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Zinc in PDB 6lfd: Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)

Protein crystallography data

The structure of Crystal Structure of Vmb-1 at PH5.5(Bis-Tris), PDB code: 6lfd 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) 38.69 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.110, 97.110, 132.660, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris) (pdb code 6lfd). 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 at PH5.5(Bis-Tris), PDB code: 6lfd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6lfd

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Zinc binding site 1 out of 8 in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)


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 at PH5.5(Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:28.0
occ:1.00
ND1 A:HIS80 1.9 24.4 1.0
NE2 A:HIS140 2.0 28.5 1.0
NE2 A:HIS78 2.1 26.0 1.0
O A:HOH477 2.2 22.2 1.0
CE1 A:HIS80 2.9 26.0 1.0
CG A:HIS80 2.9 27.1 1.0
CD2 A:HIS78 3.0 27.1 1.0
CE1 A:HIS140 3.0 27.0 1.0
CD2 A:HIS140 3.0 27.7 1.0
CE1 A:HIS78 3.2 28.5 1.0
CB A:HIS80 3.3 26.8 1.0
ZN A:ZN302 3.7 32.2 1.0
OD1 A:ASP82 3.9 30.1 1.0
NE2 A:HIS80 4.0 25.0 1.0
CD2 A:HIS80 4.0 25.4 1.0
CB A:CYS159 4.1 28.2 1.0
ND1 A:HIS140 4.1 26.6 1.0
CG A:HIS140 4.1 27.5 1.0
CG A:HIS78 4.2 26.6 1.0
ND1 A:HIS78 4.2 27.0 1.0
SG A:CYS159 4.4 31.0 1.0
OD2 A:ASP82 4.5 30.9 1.0
CG A:ASP82 4.6 30.3 1.0
CA A:HIS80 4.8 28.8 1.0
CG2 A:THR141 4.8 27.8 1.0
O A:HOH490 4.9 43.0 1.0

Zinc binding site 2 out of 8 in 6lfd

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Zinc binding site 2 out of 8 in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)


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 at PH5.5(Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:32.2
occ:1.00
OD2 A:ASP82 2.0 30.9 1.0
NE2 A:HIS201 2.1 31.1 1.0
O A:HOH477 2.2 22.2 1.0
SG A:CYS159 2.3 31.0 1.0
CG A:ASP82 3.0 30.3 1.0
CE1 A:HIS201 3.0 30.7 1.0
CD2 A:HIS201 3.2 32.4 1.0
CB A:CYS159 3.4 28.2 1.0
OD1 A:ASP82 3.4 30.1 1.0
O A:HOH460 3.6 31.5 1.0
ZN A:ZN301 3.7 28.0 1.0
ND1 A:HIS201 4.2 32.5 1.0
CE1 A:HIS78 4.2 28.5 1.0
CG A:HIS201 4.2 29.6 1.0
CB A:ASP82 4.3 32.4 1.0
NE2 A:HIS78 4.3 26.0 1.0
NE2 A:HIS140 4.5 28.5 1.0
CA A:CYS159 4.7 27.6 1.0
O A:HOH447 4.8 40.1 1.0
O A:HOH490 5.0 43.0 1.0
CE1 A:HIS140 5.0 27.0 1.0

Zinc binding site 3 out of 8 in 6lfd

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Zinc binding site 3 out of 8 in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)


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 at PH5.5(Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:26.0
occ:1.00
ND1 B:HIS80 2.0 24.7 1.0
NE2 B:HIS140 2.1 24.8 1.0
NE2 B:HIS78 2.1 24.1 1.0
O B:HOH501 2.2 19.6 1.0
CE1 B:HIS80 3.0 23.9 1.0
CG B:HIS80 3.0 26.2 1.0
CE1 B:HIS140 3.0 24.9 1.0
CD2 B:HIS78 3.1 25.3 1.0
CD2 B:HIS140 3.1 24.7 1.0
CE1 B:HIS78 3.1 25.9 1.0
CB B:HIS80 3.4 27.3 1.0
ZN B:ZN302 3.6 32.9 1.0
OD1 B:ASP82 3.7 28.8 1.0
CB B:CYS159 4.0 28.3 1.0
NE2 B:HIS80 4.1 25.6 1.0
ND1 B:HIS140 4.2 25.1 1.0
CD2 B:HIS80 4.2 26.1 1.0
CG B:HIS140 4.2 24.7 1.0
ND1 B:HIS78 4.2 26.1 1.0
CG B:HIS78 4.2 23.6 1.0
SG B:CYS159 4.3 30.1 1.0
CG2 B:THR141 4.5 25.1 1.0
OD2 B:ASP82 4.6 30.0 1.0
CG B:ASP82 4.6 27.6 1.0
CA B:HIS80 4.8 27.3 1.0

Zinc binding site 4 out of 8 in 6lfd

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Zinc binding site 4 out of 8 in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)


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 at PH5.5(Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:32.9
occ:1.00
OD2 B:ASP82 2.0 30.0 1.0
O B:HOH501 2.2 19.6 1.0
NE2 B:HIS201 2.2 28.8 1.0
SG B:CYS159 2.3 30.1 1.0
CG B:ASP82 3.0 27.6 1.0
CE1 B:HIS201 3.1 27.5 1.0
CD2 B:HIS201 3.1 28.7 1.0
OD1 B:ASP82 3.3 28.8 1.0
CB B:CYS159 3.4 28.3 1.0
ZN B:ZN301 3.6 26.0 1.0
O B:HOH480 3.8 33.2 1.0
ND1 B:HIS201 4.2 27.0 1.0
CG B:HIS201 4.3 28.9 1.0
CE1 B:HIS78 4.3 25.9 1.0
CB B:ASP82 4.3 28.8 1.0
NE2 B:HIS140 4.4 24.8 1.0
NE2 B:HIS78 4.4 24.1 1.0
CA B:CYS159 4.6 26.3 1.0
CE1 B:HIS140 4.7 24.9 1.0

Zinc binding site 5 out of 8 in 6lfd

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Zinc binding site 5 out of 8 in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)


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 at PH5.5(Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:29.3
occ:1.00
NE2 C:HIS140 2.0 31.7 1.0
ND1 C:HIS80 2.0 29.4 1.0
NE2 C:HIS78 2.1 27.2 1.0
O C:HOH493 2.2 24.5 1.0
CE1 C:HIS80 2.9 28.5 1.0
CE1 C:HIS140 3.0 33.2 1.0
CD2 C:HIS140 3.0 30.9 1.0
CG C:HIS80 3.0 29.3 1.0
CD2 C:HIS78 3.1 30.0 1.0
CE1 C:HIS78 3.2 27.7 1.0
CB C:HIS80 3.4 30.3 1.0
ZN C:ZN302 3.6 37.2 1.0
OD1 C:ASP82 3.9 32.1 1.0
CB C:CYS159 4.0 31.5 1.0
ND1 C:HIS140 4.1 30.3 1.0
NE2 C:HIS80 4.1 28.1 1.0
CG C:HIS140 4.1 31.6 1.0
CD2 C:HIS80 4.1 29.3 1.0
CG C:HIS78 4.2 28.7 1.0
ND1 C:HIS78 4.2 29.4 1.0
SG C:CYS159 4.2 35.9 1.0
CG2 C:THR141 4.7 27.6 1.0
CG C:ASP82 4.7 33.8 1.0
OD2 C:ASP82 4.7 34.7 1.0
CA C:HIS80 4.8 31.1 1.0

Zinc binding site 6 out of 8 in 6lfd

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Zinc binding site 6 out of 8 in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)


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 at PH5.5(Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:37.2
occ:1.00
OD2 C:ASP82 2.0 34.7 1.0
O C:HOH493 2.2 24.5 1.0
NE2 C:HIS201 2.2 33.8 1.0
SG C:CYS159 2.3 35.9 1.0
CG C:ASP82 3.0 33.8 1.0
CE1 C:HIS201 3.1 32.7 1.0
CD2 C:HIS201 3.2 33.9 1.0
OD1 C:ASP82 3.2 32.1 1.0
CB C:CYS159 3.4 31.5 1.0
ZN C:ZN301 3.6 29.3 1.0
O C:HOH456 3.7 35.6 1.0
ND1 C:HIS201 4.2 31.7 1.0
CE1 C:HIS78 4.3 27.7 1.0
CG C:HIS201 4.3 33.2 1.0
CB C:ASP82 4.3 34.8 1.0
NE2 C:HIS78 4.4 27.2 1.0
NE2 C:HIS140 4.5 31.7 1.0
CA C:CYS159 4.7 29.2 1.0
CE1 C:HIS140 4.8 33.2 1.0

Zinc binding site 7 out of 8 in 6lfd

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Zinc binding site 7 out of 8 in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)


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 at PH5.5(Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:26.5
occ:1.00
ND1 D:HIS80 2.0 28.0 1.0
NE2 D:HIS140 2.0 25.4 1.0
NE2 D:HIS78 2.1 26.6 1.0
O D:HOH486 2.2 17.5 1.0
CE1 D:HIS80 3.0 29.7 1.0
CD2 D:HIS140 3.0 24.5 1.0
CG D:HIS80 3.0 27.8 1.0
CD2 D:HIS78 3.0 26.2 1.0
CE1 D:HIS140 3.0 23.8 1.0
CE1 D:HIS78 3.1 27.1 1.0
CB D:HIS80 3.3 28.5 1.0
ZN D:ZN302 3.6 28.0 1.0
OD1 D:ASP82 3.8 25.6 1.0
CB D:CYS159 4.0 30.4 1.0
NE2 D:HIS80 4.1 29.7 1.0
CD2 D:HIS80 4.1 30.4 1.0
CG D:HIS140 4.1 23.4 1.0
ND1 D:HIS140 4.1 25.3 1.0
CG D:HIS78 4.2 26.2 1.0
ND1 D:HIS78 4.2 26.3 1.0
SG D:CYS159 4.3 29.5 1.0
CG D:ASP82 4.6 27.8 1.0
OD2 D:ASP82 4.6 28.4 1.0
CA D:HIS80 4.8 27.7 1.0
CG2 D:THR141 4.8 27.6 1.0

Zinc binding site 8 out of 8 in 6lfd

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Zinc binding site 8 out of 8 in the Crystal Structure of Vmb-1 at PH5.5(Bis-Tris)


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 at PH5.5(Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:28.0
occ:1.00
OD2 D:ASP82 2.0 28.4 1.0
O D:HOH486 2.1 17.5 1.0
NE2 D:HIS201 2.2 24.8 1.0
SG D:CYS159 2.3 29.5 1.0
CG D:ASP82 2.9 27.8 1.0
CD2 D:HIS201 3.1 27.1 1.0
CE1 D:HIS201 3.1 26.9 1.0
OD1 D:ASP82 3.2 25.6 1.0
CB D:CYS159 3.4 30.4 1.0
O D:HOH422 3.6 31.0 1.0
ZN D:ZN301 3.6 26.5 1.0
ND1 D:HIS201 4.2 26.4 1.0
CE1 D:HIS78 4.2 27.1 1.0
CG D:HIS201 4.2 25.7 1.0
CB D:ASP82 4.2 28.2 1.0
NE2 D:HIS78 4.4 26.6 1.0
NE2 D:HIS140 4.5 25.4 1.0
CA D:CYS159 4.7 28.6 1.0
CE1 D:HIS140 4.9 23.8 1.0
O D:HOH443 4.9 32.6 1.0
O D:HOH410 5.0 40.5 1.0

Reference:

S.Chen, Q.Cheng. Crystal Structure of Vmb-1 at pH 5.5(Bis-Tris) To Be Published.
Page generated: Wed Dec 16 12:15:01 2020

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