Zinc in PDB 6vd8: Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa

Protein crystallography data

The structure of Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa, PDB code: 6vd8 was solved by M.J.Maher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.29 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.916, 58.247, 72.014, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 27.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa (pdb code 6vd8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa, PDB code: 6vd8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6vd8

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Zinc binding site 1 out of 5 in the Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:29.1
occ:1.00
NE2 B:HIS280 1.9 29.4 1.0
NE2 A:HIS237 1.9 29.1 1.0
OD1 A:ASP235 2.0 28.1 1.0
CE1 A:HIS237 2.9 29.1 1.0
CE1 B:HIS280 2.9 29.9 1.0
CG A:ASP235 2.9 28.5 1.0
CD2 B:HIS280 2.9 29.6 1.0
CD2 A:HIS237 3.0 29.0 1.0
OD2 A:ASP235 3.3 28.4 1.0
ND1 B:HIS280 4.0 30.1 1.0
ND1 A:HIS237 4.0 29.0 1.0
O A:HOH402 4.0 40.6 1.0
CG B:HIS280 4.1 29.6 1.0
CG A:HIS237 4.1 29.0 1.0
CB A:ASP235 4.2 28.6 1.0
CA A:ASP235 4.5 28.9 1.0
O B:HOH404 4.5 28.0 1.0
O A:ASP235 4.6 29.6 1.0
C A:ASP235 4.7 28.9 1.0

Zinc binding site 2 out of 5 in 6vd8

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Zinc binding site 2 out of 5 in the Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:29.1
occ:1.00
ND1 A:HIS251 2.1 27.9 1.0
NE2 A:HIS234 2.2 29.2 1.0
OE1 A:GLU286 2.2 32.5 1.0
SG A:CYS290 2.3 39.6 1.0
CD A:GLU286 3.0 33.0 1.0
CG A:HIS251 3.0 28.1 1.0
CE1 A:HIS234 3.1 29.2 1.0
CE1 A:HIS251 3.1 27.9 1.0
OE2 A:GLU286 3.1 33.9 1.0
CD2 A:HIS234 3.2 29.6 1.0
CB A:HIS251 3.2 28.3 1.0
CB A:CYS290 3.6 41.4 1.0
N A:CYS290 4.0 42.0 1.0
NE2 A:GLN284 4.1 27.8 1.0
CD2 A:HIS251 4.1 28.0 1.0
NE2 A:HIS251 4.2 28.0 1.0
ND1 A:HIS234 4.2 29.1 1.0
CG A:HIS234 4.3 29.5 1.0
CA A:CYS290 4.4 42.1 1.0
CG A:GLU286 4.4 33.1 1.0
CA A:HIS251 4.7 28.4 1.0
O A:HOH408 4.9 34.3 1.0
C A:ALA289 5.0 41.2 1.0

Zinc binding site 3 out of 5 in 6vd8

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Zinc binding site 3 out of 5 in the Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:35.8
occ:1.00
OE2 A:GLU279 1.8 42.2 1.0
NE2 A:HIS273 2.2 36.6 1.0
CD A:GLU279 2.5 41.3 1.0
OE1 A:GLU279 2.5 40.6 1.0
CD2 A:HIS273 2.9 36.1 1.0
CE1 A:HIS273 3.3 36.9 1.0
CG A:GLU279 3.9 41.3 1.0
CG A:HIS273 4.2 36.6 1.0
ND1 A:HIS273 4.3 36.9 1.0
CB A:GLU279 5.0 41.1 1.0

Zinc binding site 4 out of 5 in 6vd8

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Zinc binding site 4 out of 5 in the Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:31.8
occ:1.00
OE1 B:GLU286 2.1 32.6 1.0
ND1 B:HIS251 2.2 29.9 1.0
NE2 B:HIS234 2.2 25.9 1.0
SG B:CYS290 2.3 39.7 1.0
CD B:GLU286 2.9 32.7 1.0
OE2 B:GLU286 3.0 33.0 1.0
CE1 B:HIS234 3.0 25.9 1.0
CG B:HIS251 3.1 29.6 1.0
CE1 B:HIS251 3.2 30.0 1.0
CD2 B:HIS234 3.2 26.2 1.0
CB B:HIS251 3.3 29.2 1.0
CB B:CYS290 3.4 40.9 1.0
N B:CYS290 3.8 41.0 1.0
NE2 B:GLN284 4.1 25.8 1.0
CA B:CYS290 4.2 41.5 1.0
ND1 B:HIS234 4.2 26.2 1.0
CD2 B:HIS251 4.2 29.9 1.0
NE2 B:HIS251 4.3 29.7 1.0
CG B:GLU286 4.3 33.0 1.0
CG B:HIS234 4.3 26.6 1.0
CA B:HIS251 4.7 28.9 1.0
C B:ALA289 4.8 40.5 1.0

Zinc binding site 5 out of 5 in 6vd8

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Zinc binding site 5 out of 5 in the Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Metal-Bound C-Terminal Domain of Czcd Transporter From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:48.1
occ:1.00
NE2 A:HIS280 2.0 39.1 1.0
OD1 B:ASP235 2.0 32.6 1.0
NE2 B:HIS237 2.0 31.4 1.0
O B:HOH417 2.2 44.5 1.0
CD2 A:HIS280 2.9 38.7 1.0
CE1 B:HIS237 2.9 31.4 1.0
CE1 A:HIS280 2.9 39.6 1.0
CG B:ASP235 3.0 31.6 1.0
CD2 B:HIS237 3.1 31.1 1.0
O A:HOH409 3.3 72.3 1.0
OD2 B:ASP235 3.4 32.4 1.0
ND1 A:HIS280 4.0 38.9 1.0
CG A:HIS280 4.0 38.1 1.0
ND1 B:HIS237 4.1 31.4 1.0
CG B:HIS237 4.2 31.1 1.0
CB B:ASP235 4.2 30.4 1.0
CA B:ASP235 4.5 29.0 1.0
O B:ASP235 4.6 27.9 1.0
C B:ASP235 4.8 28.5 1.0
O A:HOH406 5.0 39.1 1.0

Reference:

S.R.Udagedara, D.M.La Porta, C.Spehar, G.Purohit, M.J.A.Hein, M.E.Fatmous, G.P.Casas Garcia, K.Ganio, C.A.Mcdevitt, M.J.Maher. Structural and Functional Characterizations of the C-Terminal Domains of Czcd Proteins. J.Inorg.Biochem. V. 208 11087 2020.
ISSN: ISSN 0162-0134
PubMed: 32505855
DOI: 10.1016/J.JINORGBIO.2020.111087
Page generated: Wed Dec 16 13:01:29 2020

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