Atomistry » Zinc » PDB 6l72-6lj4 » 6lf4
Atomistry »
  Zinc »
    PDB 6l72-6lj4 »
      6lf4 »

Zinc in PDB 6lf4: Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem

Protein crystallography data

The structure of Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem, PDB code: 6lf4 was solved by Q.Cheng, S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.99 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.108, 96.777, 131.716, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem (pdb code 6lf4). 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 Vmb-1 Bound to Hydrolyzed Meropenem, PDB code: 6lf4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6lf4

Go back to Zinc Binding Sites List in 6lf4
Zinc binding site 1 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:30.7
occ:1.00
ND1 A:HIS80 1.8 26.0 1.0
NE2 A:HIS140 2.0 32.9 1.0
NE2 A:HIS78 2.1 29.8 1.0
O72 A:LMP303 2.4 40.5 1.0
CE1 A:HIS80 2.7 28.2 1.0
CG A:HIS80 2.9 28.5 1.0
CD2 A:HIS140 3.0 30.7 1.0
C7 A:LMP303 3.0 63.7 1.0
CE1 A:HIS140 3.0 30.5 1.0
O71 A:LMP303 3.0 60.6 1.0
CD2 A:HIS78 3.0 28.9 1.0
CE1 A:HIS78 3.1 31.2 1.0
CB A:HIS80 3.3 30.8 1.0
NE2 A:HIS80 3.9 26.1 1.0
OD1 A:ASP82 3.9 37.4 1.0
CD2 A:HIS80 3.9 25.6 1.0
ZN A:ZN302 4.0 50.8 1.0
ND1 A:HIS140 4.1 28.7 1.0
CG A:HIS140 4.1 28.5 1.0
CG A:HIS78 4.2 31.0 1.0
CB A:CYS159 4.2 34.3 1.0
ND1 A:HIS78 4.2 31.1 1.0
SG A:CYS159 4.4 40.7 1.0
C62 A:LMP303 4.4 69.7 1.0
C6 A:LMP303 4.4 73.0 1.0
OD2 A:ASP82 4.5 36.7 1.0
CG A:ASP82 4.6 34.4 1.0
CG2 A:THR141 4.7 29.2 1.0
CA A:HIS80 4.8 31.6 1.0
C61 A:LMP303 4.8 74.5 1.0
N4 A:LMP303 5.0 74.5 1.0

Zinc binding site 2 out of 8 in 6lf4

Go back to Zinc Binding Sites List in 6lf4
Zinc binding site 2 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:50.8
occ:1.00
OD2 A:ASP82 2.1 36.7 1.0
NE2 A:HIS201 2.1 35.3 1.0
O72 A:LMP303 2.3 40.5 1.0
SG A:CYS159 2.3 40.7 1.0
N4 A:LMP303 2.5 74.5 1.0
CE1 A:HIS201 3.1 34.4 1.0
CD2 A:HIS201 3.1 35.2 1.0
C7 A:LMP303 3.1 63.7 1.0
CG A:ASP82 3.2 34.4 1.0
O32 A:LMP303 3.2 66.7 1.0
C5 A:LMP303 3.4 78.9 1.0
C3 A:LMP303 3.5 75.8 1.0
CB A:CYS159 3.5 34.3 1.0
C6 A:LMP303 3.7 73.0 1.0
O A:HOH446 3.7 45.9 1.0
C31 A:LMP303 3.7 60.3 1.0
OD1 A:ASP82 3.8 37.4 1.0
ZN A:ZN301 4.0 30.7 1.0
O71 A:LMP303 4.1 60.6 1.0
C61 A:LMP303 4.2 74.5 1.0
ND1 A:HIS201 4.2 34.6 1.0
CG A:HIS201 4.2 31.7 1.0
CB A:ASP82 4.4 34.4 1.0
CE1 A:HIS78 4.6 31.2 1.0
CA A:CYS159 4.7 31.0 1.0
NE2 A:HIS140 4.7 32.9 1.0
C1 A:LMP303 4.8 80.3 1.0
NE2 A:HIS78 4.8 29.8 1.0
C2 A:LMP303 4.8 80.0 1.0
O31 A:LMP303 4.8 60.7 1.0
CE1 A:HIS140 4.9 30.5 1.0
C62 A:LMP303 5.0 69.7 1.0

Zinc binding site 3 out of 8 in 6lf4

Go back to Zinc Binding Sites List in 6lf4
Zinc binding site 3 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:34.7
occ:1.00
ND1 B:HIS80 2.0 30.8 1.0
NE2 B:HIS140 2.0 32.4 1.0
O72 B:LMP303 2.2 45.7 1.0
NE2 B:HIS78 2.2 33.0 1.0
C7 B:LMP303 2.8 59.4 1.0
O71 B:LMP303 2.9 58.9 1.0
CE1 B:HIS80 2.9 33.0 1.0
CE1 B:HIS140 2.9 34.5 1.0
CG B:HIS80 3.0 32.2 1.0
CD2 B:HIS140 3.0 31.2 1.0
CD2 B:HIS78 3.1 32.0 1.0
CE1 B:HIS78 3.2 32.9 1.0
CB B:HIS80 3.4 34.0 1.0
OD1 B:ASP82 3.8 40.9 1.0
ZN B:ZN302 3.9 54.4 1.0
NE2 B:HIS80 4.0 30.8 1.0
ND1 B:HIS140 4.1 32.1 1.0
CB B:CYS159 4.1 36.6 1.0
CD2 B:HIS80 4.1 33.6 1.0
CG B:HIS140 4.1 32.9 1.0
SG B:CYS159 4.2 43.0 1.0
CG B:HIS78 4.2 29.4 1.0
ND1 B:HIS78 4.2 30.7 1.0
C6 B:LMP303 4.3 63.4 1.0
N4 B:LMP303 4.4 59.4 1.0
OD2 B:ASP82 4.5 43.7 1.0
O31 B:LMP303 4.5 52.3 1.0
CG B:ASP82 4.5 39.1 1.0
O62 B:LMP303 4.6 72.8 1.0
C62 B:LMP303 4.6 69.0 1.0
C61 B:LMP303 4.7 71.7 1.0
CG2 B:THR141 4.7 32.2 1.0
C31 B:LMP303 4.8 52.0 1.0
CA B:HIS80 4.8 33.6 1.0
C3 B:LMP303 4.8 62.1 1.0
C5 B:LMP303 4.9 62.6 1.0

Zinc binding site 4 out of 8 in 6lf4

Go back to Zinc Binding Sites List in 6lf4
Zinc binding site 4 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:54.4
occ:1.00
N4 B:LMP303 2.0 59.4 1.0
O31 B:LMP303 2.0 52.3 1.0
NE2 B:HIS201 2.1 39.2 1.0
OD2 B:ASP82 2.1 43.7 1.0
SG B:CYS159 2.3 43.0 1.0
C3 B:LMP303 2.6 62.1 1.0
C31 B:LMP303 2.7 52.0 1.0
O72 B:LMP303 2.8 45.7 1.0
CE1 B:HIS201 3.1 39.8 1.0
CD2 B:HIS201 3.1 41.5 1.0
CG B:ASP82 3.3 39.1 1.0
C5 B:LMP303 3.3 62.6 1.0
CB B:CYS159 3.4 36.6 1.0
C7 B:LMP303 3.5 59.4 1.0
O B:HOH426 3.7 44.3 1.0
O32 B:LMP303 3.8 57.5 1.0
OD1 B:ASP82 3.8 40.9 1.0
ZN B:ZN301 3.9 34.7 1.0
C2 B:LMP303 4.1 69.6 1.0
C6 B:LMP303 4.1 63.4 1.0
ND1 B:HIS201 4.2 35.9 1.0
CG B:HIS201 4.2 36.3 1.0
O71 B:LMP303 4.3 58.9 1.0
C1 B:LMP303 4.3 66.1 1.0
NE2 B:HIS140 4.5 32.4 1.0
CA B:CYS159 4.5 33.1 1.0
CB B:ASP82 4.6 39.5 1.0
CE1 B:HIS140 4.7 34.5 1.0
C2A B:LMP303 4.8 78.9 1.0
CE1 B:HIS78 4.9 32.9 1.0
NE2 B:HIS78 4.9 33.0 1.0
C62 B:LMP303 4.9 69.0 1.0

Zinc binding site 5 out of 8 in 6lf4

Go back to Zinc Binding Sites List in 6lf4
Zinc binding site 5 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:29.2
occ:1.00
ND1 C:HIS80 2.0 23.8 1.0
NE2 C:HIS140 2.0 33.1 1.0
NE2 C:HIS78 2.0 26.7 1.0
O72 C:LMP303 2.2 42.9 1.0
O71 C:LMP303 2.7 41.5 1.0
C7 C:LMP303 2.8 47.2 1.0
CG C:HIS80 3.0 25.6 1.0
CE1 C:HIS80 3.0 27.3 1.0
CD2 C:HIS140 3.0 28.8 1.0
CD2 C:HIS78 3.0 27.4 1.0
CE1 C:HIS78 3.0 27.7 1.0
CE1 C:HIS140 3.1 31.7 1.0
CB C:HIS80 3.3 27.9 1.0
OD1 C:ASP82 3.7 32.4 1.0
SG C:CYS159 4.0 34.7 1.0
NE2 C:HIS80 4.1 25.2 1.0
CB C:CYS159 4.1 32.2 1.0
CD2 C:HIS80 4.1 23.9 1.0
ZN C:ZN302 4.1 41.6 1.0
ND1 C:HIS78 4.1 28.5 1.0
CG C:HIS140 4.1 31.4 1.0
CG C:HIS78 4.1 26.6 1.0
ND1 C:HIS140 4.1 31.7 1.0
C6 C:LMP303 4.3 52.7 1.0
OD2 C:ASP82 4.3 35.8 1.0
CG2 C:THR141 4.5 27.5 1.0
CG C:ASP82 4.5 32.6 1.0
O62 C:LMP303 4.7 63.0 1.0
CA C:HIS80 4.7 29.8 1.0
N4 C:LMP303 4.8 51.4 1.0

Zinc binding site 6 out of 8 in 6lf4

Go back to Zinc Binding Sites List in 6lf4
Zinc binding site 6 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:41.6
occ:1.00
NE2 C:HIS201 2.0 32.5 1.0
OD2 C:ASP82 2.2 35.8 1.0
N4 C:LMP303 2.2 51.4 1.0
SG C:CYS159 2.3 34.7 1.0
O32 C:LMP303 2.6 44.3 1.0
O72 C:LMP303 2.7 42.9 1.0
CE1 C:HIS201 2.9 32.6 1.0
CD2 C:HIS201 3.0 34.7 1.0
C3 C:LMP303 3.1 50.5 1.0
C31 C:LMP303 3.2 46.5 1.0
CB C:CYS159 3.3 32.2 1.0
C5 C:LMP303 3.3 52.5 1.0
CG C:ASP82 3.4 32.6 1.0
C7 C:LMP303 3.4 47.2 1.0
C6 C:LMP303 3.9 52.7 1.0
OD1 C:ASP82 4.0 32.4 1.0
O C:HOH469 4.0 43.7 1.0
ND1 C:HIS201 4.1 33.4 1.0
CG C:HIS201 4.1 35.1 1.0
ZN C:ZN301 4.1 29.2 1.0
O71 C:LMP303 4.3 41.5 1.0
O31 C:LMP303 4.3 42.3 1.0
CA C:CYS159 4.4 31.2 1.0
C2 C:LMP303 4.5 55.4 1.0
NE2 C:HIS140 4.5 33.1 1.0
C1 C:LMP303 4.5 55.8 1.0
CE1 C:HIS140 4.5 31.7 1.0
CB C:ASP82 4.6 34.5 1.0
CE1 C:HIS78 5.0 27.7 1.0

Zinc binding site 7 out of 8 in 6lf4

Go back to Zinc Binding Sites List in 6lf4
Zinc binding site 7 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:35.4
occ:1.00
ND1 D:HIS80 2.0 35.7 1.0
NE2 D:HIS140 2.0 35.2 1.0
NE2 D:HIS78 2.2 33.1 1.0
O72 D:LMP303 2.5 42.0 1.0
CE1 D:HIS80 2.9 39.2 1.0
CD2 D:HIS140 3.0 34.1 1.0
CG D:HIS80 3.0 36.7 1.0
CE1 D:HIS140 3.0 33.2 1.0
CD2 D:HIS78 3.1 35.1 1.0
CE1 D:HIS78 3.2 36.4 1.0
C7 D:LMP303 3.2 61.5 1.0
O71 D:LMP303 3.3 62.3 1.0
CB D:HIS80 3.3 33.5 1.0
ZN D:ZN302 3.8 40.6 1.0
OD1 D:ASP82 3.8 37.1 1.0
CB D:CYS159 4.0 32.2 1.0
NE2 D:HIS80 4.1 36.8 1.0
CD2 D:HIS80 4.1 38.1 1.0
CG D:HIS140 4.1 31.6 1.0
ND1 D:HIS140 4.1 34.6 1.0
SG D:CYS159 4.3 36.6 1.0
CG D:HIS78 4.3 34.4 1.0
ND1 D:HIS78 4.3 35.3 1.0
O31 D:LMP303 4.5 62.8 1.0
N4 D:LMP303 4.5 72.4 1.0
CG D:ASP82 4.6 37.5 1.0
OD2 D:ASP82 4.7 35.7 1.0
C6 D:LMP303 4.7 68.0 1.0
CA D:HIS80 4.8 33.0 1.0
CG2 D:THR141 4.8 33.4 1.0

Zinc binding site 8 out of 8 in 6lf4

Go back to Zinc Binding Sites List in 6lf4
Zinc binding site 8 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:40.6
occ:1.00
OD2 D:ASP82 2.1 35.7 1.0
NE2 D:HIS201 2.2 33.2 1.0
SG D:CYS159 2.3 36.6 1.0
N4 D:LMP303 2.8 72.4 1.0
O31 D:LMP303 3.0 62.8 1.0
CG D:ASP82 3.0 37.5 1.0
O72 D:LMP303 3.1 42.0 1.0
CE1 D:HIS201 3.1 33.8 1.0
CD2 D:HIS201 3.1 37.2 1.0
OD1 D:ASP82 3.3 37.1 1.0
CB D:CYS159 3.4 32.2 1.0
C3 D:LMP303 3.6 81.3 1.0
O D:HOH417 3.6 39.9 1.0
C31 D:LMP303 3.7 67.1 1.0
ZN D:ZN301 3.8 35.4 1.0
C5 D:LMP303 3.9 76.1 1.0
C7 D:LMP303 4.0 61.5 1.0
ND1 D:HIS201 4.2 32.9 1.0
CG D:HIS201 4.3 35.6 1.0
CB D:ASP82 4.4 37.3 1.0
CE1 D:HIS78 4.5 36.4 1.0
NE2 D:HIS140 4.6 35.2 1.0
C6 D:LMP303 4.6 68.0 1.0
CA D:CYS159 4.6 31.4 1.0
NE2 D:HIS78 4.6 33.1 1.0
CE1 D:HIS140 4.8 33.2 1.0
C2 D:LMP303 4.8 84.4 1.0
O32 D:LMP303 4.9 65.9 1.0
O71 D:LMP303 5.0 62.3 1.0

Reference:

S.Chen, Q.Cheng. Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem To Be Published.
Page generated: Wed Dec 16 12:14:59 2020

Last articles

Zn in 7NN0
Zn in 7NIO
Zn in 7LUP
Zn in 7M1Y
Zn in 7LO4
Zn in 7KWO
Zn in 7KJY
Zn in 7KCQ
Zn in 7KC2
Zn in 7KCB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy