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

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Zinc binding site 1 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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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

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Zinc binding site 2 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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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

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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

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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

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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

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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

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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

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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

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