Atomistry » Zinc » PDB 6r55-6rda » 6r79
Atomistry »
  Zinc »
    PDB 6r55-6rda »
      6r79 »

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

Go back to Zinc Binding Sites List in 6r79
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

Go back to Zinc Binding Sites List in 6r79
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

Go back to Zinc Binding Sites List in 6r79
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

Go back to Zinc Binding Sites List in 6r79
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

Go back to Zinc Binding Sites List in 6r79
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

Go back to Zinc Binding Sites List in 6r79
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

Go back to Zinc Binding Sites List in 6r79
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

Go back to Zinc Binding Sites List in 6r79
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: Tue Oct 29 06:06:01 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy