 4.0 7.7 1.0
NE2 B:HIS122 4.1 4.9 1.0
CG B:GLU152 4.2 5.0 1.0
CB B:ASP223 4.3 5.5 1.0
O B:HOH491 4.3 13.5 1.0
O B:HOH433 4.5 16.7 1.0
CD2 B:HIS122 4.8 5.2 1.0

Reference:

D.T.King, L.J.Worrall, R.Gruninger, N.C.Strynadka. New Delhi Metallo-Beta-Lactamase: Structural Insights Into Beta-Lactam Recognition and Inhibition J.Am.Chem.Soc. V. 134 11362 2012.
ISSN: ISSN 0002-7863
PubMed: 22713171
DOI: 10.1021/JA303579D
Page generated: Sat Oct 26 22:09:57 2024

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