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Zinc in PDB 1wup: Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E):
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E), PDB code: 1wup was solved by Y.Yamaguchi, Y.Yamagata, M.Goto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.213, 73.061, 80.890, 84.81, 76.10, 74.00
R / Rfree (%) 22.4 / 29.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E) (pdb code 1wup). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E), PDB code: 1wup:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1wup

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Zinc binding site 1 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)


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 Metallo-Beta-Lactamase Imp-1 Mutant (D81E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:17.8
occ:1.00
 NE2 A:HIS77 2.0 13.4 1.0
ND1 A:HIS79 2.1 17.7 1.0
NE2 A:HIS139 2.2 7.4 1.0
OXT A:ACY401 2.9 17.4 1.0
CD2 A:HIS77 2.9 12.8 1.0
CE1 A:HIS79 2.9 17.9 1.0
CE1 A:HIS77 3.0 15.7 1.0
CD2 A:HIS139 3.1 6.3 1.0
OE1 A:GLU81 3.1 16.9 1.0
CG A:HIS79 3.2 17.1 1.0
CE1 A:HIS139 3.2 8.9 1.0
CD A:GLU81 3.4 17.5 1.0
ZN A:ZN302 3.5 21.1 1.0
SG A:CYS158 3.6 9.8 1.0
CB A:HIS79 3.6 15.8 1.0
OE2 A:GLU81 3.7 16.7 1.0
CB A:CYS158 3.9 8.5 1.0
CG A:HIS77 4.1 14.1 1.0
ND1 A:HIS77 4.1 15.2 1.0
NE2 A:HIS79 4.1 16.5 1.0
C A:ACY401 4.1 18.5 1.0
CD2 A:HIS79 4.2 16.9 1.0
CG A:HIS139 4.3 7.4 1.0
CG A:GLU81 4.3 15.8 1.0
ND1 A:HIS139 4.3 9.9 1.0
OG1 A:THR140 4.7 11.4 1.0
CH3 A:ACY401 4.9 16.1 1.0
CB A:GLU81 4.9 13.1 1.0

Zinc binding site 2 out of 8 in 1wup

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Zinc binding site 2 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)


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 Metallo-Beta-Lactamase Imp-1 Mutant (D81E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:21.1
occ:1.00
 OE2 A:GLU81 2.0 16.7 1.0
SG A:CYS158 2.1 9.8 1.0
NE2 A:HIS197 2.2 7.7 1.0
OXT A:ACY401 2.2 17.4 1.0
C A:ACY401 2.5 18.5 1.0
OE1 A:GLU81 2.6 16.9 1.0
CD A:GLU81 2.6 17.5 1.0
O A:ACY401 2.9 14.0 1.0
CE1 A:HIS197 3.0 8.5 1.0
CD2 A:HIS197 3.3 8.0 1.0
CH3 A:ACY401 3.5 16.1 1.0
CB A:CYS158 3.5 8.5 1.0
ZN A:ZN301 3.5 17.8 1.0
NZ A:LYS161 3.8 14.7 1.0
NE2 A:HIS139 4.0 7.4 1.0
CG A:GLU81 4.1 15.8 1.0
ND1 A:HIS197 4.2 9.1 1.0
OG A:SER196 4.3 1.3 1.0
CE1 A:HIS139 4.3 8.9 1.0
CG A:HIS197 4.3 9.7 1.0
CE A:LYS161 4.4 12.5 1.0
CA A:CYS158 4.5 10.5 1.0
CB A:SER196 4.7 2.6 1.0
NE2 A:HIS77 4.8 13.4 1.0
CB A:GLU81 4.8 13.1 1.0
CE1 A:HIS77 4.9 15.7 1.0

Zinc binding site 3 out of 8 in 1wup

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Zinc binding site 3 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)


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 Metallo-Beta-Lactamase Imp-1 Mutant (D81E) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:23.5
occ:1.00
 NE2 B:HIS139 1.9 18.1 1.0
OE1 B:GLU81 2.1 22.6 1.0
ND1 B:HIS79 2.1 23.7 1.0
NE2 B:HIS77 2.3 11.5 1.0
OXT B:ACY402 2.5 3.7 1.0
CD2 B:HIS139 2.8 17.9 1.0
CD2 B:HIS77 3.0 9.7 1.0
CE1 B:HIS79 3.0 25.7 1.0
CE1 B:HIS139 3.0 18.8 1.0
CG B:HIS79 3.2 22.2 1.0
CD B:GLU81 3.2 23.4 1.0
CE1 B:HIS77 3.5 11.7 1.0
SG B:CYS158 3.5 14.5 1.0
CB B:HIS79 3.5 20.4 1.0
ZN B:ZN304 3.7 23.5 1.0
C B:ACY402 3.8 6.1 1.0
CB B:CYS158 3.8 16.3 1.0
OE2 B:GLU81 3.9 21.6 1.0
CG B:HIS139 4.0 18.9 1.0
ND1 B:HIS139 4.1 19.9 1.0
NE2 B:HIS79 4.2 23.4 1.0
CG B:GLU81 4.2 23.6 1.0
CG B:HIS77 4.2 10.7 1.0
CD2 B:HIS79 4.3 23.4 1.0
OG1 B:THR140 4.4 17.5 1.0
ND1 B:HIS77 4.5 10.1 1.0
CH3 B:ACY402 4.6 3.3 1.0
O B:ACY402 4.6 3.9 1.0
ND2 B:ASN167 4.7 31.9 1.0
CB B:GLU81 4.9 21.8 1.0

Zinc binding site 4 out of 8 in 1wup

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Zinc binding site 4 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)


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 Metallo-Beta-Lactamase Imp-1 Mutant (D81E) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:23.5
occ:1.00
 OE2 B:GLU81 1.8 21.6 1.0
NE2 B:HIS197 1.9 20.9 1.0
CD B:GLU81 2.4 23.4 1.0
SG B:CYS158 2.5 14.5 1.0
OXT B:ACY402 2.5 3.7 1.0
OE1 B:GLU81 2.5 22.6 1.0
C B:ACY402 2.6 6.1 1.0
CE1 B:HIS197 2.8 21.1 1.0
O B:ACY402 2.9 3.9 1.0
CD2 B:HIS197 3.0 20.0 1.0
CB B:CYS158 3.4 16.3 1.0
CH3 B:ACY402 3.5 3.3 1.0
ZN B:ZN303 3.7 23.5 1.0
OG B:SER196 3.8 7.8 1.0
CG B:GLU81 3.9 23.6 1.0
ND1 B:HIS197 3.9 20.9 1.0
CG B:HIS197 4.1 19.1 1.0
NZ B:LYS161 4.1 24.8 1.0
CB B:SER196 4.2 11.3 1.0
NE2 B:HIS139 4.3 18.1 1.0
CA B:CYS158 4.4 17.6 1.0
CB B:GLU81 4.6 21.8 1.0
CE1 B:HIS139 4.8 18.8 1.0
NE2 B:HIS77 4.8 11.5 1.0
CE B:LYS161 4.8 23.7 1.0
CD2 B:HIS139 4.9 17.9 1.0

Zinc binding site 5 out of 8 in 1wup

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Zinc binding site 5 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)


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 Metallo-Beta-Lactamase Imp-1 Mutant (D81E) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn305

b:21.1
occ:1.00
 OE1 C:GLU81 1.9 5.5 1.0
NE2 C:HIS139 1.9 22.8 1.0
ND1 C:HIS79 2.0 12.8 1.0
NE2 C:HIS77 2.2 12.5 1.0
CD2 C:HIS77 2.8 11.2 1.0
OXT C:ACY403 2.8 18.9 1.0
CD2 C:HIS139 2.9 21.8 1.0
CE1 C:HIS79 2.9 12.1 1.0
CE1 C:HIS139 3.0 24.8 1.0
CG C:HIS79 3.1 11.1 1.0
CD C:GLU81 3.1 5.4 1.0
CE1 C:HIS77 3.5 13.6 1.0
SG C:CYS158 3.5 12.5 1.0
CB C:HIS79 3.5 11.1 1.0
CB C:CYS158 3.7 12.8 1.0
ZN C:ZN306 3.7 17.0 1.0
OE2 C:GLU81 3.8 1.0 1.0
C C:ACY403 4.0 19.6 1.0
CG C:HIS139 4.0 22.1 1.0
NE2 C:HIS79 4.1 10.5 1.0
CG C:HIS77 4.1 12.0 1.0
ND1 C:HIS139 4.1 24.0 1.0
CD2 C:HIS79 4.2 10.4 1.0
CG C:GLU81 4.2 7.8 1.0
ND1 C:HIS77 4.4 12.6 1.0
OG1 C:THR140 4.4 22.6 1.0
CH3 C:ACY403 4.7 13.5 1.0
CB C:GLU81 4.8 10.4 1.0
O C:ACY403 4.9 17.9 1.0
CA C:HIS79 5.0 12.0 1.0

Zinc binding site 6 out of 8 in 1wup

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Zinc binding site 6 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)


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 Metallo-Beta-Lactamase Imp-1 Mutant (D81E) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn306

b:17.0
occ:1.00
 OE2 C:GLU81 1.8 1.0 1.0
NE2 C:HIS197 2.0 6.7 1.0
SG C:CYS158 2.2 12.5 1.0
OXT C:ACY403 2.3 18.9 1.0
CD C:GLU81 2.7 5.4 1.0
C C:ACY403 2.8 19.6 1.0
OE1 C:GLU81 2.9 5.5 1.0
CD2 C:HIS197 2.9 8.4 1.0
O C:ACY403 3.1 17.9 1.0
CE1 C:HIS197 3.2 7.5 1.0
CB C:CYS158 3.2 12.8 1.0
NZ C:LYS161 3.3 20.9 1.0
ZN C:ZN305 3.7 21.1 1.0
CH3 C:ACY403 3.9 13.5 1.0
NE2 C:HIS139 4.0 22.8 1.0
OG C:SER196 4.1 9.8 1.0
CG C:HIS197 4.1 9.6 1.0
CG C:GLU81 4.1 7.8 1.0
ND1 C:HIS197 4.2 8.0 1.0
CE1 C:HIS139 4.2 24.8 1.0
CA C:CYS158 4.2 12.6 1.0
CB C:SER196 4.3 11.4 1.0
CE C:LYS161 4.3 20.7 1.0
CD2 C:HIS139 4.8 21.8 1.0
NE2 C:HIS77 4.9 12.5 1.0

Zinc binding site 7 out of 8 in 1wup

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Zinc binding site 7 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn307

b:16.0
occ:1.00
 ND1 D:HIS79 2.0 28.7 1.0
NE2 D:HIS139 2.2 19.9 1.0
NE2 D:HIS77 2.4 20.6 1.0
CD2 D:HIS77 2.8 18.4 1.0
CE1 D:HIS79 2.8 28.5 1.0
OE1 D:GLU81 2.8 29.0 1.0
CG D:HIS79 3.0 27.5 1.0
CE1 D:HIS139 3.1 19.8 1.0
CD2 D:HIS139 3.3 16.6 1.0
OXT D:ACY404 3.4 17.9 1.0
CB D:HIS79 3.5 25.6 1.0
CD D:GLU81 3.5 27.3 1.0
ZN D:ZN308 3.5 21.7 1.0
CE1 D:HIS77 3.6 21.7 1.0
SG D:CYS158 3.7 2.8 1.0
NE2 D:HIS79 3.9 29.5 1.0
CB D:CYS158 3.9 2.9 1.0
OE2 D:GLU81 4.0 24.9 1.0
CD2 D:HIS79 4.0 27.3 1.0
CG D:HIS77 4.1 19.2 1.0
C D:ACY404 4.2 18.5 1.0
CG D:GLU81 4.2 25.3 1.0
ND1 D:HIS139 4.3 19.4 1.0
CG D:HIS139 4.4 17.4 1.0
ND1 D:HIS77 4.5 19.7 1.0
OG1 D:THR140 4.6 17.1 1.0
O D:ACY404 4.7 17.4 1.0
CA D:HIS79 4.9 22.5 1.0
CB D:GLU81 5.0 21.4 1.0

Zinc binding site 8 out of 8 in 1wup

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Zinc binding site 8 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81E) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn308

b:21.7
occ:1.00
 OE1 D:GLU81 2.1 29.0 1.0
OE2 D:GLU81 2.2 24.9 1.0
NE2 D:HIS197 2.3 7.8 1.0
SG D:CYS158 2.3 2.8 1.0
O D:ACY404 2.4 17.4 1.0
C D:ACY404 2.5 18.5 1.0
CD D:GLU81 2.5 27.3 1.0
CE1 D:HIS197 3.0 8.8 1.0
OXT D:ACY404 3.0 17.9 1.0
CH3 D:ACY404 3.0 16.6 1.0
CB D:CYS158 3.4 2.9 1.0
CD2 D:HIS197 3.4 8.3 1.0
ZN D:ZN307 3.5 16.0 1.0
NZ D:LYS161 3.6 13.3 1.0
NE2 D:HIS139 3.9 19.9 1.0
CG D:GLU81 4.0 25.3 1.0
CE1 D:HIS139 4.0 19.8 1.0
ND1 D:HIS197 4.1 8.6 1.0
CG D:HIS197 4.4 9.3 1.0
CA D:CYS158 4.5 6.5 1.0
CE D:LYS161 4.6 15.2 1.0
NE2 D:HIS77 4.6 20.6 1.0
CB D:SER196 4.7 11.5 1.0
OG D:SER196 4.8 13.7 1.0
CB D:GLU81 4.8 21.4 1.0

Reference:

Y.Yamaguchi, T.Kuroki, H.Yasuzawa, T.Higashi, W.Jin, A.Kawanami, Y.Yamagata, Y.Arakawa, M.Goto, H.Kurosaki. Probing the Role of Asp-120(81) of Metallo-Beta-Lactamase (Imp-1) By Site-Directed Mutagenesis, Kinetic Studies, and X-Ray Crystallography. J.Biol.Chem. V. 280 20824 2005.
ISSN: ISSN 0021-9258
PubMed: 15788415
DOI: 10.1074/JBC.M414314200
Page generated: Wed Oct 16 20:09:15 2024

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