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Zinc in PDB 3spu: Apo Ndm-1 Crystal Structure

Enzymatic activity of Apo Ndm-1 Crystal Structure

All present enzymatic activity of Apo Ndm-1 Crystal Structure:
3.5.2.6;

Protein crystallography data

The structure of Apo Ndm-1 Crystal Structure, PDB code: 3spu 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) 43.67 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.536, 73.904, 77.407, 70.32, 75.86, 65.30
R / Rfree (%) 21.6 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Apo Ndm-1 Crystal Structure (pdb code 3spu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Apo Ndm-1 Crystal Structure, PDB code: 3spu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3spu

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Zinc binding site 1 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:24.1
occ:1.00
 ND1 A:HIS122 1.8 14.3 1.0
NE2 A:HIS120 2.0 16.7 1.0
NE2 A:HIS189 2.0 24.6 1.0
CE1 A:HIS122 2.8 20.1 1.0
CG A:HIS122 2.9 18.4 1.0
CE1 A:HIS120 2.9 17.4 1.0
CD2 A:HIS189 2.9 22.8 1.0
CD2 A:HIS120 3.0 17.1 1.0
CE1 A:HIS189 3.1 22.7 1.0
CB A:HIS122 3.3 17.7 1.0
ZN A:ZN302 3.8 32.6 1.0
NE2 A:HIS122 3.9 18.8 1.0
CD2 A:HIS122 4.0 16.3 1.0
ND1 A:HIS120 4.0 18.2 1.0
CG A:HIS120 4.1 17.1 1.0
OD2 A:ASP124 4.1 26.2 1.0
CG A:HIS189 4.1 21.4 1.0
ND1 A:HIS189 4.2 21.4 1.0
O A:HOH483 4.2 24.7 1.0
SG A:CYS208 4.2 27.1 1.0
CB A:CYS208 4.4 23.4 1.0
OD1 A:ASP124 4.7 27.3 1.0
CA A:HIS122 4.8 18.0 1.0
CG A:ASP124 4.9 22.9 1.0
O A:HOH423 4.9 15.8 1.0

Zinc binding site 2 out of 10 in 3spu

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Zinc binding site 2 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:32.6
occ:1.00
 NE2 A:HIS250 2.2 24.9 1.0
OD1 A:ASP124 2.3 27.3 1.0
SG A:CYS208 2.3 27.1 1.0
O A:HOH483 2.5 24.7 1.0
CD2 A:HIS250 3.1 24.8 1.0
CE1 A:HIS250 3.2 26.2 1.0
CB A:CYS208 3.3 23.4 1.0
CG A:ASP124 3.4 22.9 1.0
OD2 A:ASP124 3.7 26.2 1.0
ZN A:ZN301 3.8 24.1 1.0
CB A:SER249 4.2 26.4 1.0
ND1 A:HIS250 4.3 25.5 1.0
CG A:HIS250 4.3 27.1 1.0
NE2 A:HIS189 4.3 24.6 1.0
CE1 A:HIS189 4.4 22.7 1.0
CA A:CYS208 4.6 23.4 1.0
CE1 A:HIS120 4.6 17.4 1.0
CB A:ASP124 4.6 20.5 1.0
OG A:SER249 4.7 26.3 1.0
NE2 A:HIS120 4.7 16.7 1.0

Zinc binding site 3 out of 10 in 3spu

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Zinc binding site 3 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:25.1
occ:1.00
 ND1 B:HIS122 1.8 14.1 1.0
O B:HOH404 1.9 22.0 1.0
NE2 B:HIS120 2.1 18.1 1.0
NE2 B:HIS189 2.2 24.4 1.0
CE1 B:HIS122 2.8 19.8 1.0
CG B:HIS122 2.8 18.0 1.0
CE1 B:HIS120 3.0 17.5 1.0
CD2 B:HIS120 3.1 17.4 1.0
CD2 B:HIS189 3.1 22.3 1.0
CB B:HIS122 3.2 18.2 1.0
CE1 B:HIS189 3.2 22.6 1.0
OD2 B:ASP124 3.9 25.9 1.0
NE2 B:HIS122 3.9 18.9 1.0
ZN B:ZN302 3.9 34.2 1.0
CD2 B:HIS122 3.9 16.3 1.0
ND1 B:HIS120 4.1 17.9 1.0
CG B:HIS120 4.2 17.3 1.0
SG B:CYS208 4.2 27.3 1.0
CD2 A:LEU272 4.2 31.0 1.0
ND1 B:HIS189 4.3 20.7 1.0
CG B:HIS189 4.3 21.3 1.0
O B:HOH481 4.3 24.6 1.0
CB B:CYS208 4.5 23.5 1.0
CA B:HIS122 4.6 17.6 1.0
OD1 B:ASP124 4.7 27.4 1.0
CG B:ASP124 4.7 22.9 1.0

Zinc binding site 4 out of 10 in 3spu

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Zinc binding site 4 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

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

b:34.2
occ:1.00
 OD1 B:ASP124 2.1 27.4 1.0
NE2 B:HIS250 2.1 25.1 1.0
SG B:CYS208 2.4 27.3 1.0
O B:HOH404 2.6 22.0 1.0
O B:HOH481 2.7 24.6 1.0
CE1 B:HIS250 3.0 26.6 1.0
CG B:ASP124 3.1 22.9 1.0
CD2 B:HIS250 3.1 25.2 1.0
OD2 B:ASP124 3.4 25.9 1.0
CB B:CYS208 3.4 23.5 1.0
ZN B:ZN301 3.9 25.1 1.0
ND1 B:HIS250 4.1 24.8 1.0
CB B:SER249 4.2 26.3 1.0
CG B:HIS250 4.2 27.3 1.0
CB B:ASP124 4.4 20.9 1.0
NE2 B:HIS189 4.4 24.4 1.0
OG B:SER249 4.5 26.0 1.0
CE1 B:HIS189 4.6 22.6 1.0
CE1 B:HIS120 4.7 17.5 1.0
CA B:CYS208 4.7 23.7 1.0
NE2 B:HIS120 4.8 18.1 1.0

Zinc binding site 5 out of 10 in 3spu

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Zinc binding site 5 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:25.0
occ:1.00
 ND1 C:HIS122 1.8 14.2 1.0
NE2 C:HIS120 1.9 17.6 1.0
O C:HOH448 2.1 22.8 1.0
NE2 C:HIS189 2.1 24.5 1.0
CE1 C:HIS122 2.7 20.0 1.0
CG C:HIS122 2.9 18.4 1.0
CE1 C:HIS120 2.9 17.6 1.0
CD2 C:HIS120 2.9 17.8 1.0
CD2 C:HIS189 3.0 22.2 1.0
CE1 C:HIS189 3.2 22.2 1.0
CB C:HIS122 3.3 17.9 1.0
NE2 C:HIS122 3.9 19.2 1.0
CD2 C:HIS122 3.9 16.6 1.0
ZN C:ZN302 4.0 30.5 1.0
ND1 C:HIS120 4.0 19.4 1.0
OD2 C:ASP124 4.0 25.6 1.0
CG C:HIS120 4.1 17.3 1.0
SG C:CYS208 4.1 27.2 1.0
CG C:HIS189 4.2 21.2 1.0
ND1 C:HIS189 4.2 21.1 1.0
O C:HOH491 4.3 23.5 1.0
CB C:CYS208 4.4 23.7 1.0
OD1 C:ASP124 4.7 27.1 1.0
CA C:HIS122 4.7 17.9 1.0
CG C:ASP124 4.8 23.3 1.0

Zinc binding site 6 out of 10 in 3spu

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Zinc binding site 6 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:30.5
occ:1.00
 NE2 C:HIS250 2.1 25.1 1.0
OD1 C:ASP124 2.1 27.1 1.0
O C:HOH448 2.2 22.8 1.0
SG C:CYS208 2.4 27.2 1.0
O C:HOH491 2.6 23.5 1.0
CE1 C:HIS250 3.0 26.4 1.0
CD2 C:HIS250 3.1 24.6 1.0
CG C:ASP124 3.2 23.3 1.0
CB C:CYS208 3.4 23.7 1.0
OD2 C:ASP124 3.6 25.6 1.0
ZN C:ZN301 4.0 25.0 1.0
ND1 C:HIS250 4.1 25.2 1.0
CG C:HIS250 4.2 26.9 1.0
CB C:SER249 4.2 26.3 1.0
NE2 C:HIS189 4.4 24.5 1.0
CB C:ASP124 4.5 20.5 1.0
CE1 C:HIS189 4.6 22.2 1.0
OG C:SER249 4.6 26.8 1.0
CE1 C:HIS120 4.7 17.6 1.0
CA C:CYS208 4.7 23.4 1.0
NE2 C:HIS120 4.8 17.6 1.0

Zinc binding site 7 out of 10 in 3spu

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Zinc binding site 7 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:24.2
occ:1.00
 ND1 D:HIS122 1.9 13.8 1.0
NE2 D:HIS189 2.0 24.7 1.0
NE2 D:HIS120 2.1 17.4 1.0
O D:HOH403 2.1 16.9 1.0
CE1 D:HIS122 2.8 20.4 1.0
CG D:HIS122 2.9 18.0 1.0
CD2 D:HIS189 2.9 22.2 1.0
CE1 D:HIS120 3.0 17.3 1.0
CE1 D:HIS189 3.0 22.1 1.0
CD2 D:HIS120 3.1 17.2 1.0
CB D:HIS122 3.3 17.8 1.0
ZN D:ZN302 3.8 33.8 1.0
NE2 D:HIS122 4.0 18.7 1.0
CD2 D:HIS122 4.0 16.6 1.0
ND1 D:HIS120 4.1 19.0 1.0
OD2 D:ASP124 4.1 26.4 1.0
SG D:CYS208 4.1 26.9 1.0
CG D:HIS189 4.1 20.9 1.0
ND1 D:HIS189 4.1 20.6 1.0
CG D:HIS120 4.2 17.2 1.0
CB D:CYS208 4.3 23.6 1.0
OD1 D:ASP124 4.8 26.4 1.0
CA D:HIS122 4.8 17.9 1.0
CG D:ASP124 4.9 23.0 1.0

Zinc binding site 8 out of 10 in 3spu

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Zinc binding site 8 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:33.8
occ:1.00
 NE2 D:HIS250 2.1 25.8 1.0
OD1 D:ASP124 2.2 26.4 1.0
SG D:CYS208 2.3 26.9 1.0
O D:HOH403 2.4 16.9 1.0
CE1 D:HIS250 3.1 26.2 1.0
CD2 D:HIS250 3.1 25.3 1.0
CG D:ASP124 3.2 23.0 1.0
CB D:CYS208 3.3 23.6 1.0
OD2 D:ASP124 3.6 26.4 1.0
O D:HOH485 3.6 26.7 1.0
ZN D:ZN301 3.8 24.2 1.0
CB D:SER249 4.1 26.2 1.0
ND1 D:HIS250 4.2 25.1 1.0
CG D:HIS250 4.2 27.0 1.0
NE2 D:HIS189 4.4 24.7 1.0
CB D:ASP124 4.5 20.6 1.0
OG D:SER249 4.5 26.3 1.0
CA D:CYS208 4.5 23.7 1.0
CE1 D:HIS189 4.5 22.1 1.0
CE1 D:HIS120 4.6 17.3 1.0
NE2 D:HIS120 4.8 17.4 1.0

Zinc binding site 9 out of 10 in 3spu

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Zinc binding site 9 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:33.2
occ:1.00
 O E:HOH1125 2.0 44.3 1.0
NE2 E:HIS189 2.0 24.6 1.0
ND1 E:HIS122 2.0 14.9 1.0
NE2 E:HIS120 2.1 18.6 1.0
CE1 E:HIS120 2.9 18.7 1.0
CD2 E:HIS189 3.0 23.2 1.0
CE1 E:HIS122 3.0 20.9 1.0
CE1 E:HIS189 3.0 23.1 1.0
CG E:HIS122 3.1 18.6 1.0
CD2 E:HIS120 3.2 18.5 1.0
CB E:HIS122 3.4 18.3 1.0
ZN E:ZN1002 3.6 37.5 1.0
SG E:CYS208 4.0 28.4 1.0
ND1 E:HIS120 4.0 19.4 1.0
OD2 E:ASP124 4.1 26.0 1.0
ND1 E:HIS189 4.1 21.9 1.0
CG E:HIS189 4.1 21.5 1.0
NE2 E:HIS122 4.1 19.4 1.0
CD2 E:HIS122 4.2 16.5 1.0
CB E:CYS208 4.2 23.7 1.0
CG E:HIS120 4.2 17.4 1.0
OD1 E:ASP124 4.6 27.4 1.0
CG E:ASP124 4.8 22.8 1.0
CA E:HIS122 4.9 18.3 1.0

Zinc binding site 10 out of 10 in 3spu

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Zinc binding site 10 out of 10 in the Apo Ndm-1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Apo Ndm-1 Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:37.5
occ:1.00
 OD1 E:ASP124 2.0 27.4 1.0
O E:HOH1125 2.1 44.3 1.0
SG E:CYS208 2.3 28.4 1.0
NE2 E:HIS250 2.4 25.0 1.0
CG E:ASP124 3.0 22.8 1.0
CE1 E:HIS250 3.2 25.9 1.0
CD2 E:HIS250 3.4 24.4 1.0
CB E:CYS208 3.4 23.7 1.0
OD2 E:ASP124 3.4 26.0 1.0
ZN E:ZN1001 3.6 33.2 1.0
CB E:SER249 4.0 26.6 1.0
OG E:SER249 4.3 26.8 1.0
CB E:ASP124 4.3 21.0 1.0
CE1 E:HIS120 4.3 18.7 1.0
ND1 E:HIS250 4.4 26.1 1.0
CG E:HIS250 4.4 27.2 1.0
NE2 E:HIS189 4.5 24.6 1.0
NE2 E:HIS120 4.5 18.6 1.0
CA E:CYS208 4.6 23.8 1.0
CE1 E:HIS189 4.7 23.1 1.0
CE E:LYS125 4.8 24.3 1.0
CG E:LYS125 4.8 21.0 1.0
CD E:LYS125 4.9 22.5 1.0

Reference:

D.King, N.Strynadka. Crystal Structure of New Delhi Metallo-Beta-Lactamase Reveals Molecular Basis For Antibiotic Resistance Protein Sci. V. 20 1484 2011.
ISSN: ISSN 0961-8368
PubMed: 21774017
DOI: 10.1002/PRO.697
Page generated: Wed Dec 16 04:50:46 2020

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