Zinc in PDB 4eyb: Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin

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

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

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin, PDB code: 4eyb 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) 25.42 / 1.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.200, 79.370, 134.150, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 16.4

Zinc Binding Sites:

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

Zinc binding site 1 out of 5 in 4eyb

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


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 Oxacillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:7.6
occ:0.90
NE2 A:HIS250 2.0 7.1 1.0
NAP A:0WO303 2.1 8.6 1.0
OD2 A:ASP124 2.1 8.0 1.0
OAH A:0WO303 2.2 9.1 1.0
SG A:CYS208 2.4 7.1 1.0
O A:HOH598 2.9 10.8 1.0
CAT A:0WO303 3.0 8.9 1.0
CD2 A:HIS250 3.0 7.8 1.0
CE1 A:HIS250 3.0 7.5 1.0
CBB A:0WO303 3.0 8.8 1.0
CB A:0WO303 3.2 10.2 1.0
CG A:ASP124 3.3 7.5 1.0
CB A:CYS208 3.4 6.9 1.0
CAC A:0WO303 3.6 10.8 1.0
OD1 A:ASP124 3.8 8.2 1.0
CBC A:0WO303 3.9 8.9 1.0
ND1 A:HIS250 4.1 8.2 1.0
CG A:HIS250 4.1 8.0 1.0
OAE A:0WO303 4.2 10.7 1.0
CB A:SER249 4.2 7.9 1.0
CA A:0WO303 4.3 10.3 1.0
O A:0WO303 4.4 11.1 1.0
SAR A:0WO303 4.5 11.8 1.0
CA A:CYS208 4.5 6.6 1.0
CB A:ASP124 4.5 7.8 1.0
ZN A:ZN302 4.5 7.7 0.9
OG A:SER249 4.6 7.6 1.0
NE2 A:HIS189 4.8 7.1 1.0
CE1 A:HIS189 4.8 7.0 1.0
C A:0WO303 4.8 10.4 1.0

Zinc binding site 2 out of 5 in 4eyb

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Zinc binding site 2 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Oxacillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:7.7
occ:0.90
ND1 A:HIS122 1.9 7.9 1.0
O A:HOH598 2.0 10.8 1.0
NE2 A:HIS189 2.0 7.1 1.0
NE2 A:HIS120 2.1 8.1 1.0
O A:0WO303 2.5 11.1 1.0
CE1 A:HIS122 2.9 8.1 1.0
CG A:HIS122 3.0 7.3 1.0
CD2 A:HIS189 3.0 7.1 1.0
CE1 A:HIS189 3.0 7.0 1.0
CE1 A:HIS120 3.1 7.4 1.0
CD2 A:HIS120 3.1 8.3 1.0
CB A:HIS122 3.3 6.7 1.0
C A:0WO303 3.3 10.4 1.0
CA A:0WO303 3.9 10.3 1.0
NAP A:0WO303 4.0 8.6 1.0
NE2 A:HIS122 4.0 11.0 1.0
CD2 A:HIS122 4.1 9.1 1.0
ND1 A:HIS189 4.1 6.7 1.0
CG A:HIS189 4.2 6.0 1.0
OD1 A:ASP124 4.2 8.2 1.0
ND1 A:HIS120 4.2 7.4 1.0
OXT A:0WO303 4.2 13.2 1.0
CG A:HIS120 4.3 6.5 1.0
CG2 A:THR190 4.4 8.1 1.0
SG A:CYS208 4.4 7.1 1.0
CB A:CYS208 4.5 6.9 1.0
ZN A:ZN301 4.5 7.6 0.9
CB A:0WO303 4.6 10.2 1.0
O A:HOH449 4.7 18.7 1.0
CA A:HIS122 4.8 6.9 1.0
CBB A:0WO303 4.9 8.8 1.0

Zinc binding site 3 out of 5 in 4eyb

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Zinc binding site 3 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Oxacillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:7.7
occ:0.90
ND1 B:HIS122 1.9 8.0 1.0
O B:HOH558 2.0 12.1 1.0
NE2 B:HIS189 2.0 7.6 1.0
NE2 B:HIS120 2.1 8.1 1.0
O B:0WO301 2.5 12.1 1.0
CE1 B:HIS122 2.9 9.2 1.0
CG B:HIS122 3.0 6.9 1.0
CD2 B:HIS189 3.0 7.2 1.0
CE1 B:HIS189 3.0 6.8 1.0
CE1 B:HIS120 3.1 8.2 1.0
CD2 B:HIS120 3.1 7.2 1.0
CB B:HIS122 3.3 6.1 1.0
C B:0WO301 3.4 10.7 1.0
CA B:0WO301 3.9 9.8 1.0
NAP B:0WO301 4.0 9.8 1.0
NE2 B:HIS122 4.1 9.9 1.0
CD2 B:HIS122 4.1 9.0 1.0
ND1 B:HIS189 4.1 7.0 1.0
CG B:HIS189 4.2 6.2 1.0
OD1 B:ASP124 4.2 8.7 1.0
ND1 B:HIS120 4.2 8.2 1.0
CG B:HIS120 4.3 6.9 1.0
CG2 B:THR190 4.3 7.9 1.0
OXT B:0WO301 4.3 16.3 1.0
SG B:CYS208 4.4 7.8 1.0
CB B:CYS208 4.5 7.2 1.0
CB B:0WO301 4.5 10.9 1.0
ZN B:ZN303 4.6 8.0 0.9
O B:HOH561 4.6 18.8 1.0
CA B:HIS122 4.8 6.2 1.0
CBB B:0WO301 4.9 10.1 1.0
OD2 B:ASP124 5.0 8.6 1.0

Zinc binding site 4 out of 5 in 4eyb

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Zinc binding site 4 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Oxacillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:8.0
occ:0.90
NE2 B:HIS250 2.0 7.8 1.0
NAP B:0WO301 2.1 9.8 1.0
OAH B:0WO301 2.1 10.6 1.0
OD2 B:ASP124 2.2 8.6 1.0
SG B:CYS208 2.4 7.8 1.0
CAT B:0WO301 2.9 8.9 1.0
CD2 B:HIS250 3.0 9.3 1.0
O B:HOH558 3.0 12.1 1.0
CE1 B:HIS250 3.0 8.8 1.0
CBB B:0WO301 3.0 10.1 1.0
CB B:0WO301 3.2 10.9 1.0
CG B:ASP124 3.3 8.4 1.0
CB B:CYS208 3.4 7.2 1.0
CAC B:0WO301 3.7 11.8 1.0
OD1 B:ASP124 3.8 8.7 1.0
CBC B:0WO301 3.9 9.4 1.0
ND1 B:HIS250 4.1 9.2 1.0
CG B:HIS250 4.1 10.0 1.0
OAE B:0WO301 4.2 10.6 1.0
CB B:SER249 4.2 8.2 1.0
CA B:0WO301 4.3 9.8 1.0
O B:0WO301 4.4 12.1 1.0
CA B:CYS208 4.5 7.3 1.0
SAR B:0WO301 4.5 12.2 1.0
CB B:ASP124 4.5 7.6 1.0
ZN B:ZN302 4.6 7.7 0.9
OG B:SER249 4.6 8.7 1.0
NE2 B:HIS189 4.8 7.6 1.0
C B:0WO301 4.8 10.7 1.0
CE1 B:HIS189 4.8 6.8 1.0

Zinc binding site 5 out of 5 in 4eyb

Go back to Zinc Binding Sites List in 4eyb
Zinc binding site 5 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Oxacillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:12.5
occ:0.50
O B:HOH562 1.9 27.5 1.0
OD2 B:ASP223 2.0 14.3 1.0
OE2 B:GLU152 2.5 25.8 1.0
OE1 B:GLU152 2.6 17.4 1.0
CD B:GLU152 2.8 13.7 1.0
CG B:ASP223 2.9 13.0 1.0
OD1 B:ASP223 2.9 20.6 1.0
NE2 B:HIS122 4.0 9.9 1.0
O B:HOH413 4.0 13.4 1.0
CB B:ASP223 4.3 11.5 1.0
CG B:GLU152 4.3 10.7 1.0
O B:HOH525 4.5 33.7 1.0
CD2 B:HIS122 4.7 9.0 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: Wed Dec 16 05:16:30 2020

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