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Zinc in PDB 6bie: Misreading Chaperone-Substrate Complexes From Random Noise

Protein crystallography data

The structure of Misreading Chaperone-Substrate Complexes From Random Noise, PDB code: 6bie was solved by J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.54 / 1.77
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 42.960, 42.960, 258.169, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 24.8

Other elements in 6bie:

The structure of Misreading Chaperone-Substrate Complexes From Random Noise also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 7 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Misreading Chaperone-Substrate Complexes From Random Noise (pdb code 6bie). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Misreading Chaperone-Substrate Complexes From Random Noise, PDB code: 6bie:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 6bie

Go back to Zinc Binding Sites List in 6bie
Zinc binding site 1 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:32.9
occ:1.00
OE1 A:GLU86 2.0 34.5 1.0
N1 A:IMD215 2.1 26.3 0.8
CL A:CL211 2.2 62.5 1.0
H5 A:IMD215 2.7 26.9 0.8
CD A:GLU86 2.7 32.7 1.0
OE2 A:GLU86 2.8 32.6 1.0
C5 A:IMD215 2.9 26.9 0.8
C2 A:IMD215 3.3 26.5 0.8
H2 A:IMD215 3.6 26.5 0.8
O A:HOH339 3.7 41.8 1.0
C4 A:IMD215 4.2 26.1 0.8
CG A:GLU86 4.2 31.1 1.0
O A:HOH354 4.3 31.1 1.0
N3 A:IMD215 4.3 26.4 0.8
HB3 A:GLU86 4.3 31.4 1.0
HB2 A:ALA83 4.5 28.8 1.0
HB2 A:GLU86 4.6 31.4 1.0
HG3 A:GLU86 4.6 31.1 1.0
CB A:GLU86 4.7 31.4 1.0
HG2 A:GLU86 4.7 31.1 1.0

Zinc binding site 2 out of 14 in 6bie

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Zinc binding site 2 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:64.3
occ:0.90
ND1 A:HIS96 1.9 51.1 1.0
O A:HOH385 2.3 62.3 1.0
O A:HOH373 2.4 51.8 1.0
CE1 A:HIS96 2.8 46.9 1.0
CG A:HIS96 2.9 43.2 1.0
HE1 A:HIS96 2.9 46.9 1.0
O A:HOH318 3.0 69.3 1.0
HB2 A:HIS96 3.1 39.2 1.0
HA A:HIS96 3.1 33.4 1.0
CB A:HIS96 3.4 39.2 1.0
CA A:HIS96 3.7 33.4 1.0
HE22 A:GLN100 3.8 49.5 1.0
NE2 A:HIS96 3.9 53.2 1.0
O A:HOH390 3.9 58.0 1.0
CD2 A:HIS96 4.0 47.5 1.0
HB3 A:HIS96 4.3 39.2 1.0
HG2 A:GLN100 4.5 33.9 1.0
NE2 A:GLN100 4.5 49.5 1.0
O A:HIS96 4.6 28.2 1.0
C A:HIS96 4.6 32.0 1.0
HB A:THR99 4.6 31.6 1.0
N A:HIS96 4.8 31.7 1.0
HD2 A:HIS96 4.9 47.5 1.0
HE21 A:GLN100 4.9 49.5 1.0

Zinc binding site 3 out of 14 in 6bie

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Zinc binding site 3 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:87.9
occ:1.00
O A:HOH401 2.0 66.2 1.0
NE2 A:HIS96 2.1 53.2 1.0
O A:HOH393 2.7 58.6 1.0
HE2 B:MET64 2.8 46.5 1.0
CE1 A:HIS96 3.1 46.9 1.0
HE1 B:MET64 3.1 46.5 1.0
CD2 A:HIS96 3.2 47.5 1.0
HE1 A:HIS96 3.2 46.9 1.0
O A:HOH381 3.2 83.4 1.0
HD2 A:HIS96 3.4 47.5 1.0
CE B:MET64 3.4 46.5 1.0
HG3 A:GLN100 3.5 33.9 1.0
HE3 B:MET64 4.0 46.5 1.0
ND1 A:HIS96 4.2 51.1 1.0
CG A:HIS96 4.3 43.2 1.0
HD12 B:ILE68 4.3 41.0 1.0
CG A:GLN100 4.4 33.9 1.0
HD13 B:ILE68 4.6 41.0 1.0
HG2 A:GLN100 4.7 33.9 1.0
CD A:GLN100 4.7 40.7 1.0
SD B:MET64 4.7 60.7 1.0
HE2 A:PHE119 4.8 45.8 1.0
OE1 A:GLN100 4.9 52.6 1.0
CD1 B:ILE68 4.9 41.0 1.0
HH12 B:ARG61 5.0 79.4 1.0

Zinc binding site 4 out of 14 in 6bie

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Zinc binding site 4 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:43.8
occ:1.00
OD1 A:ASP66 2.0 42.2 1.0
CG A:ASP66 2.8 41.4 1.0
OD2 A:ASP66 3.0 48.9 1.0
HN1 A:IMD217 3.6 29.0 0.8
H2 A:IMD217 4.0 29.0 0.8
CB A:ASP66 4.2 36.4 1.0
HA A:ASP66 4.3 33.7 1.0
N1 A:IMD217 4.4 29.0 0.8
HB3 A:ASP66 4.5 36.4 1.0
C2 A:IMD217 4.6 29.0 0.8
CA A:ASP66 4.7 33.7 1.0
HB2 A:ASP66 4.8 36.4 1.0
O A:ARG62 4.8 32.6 1.0

Zinc binding site 5 out of 14 in 6bie

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Zinc binding site 5 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:86.6
occ:0.55
ZN A:ZN205 0.0 86.6 0.6
OE2 A:GLU79 2.0 50.8 0.6
OE1 A:GLU79 2.2 34.4 0.4
HZ2 A:LYS75 2.4 71.5 1.0
HZ2 B:LYS90 2.4 58.4 1.0
O A:HOH400 2.6 64.2 1.0
HZ3 A:LYS75 2.8 71.5 1.0
O A:HOH394 2.9 68.5 1.0
CD A:GLU79 3.0 39.1 0.6
NZ A:LYS75 3.0 71.5 1.0
ZN A:ZN205 3.1 77.1 0.5
CD A:GLU79 3.1 36.6 0.4
HZ3 B:LYS90 3.2 58.4 1.0
NZ B:LYS90 3.2 58.4 1.0
OE1 A:GLU79 3.3 37.6 0.6
HE2 B:LYS90 3.4 42.7 1.0
OE2 A:GLU79 3.6 46.1 0.4
HZ1 A:LYS75 3.7 71.5 1.0
HE2 A:LYS75 3.8 56.4 1.0
CE B:LYS90 3.8 42.7 1.0
HZ1 B:LYS90 3.9 58.4 1.0
CE A:LYS75 4.0 56.4 1.0
HE3 B:LYS90 4.2 42.7 1.0
HG2 A:GLU79 4.2 33.1 0.4
CG A:GLU79 4.3 34.3 0.6
CG A:GLU79 4.3 33.1 0.4
HD12 B:LEU94 4.4 34.0 1.0
O B:HOH301 4.5 46.1 1.0
HG2 A:GLU79 4.5 34.3 0.6
HE3 A:LYS75 4.5 56.4 1.0
HG3 A:GLU79 4.5 34.3 0.6
HG3 A:GLU79 4.8 33.1 0.4
HG2 A:LYS75 4.8 50.3 1.0
HD13 B:LEU94 4.9 34.0 1.0

Zinc binding site 6 out of 14 in 6bie

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Zinc binding site 6 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:77.1
occ:0.45
ZN A:ZN205 0.0 77.1 0.5
OE2 A:GLU79 2.0 46.1 0.4
OE1 A:GLU79 2.2 37.6 0.6
O A:HOH400 2.3 64.2 1.0
CD A:GLU79 2.9 36.6 0.4
CD A:GLU79 2.9 39.1 0.6
OE1 A:GLU79 3.1 34.4 0.4
ZN A:ZN205 3.1 86.6 0.6
OE2 A:GLU79 3.2 50.8 0.6
HZ2 B:LYS90 3.6 58.4 1.0
HZ3 A:LYS75 3.8 71.5 1.0
CG A:GLU79 4.2 34.3 0.6
CG A:GLU79 4.3 33.1 0.4
HG3 A:GLU79 4.4 34.3 0.6
NZ B:LYS90 4.5 58.4 1.0
HB3 A:GLU79 4.5 28.4 0.4
HB2 A:GLU79 4.5 28.4 0.4
HB3 A:GLU79 4.5 27.8 0.6
HB2 A:GLU79 4.5 27.8 0.6
HZ2 A:LYS75 4.5 71.5 1.0
NZ A:LYS75 4.6 71.5 1.0
HG2 A:GLU79 4.7 33.1 0.4
CB A:GLU79 4.7 28.4 0.4
O A:HOH380 4.7 64.2 1.0
HZ1 B:LYS90 4.7 58.4 1.0
CB A:GLU79 4.7 27.8 0.6
HG3 A:GLU79 4.8 33.1 0.4
HA A:VAL76 4.9 36.6 1.0
HZ1 A:LYS75 4.9 71.5 1.0
HG21 A:VAL76 4.9 44.5 1.0
HG2 A:GLU79 4.9 34.3 0.6
HZ3 B:LYS90 5.0 58.4 1.0

Zinc binding site 7 out of 14 in 6bie

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Zinc binding site 7 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:34.2
occ:1.00
HD1 B:HIS65 1.2 30.1 1.0
HN3 A:IMD216 1.5 34.9 1.0
OE2 A:GLU120 1.8 35.5 1.0
ND1 B:HIS65 2.0 30.1 1.0
N3 A:IMD216 2.2 34.9 1.0
CL A:CL214 2.3 37.9 1.0
H4 A:IMD216 2.4 39.0 1.0
C4 A:IMD216 2.6 39.0 1.0
CD A:GLU120 2.9 39.5 1.0
CE1 B:HIS65 2.9 31.5 1.0
HE1 B:HIS65 3.0 31.5 1.0
CG B:HIS65 3.1 28.7 1.0
OE1 A:GLU120 3.2 44.7 1.0
HD1 A:PHE119 3.3 40.7 1.0
HB2 B:HIS65 3.4 33.2 1.0
HB3 B:HIS65 3.4 33.2 1.0
C2 A:IMD216 3.5 38.0 1.0
CB B:HIS65 3.6 33.2 1.0
HG2 B:ARG62 3.7 39.1 0.5
HG3 B:ARG62 3.8 44.5 0.5
O A:HOH320 3.8 55.9 1.0
HA B:ARG62 3.8 41.0 0.5
HA B:ARG62 3.8 41.7 0.5
C5 A:IMD216 3.9 36.9 1.0
CD1 A:PHE119 4.0 40.7 1.0
NE2 B:HIS65 4.1 29.8 1.0
H2 A:IMD216 4.1 38.0 1.0
HA A:GLU120 4.2 39.5 1.0
CD2 B:HIS65 4.2 28.8 1.0
CG A:GLU120 4.2 37.0 1.0
HG2 A:GLU120 4.3 37.0 1.0
N1 A:IMD216 4.3 38.6 1.0
HB3 A:PHE119 4.3 37.7 1.0
HE1 A:PHE119 4.4 43.1 1.0
HG2 B:ARG62 4.5 44.5 0.5
CG B:ARG62 4.5 44.5 0.5
HE B:ARG62 4.6 46.1 0.5
CE1 A:PHE119 4.6 43.1 1.0
CG B:ARG62 4.6 39.1 0.5
CA B:ARG62 4.8 41.0 0.5
HG3 A:GLU120 4.8 37.0 1.0
H5 A:IMD216 4.8 36.9 1.0
CA B:ARG62 4.8 41.7 0.5
HE2 B:HIS65 4.8 29.8 1.0
CA A:GLU120 4.9 39.5 1.0
CG A:PHE119 4.9 38.5 1.0
HB3 B:ARG62 5.0 43.4 0.5
N A:GLU120 5.0 35.3 1.0

Zinc binding site 8 out of 14 in 6bie

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Zinc binding site 8 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:43.0
occ:1.00
OD2 A:ASP71 1.8 38.3 1.0
CL A:CL213 2.1 75.1 1.0
CL A:CL212 2.5 62.4 1.0
CG A:ASP71 2.6 40.6 1.0
OD1 A:ASP71 2.7 41.9 1.0
CB A:ASP71 4.1 41.4 1.0
O A:HOH350 4.1 51.0 1.0
O A:HOH334 4.1 53.6 1.0
O A:HOH337 4.1 61.2 1.0
HB3 A:ASP71 4.3 41.4 1.0
HB2 A:ASP71 4.4 41.4 1.0
HG23 A:THR72 4.6 37.9 1.0
H A:ASP71 4.9 40.1 1.0

Zinc binding site 9 out of 14 in 6bie

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Zinc binding site 9 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:48.6
occ:0.80
OE1 A:GLU44 1.8 48.6 1.0
CD A:GLU44 2.7 55.0 1.0
OE2 A:GLU44 2.9 62.0 1.0
HG2 A:GLN41 3.4 35.6 1.0
O A:HOH311 3.5 75.0 1.0
HA A:GLN41 3.8 35.5 1.0
CG A:GLU44 4.1 47.5 1.0
HG3 A:GLN40 4.2 37.8 1.0
HB2 A:GLU44 4.2 45.7 1.0
CG A:GLN41 4.3 35.6 1.0
HG3 A:GLN41 4.3 35.6 1.0
HB3 A:GLU44 4.5 45.7 1.0
CB A:GLU44 4.5 45.7 1.0
HG3 A:GLU44 4.6 47.5 1.0
HG2 A:GLU44 4.6 47.5 1.0
HE22 A:GLN40 4.6 44.7 1.0
HE22 A:GLN41 4.6 53.3 1.0
CA A:GLN41 4.7 35.5 1.0

Zinc binding site 10 out of 14 in 6bie

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Zinc binding site 10 out of 14 in the Misreading Chaperone-Substrate Complexes From Random Noise


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Misreading Chaperone-Substrate Complexes From Random Noise within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:32.2
occ:1.00
N3 A:IMD217 2.0 28.2 0.8
OE2 B:GLU120 2.1 34.5 1.0
ND1 A:HIS65 2.1 34.2 1.0
CL A:CL210 2.2 30.5 1.0
C2 A:IMD217 2.8 29.0 0.8
CD B:GLU120 2.8 35.2 1.0
OE1 B:GLU120 2.8 36.6 1.0
H2 A:IMD217 2.9 29.0 0.8
CE1 A:HIS65 3.0 34.3 1.0
C4 A:IMD217 3.1 28.5 0.8
HE1 A:HIS65 3.1 34.3 1.0
CG A:HIS65 3.2 34.2 1.0
HD1 B:PHE119 3.2 30.2 1.0
HB2 A:HIS65 3.2 34.6 1.0
H4 A:IMD217 3.5 28.5 0.8
CB A:HIS65 3.6 34.6 1.0
HB3 A:HIS65 3.6 34.6 1.0
HA A:ARG62 3.8 36.9 1.0
HG2 A:ARG62 3.8 49.2 1.0
CD1 B:PHE119 3.9 30.2 1.0
N1 A:IMD217 4.0 29.0 0.8
HE1 B:PHE119 4.1 33.6 1.0
NE2 A:HIS65 4.1 35.0 1.0
C5 A:IMD217 4.1 28.9 0.8
HA B:GLU120 4.2 36.5 1.0
CG B:GLU120 4.2 38.4 1.0
CD2 A:HIS65 4.2 32.9 1.0
HG2 B:GLU120 4.4 38.4 1.0
CE1 B:PHE119 4.4 33.6 1.0
HB3 B:PHE119 4.4 31.3 1.0
HG3 B:GLU120 4.7 38.4 1.0
CA A:ARG62 4.8 36.9 1.0
CG A:ARG62 4.8 49.2 1.0
HN1 A:IMD217 4.9 29.0 0.8
O A:HOH357 4.9 39.0 1.0
HE2 A:HIS65 4.9 35.0 1.0
CA B:GLU120 4.9 36.5 1.0
CG B:PHE119 4.9 30.7 1.0
N B:GLU120 5.0 32.9 1.0

Reference:

J.Wang, J.Wang. N/A N/A.
ISSN: ESSN 1545-9985
PubMed: 30297779
DOI: 10.1038/S41594-018-0144-3
Page generated: Wed Dec 16 11:32:03 2020

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