Zinc in PDB 6r79: Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)

Enzymatic activity of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)

All present enzymatic activity of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open):
3.5.2.6;

Protein crystallography data

The structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open), PDB code: 6r79 was solved by K.M.Zak, C.Softley, M.Kolonko, M.Sattler, G.M.Popowicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.55 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.762, 64.825, 86.546, 107.52, 90.99, 94.80
R / Rfree (%) 17.5 / 21.4

Other elements in 6r79:

The structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) (pdb code 6r79). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open), PDB code: 6r79:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6r79

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Zinc binding site 1 out of 8 in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn312

b:24.1
occ:1.00
 NE2 A:HIS139 2.0 18.7 1.0
ND1 A:HIS79 2.0 22.2 1.0
NE2 A:HIS77 2.1 24.1 1.0
O A:HOH562 2.1 31.6 1.0
CD2 A:HIS139 2.9 20.1 1.0
CD2 A:HIS77 3.0 21.3 1.0
CE1 A:HIS79 3.0 24.8 1.0
CG A:HIS79 3.0 21.6 1.0
CE1 A:HIS77 3.1 23.6 1.0
CE1 A:HIS139 3.1 22.2 1.0
O A:HOH585 3.3 39.0 1.0
CB A:HIS79 3.3 21.3 1.0
O A:HOH592 3.4 36.4 1.0
ZN A:ZN313 3.5 28.8 1.0
O A:HOH553 3.6 43.0 1.0
CB A:CYS158 3.9 28.0 1.0
OD1 A:ASP81 4.0 26.8 1.0
SG A:CYS158 4.0 26.3 1.0
CG A:HIS139 4.1 19.8 1.0
NE2 A:HIS79 4.1 24.0 1.0
CG A:HIS77 4.1 21.3 1.0
CD2 A:HIS79 4.1 24.0 1.0
ND1 A:HIS139 4.2 20.7 1.0
ND1 A:HIS77 4.2 21.5 1.0
O A:HOH604 4.6 45.0 1.0
OD2 A:ASP81 4.6 25.3 1.0
CG A:ASP81 4.7 23.7 1.0
CG2 A:THR140 4.7 22.1 1.0
CA A:HIS79 4.8 21.6 1.0

Zinc binding site 2 out of 8 in 6r79

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Zinc binding site 2 out of 8 in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn313

b:28.8
occ:1.00
 OD2 A:ASP81 2.1 25.3 1.0
NE2 A:HIS197 2.2 21.5 1.0
O A:HOH562 2.2 31.6 1.0
SG A:CYS158 2.2 26.3 1.0
O A:HOH553 2.5 43.0 1.0
CG A:ASP81 3.0 23.7 1.0
CD2 A:HIS197 3.1 23.9 1.0
CE1 A:HIS197 3.2 25.1 1.0
OD1 A:ASP81 3.3 26.8 1.0
CB A:CYS158 3.3 28.0 1.0
O A:HOH592 3.4 36.4 1.0
ZN A:ZN312 3.5 24.1 1.0
CE1 A:HIS77 4.1 23.6 1.0
NE2 A:HIS77 4.2 24.1 1.0
ND1 A:HIS197 4.3 24.5 1.0
CG A:HIS197 4.3 24.0 1.0
O A:HOH579 4.3 44.4 1.0
CB A:SER196 4.3 25.0 1.0
CB A:ASP81 4.4 24.2 1.0
O D:HOH1249 4.4 39.4 1.0
O A:HOH585 4.5 39.0 1.0
CA A:CYS158 4.5 24.0 1.0
CD A:LYS33 4.5 20.7 1.0
NE2 A:HIS139 4.5 18.7 1.0
CE A:LYS33 4.5 22.0 1.0
OG A:SER196 4.7 28.3 1.0
O D:GLY1101 4.9 53.1 1.0

Zinc binding site 3 out of 8 in 6r79

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Zinc binding site 3 out of 8 in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:25.7
occ:1.00
 ND1 B:HIS79 2.0 26.1 1.0
NE2 B:HIS77 2.0 28.1 1.0
NE2 B:HIS139 2.1 23.3 1.0
O C:HOH493 2.1 30.1 1.0
CD2 B:HIS139 2.9 26.6 1.0
CD2 B:HIS77 2.9 26.3 1.0
CG B:HIS79 2.9 25.5 1.0
CE1 B:HIS79 3.0 24.0 1.0
CE1 B:HIS77 3.1 28.0 1.0
CE1 B:HIS139 3.2 27.1 1.0
CB B:HIS79 3.3 25.1 1.0
O C:HOH577 3.4 39.1 1.0
O B:HOH566 3.4 33.3 1.0
ZN B:ZN304 3.6 31.8 1.0
OD1 B:ASP81 4.0 24.1 1.0
CB B:CYS158 4.0 27.3 1.0
SG B:CYS158 4.1 29.3 1.0
CD2 B:HIS79 4.1 25.2 1.0
NE2 B:HIS79 4.1 23.0 1.0
CG B:HIS77 4.1 26.6 1.0
CG B:HIS139 4.1 25.6 1.0
ND1 B:HIS77 4.2 26.0 1.0
OD1 C:ASN26 4.2 50.0 1.0
ND1 B:HIS139 4.2 24.8 1.0
CG2 B:THR140 4.7 23.8 1.0
OD2 B:ASP81 4.7 25.0 1.0
CG B:ASP81 4.7 22.4 1.0
CA B:HIS79 4.7 25.4 1.0
O B:HOH528 5.0 39.7 1.0

Zinc binding site 4 out of 8 in 6r79

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Zinc binding site 4 out of 8 in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:31.8
occ:1.00
 OD2 B:ASP81 2.0 25.0 1.0
NE2 B:HIS197 2.2 27.9 1.0
SG B:CYS158 2.2 29.3 1.0
O C:HOH493 2.3 30.1 1.0
CG B:ASP81 2.9 22.4 1.0
CD2 B:HIS197 3.1 30.3 1.0
OD1 B:ASP81 3.2 24.1 1.0
CE1 B:HIS197 3.2 29.8 1.0
CB B:CYS158 3.3 27.3 1.0
OD1 C:ASN26 3.4 50.0 1.0
O B:HOH566 3.6 33.3 1.0
ZN B:ZN303 3.6 25.7 1.0
CE1 B:HIS77 4.1 28.0 1.0
NE2 B:HIS77 4.2 28.1 1.0
CG C:ASN26 4.3 58.1 1.0
CB C:ASN26 4.3 60.9 1.0
CG B:HIS197 4.3 29.2 1.0
ND1 B:HIS197 4.3 29.6 1.0
CB B:SER196 4.3 26.4 1.0
CB B:ASP81 4.3 24.4 1.0
CA B:CYS158 4.5 27.3 1.0
CD B:LYS33 4.5 23.1 1.0
CE B:LYS33 4.5 22.8 1.0
NE2 B:HIS139 4.5 23.3 1.0
OG B:SER196 4.6 28.4 1.0
O C:HOH577 4.7 39.1 1.0

Zinc binding site 5 out of 8 in 6r79

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Zinc binding site 5 out of 8 in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn307

b:25.9
occ:1.00
 ND1 C:HIS79 2.0 26.6 1.0
NE2 C:HIS139 2.0 23.8 1.0
NE2 C:HIS77 2.1 28.4 1.0
O C:HOH507 2.2 42.1 1.0
CD2 C:HIS139 2.9 22.3 1.0
CE1 C:HIS79 2.9 25.8 1.0
CD2 C:HIS77 3.0 26.7 1.0
CG C:HIS79 3.0 25.3 1.0
CE1 C:HIS139 3.1 25.3 1.0
CE1 C:HIS77 3.2 27.6 1.0
S2 C:BME306 3.2 61.5 1.0
C2 C:BME306 3.3 55.6 1.0
CB C:HIS79 3.3 24.3 1.0
ZN C:ZN308 3.6 31.0 1.0
O1 C:BME306 3.7 63.3 1.0
CB C:CYS158 4.0 26.3 1.0
NE2 C:HIS79 4.0 23.4 1.0
OD1 C:ASP81 4.0 24.9 1.0
CD2 C:HIS79 4.1 24.5 1.0
C1 C:BME306 4.1 55.7 1.0
CG C:HIS139 4.1 23.1 1.0
SG C:CYS158 4.1 27.9 1.0
CG C:HIS77 4.2 26.6 1.0
ND1 C:HIS139 4.2 24.6 1.0
ND1 C:HIS77 4.2 25.9 1.0
O C:HOH503 4.4 40.4 1.0
CG2 C:THR140 4.6 22.8 1.0
OD2 C:ASP81 4.7 24.3 1.0
CG C:ASP81 4.8 24.6 1.0
CA C:HIS79 4.8 23.5 1.0
O C:HOH581 4.8 59.1 1.0

Zinc binding site 6 out of 8 in 6r79

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Zinc binding site 6 out of 8 in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn308

b:31.0
occ:1.00
 O C:HOH507 2.0 42.1 1.0
OD2 C:ASP81 2.0 24.3 1.0
NE2 C:HIS197 2.2 25.0 1.0
SG C:CYS158 2.2 27.9 1.0
CG C:ASP81 2.9 24.6 1.0
CD2 C:HIS197 3.1 27.8 1.0
CE1 C:HIS197 3.2 26.8 1.0
OD1 C:ASP81 3.2 24.9 1.0
CB C:CYS158 3.3 26.3 1.0
S2 C:BME306 3.3 61.5 1.0
ZN C:ZN307 3.6 25.9 1.0
O C:HOH503 3.7 40.4 1.0
C2 C:BME306 3.8 55.6 1.0
CE1 C:HIS77 4.1 27.6 1.0
NE2 C:HIS77 4.2 28.4 1.0
ND1 C:HIS197 4.3 25.3 1.0
CG C:HIS197 4.3 26.6 1.0
CB C:ASP81 4.3 24.5 1.0
CB C:SER196 4.3 27.1 1.0
CA C:CYS158 4.5 26.3 1.0
CD C:LYS33 4.5 23.2 1.0
CE C:LYS33 4.5 23.9 1.0
NE2 C:HIS139 4.6 23.8 1.0
OG C:SER196 4.6 26.2 1.0

Zinc binding site 7 out of 8 in 6r79

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Zinc binding site 7 out of 8 in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1107

b:24.6
occ:1.00
 O D:HOH1341 1.9 32.3 1.0
ND1 D:HIS79 1.9 23.9 1.0
NE2 D:HIS139 2.0 22.5 1.0
NE2 D:HIS77 2.1 22.8 1.0
CD2 D:HIS139 2.9 21.9 1.0
CE1 D:HIS79 2.9 24.8 1.0
CG D:HIS79 2.9 23.5 1.0
CD2 D:HIS77 3.0 24.5 1.0
O D:HOH1376 3.1 40.2 1.0
CE1 D:HIS139 3.2 24.7 1.0
CE1 D:HIS77 3.2 25.3 1.0
CB D:HIS79 3.3 23.7 1.0
O D:HOH1390 3.6 51.7 1.0
ZN D:ZN1108 3.6 29.5 1.0
O A:HOH539 3.8 51.1 1.0
CB D:CYS158 4.0 24.6 1.0
OD1 D:ASP81 4.0 26.4 1.0
NE2 D:HIS79 4.0 22.6 1.0
CD2 D:HIS79 4.0 25.1 1.0
SG D:CYS158 4.1 28.4 1.0
O A:HOH518 4.1 36.0 1.0
CG D:HIS139 4.1 21.2 1.0
CG D:HIS77 4.2 23.3 1.0
ND1 D:HIS139 4.2 21.9 1.0
ND1 D:HIS77 4.2 24.5 1.0
OD2 D:ASP81 4.7 26.6 1.0
CG2 D:THR140 4.7 22.4 1.0
CG D:ASP81 4.7 24.3 1.0
CA D:HIS79 4.7 24.6 1.0

Zinc binding site 8 out of 8 in 6r79

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Zinc binding site 8 out of 8 in the Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Open) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1108

b:29.5
occ:1.00
 OD2 D:ASP81 2.0 26.6 1.0
O D:HOH1341 2.2 32.3 1.0
NE2 D:HIS197 2.2 23.0 1.0
SG D:CYS158 2.2 28.4 1.0
CG D:ASP81 2.9 24.3 1.0
O A:HOH518 3.0 36.0 1.0
CD2 D:HIS197 3.1 24.8 1.0
O A:HOH539 3.1 51.1 1.0
CE1 D:HIS197 3.2 24.3 1.0
OD1 D:ASP81 3.2 26.4 1.0
CB D:CYS158 3.3 24.6 1.0
O D:HOH1376 3.5 40.2 1.0
ZN D:ZN1107 3.6 24.6 1.0
CE1 D:HIS77 4.1 25.3 1.0
NE2 D:HIS77 4.2 22.8 1.0
CG D:HIS197 4.3 24.3 1.0
ND1 D:HIS197 4.3 24.3 1.0
CB D:SER196 4.3 24.6 1.0
CB D:ASP81 4.3 23.7 1.0
OXT A:GLY311 4.3 64.8 1.0
CD D:LYS33 4.5 20.6 1.0
CA D:CYS158 4.5 22.7 1.0
CE D:LYS33 4.5 21.1 1.0
NE2 D:HIS139 4.6 22.5 1.0
OG D:SER196 4.6 26.2 1.0
O D:HOH1390 4.8 51.7 1.0

Reference:

C.Softley, K.M.Zak, R.Fino, M.Kolonko, R.Mejdi-Nitiu, H.Meyer, M.Sattler, G.M.Popowicz. Structure and Molecular Recognition Mechanism of Imp-13 B-Lactamase To Be Published.
Page generated: Wed Dec 16 12:36:26 2020

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