Zinc in PDB 5e84: Atp-Bound State of Bip

Protein crystallography data

The structure of Atp-Bound State of Bip, PDB code: 5e84 was solved by Q.Liu, J.Yang, M.Nune, Y.Zong, L.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.76 / 2.99
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 222.468, 222.468, 209.460, 90.00, 90.00, 120.00
R / Rfree (%) 24.3 / 28.7

Other elements in 5e84:

The structure of Atp-Bound State of Bip also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Atp-Bound State of Bip (pdb code 5e84). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Atp-Bound State of Bip, PDB code: 5e84:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 5e84

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Zinc binding site 1 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:65.5
occ:1.00
 O2B A:ATP801 1.9 57.7 1.0
OD2 A:ASP34 2.3 63.8 1.0
OD1 A:ASP34 2.9 70.4 1.0
CG A:ASP34 2.9 60.4 1.0
O3G A:ATP801 3.0 48.1 1.0
PB A:ATP801 3.3 42.4 1.0
O3A A:ATP801 3.8 38.5 1.0
O2A A:ATP801 3.9 43.4 1.0
O3B A:ATP801 4.0 47.0 1.0
PG A:ATP801 4.1 51.1 1.0
PA A:ATP801 4.1 37.6 1.0
O1A A:ATP801 4.3 40.5 1.0
CA A:GLY36 4.3 41.6 1.0
OE1 A:GLU201 4.4 76.5 1.0
CB A:ASP34 4.4 54.4 1.0
O1B A:ATP801 4.5 35.6 1.0
O A:TYR39 4.6 48.1 1.0
N A:GLY36 4.8 39.6 1.0
CB A:VAL394 4.9 43.4 1.0
O A:HOH906 5.0 32.1 1.0

Zinc binding site 2 out of 18 in 5e84

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Zinc binding site 2 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn806

b:65.8
occ:1.00
 OD2 A:ASP224 1.7 45.0 1.0
OD2 A:ASP231 1.7 47.2 1.0
OE1 A:GLU201 2.2 76.5 1.0
CD A:GLU201 2.8 64.3 1.0
CG A:ASP224 2.9 46.8 1.0
CG A:ASP231 3.0 52.9 1.0
OE2 A:GLU201 3.3 57.8 1.0
CB A:ASP224 3.7 45.8 1.0
CB A:GLU201 3.8 46.3 1.0
OD1 A:ASP224 3.8 46.8 1.0
CG A:GLU201 3.9 53.5 1.0
CB A:ASP231 3.9 51.5 1.0
OD1 A:ASP231 3.9 62.0 1.0
O3G A:ATP801 4.2 48.1 1.0
O A:ASP224 4.2 42.6 1.0
O A:ALA229 4.3 38.5 1.0
CB A:PRO173 4.3 52.1 1.0
N A:ASP231 4.3 46.4 1.0
CA A:PRO173 4.4 49.9 1.0
C A:ASP224 4.6 46.4 1.0
C A:ALA229 4.7 38.6 1.0
CB A:ALA229 4.7 41.5 1.0
CA A:ASP231 4.8 43.8 1.0
CA A:ASP224 4.8 45.8 1.0
CG A:PRO173 4.9 60.8 1.0
PG A:ATP801 4.9 51.1 1.0
C A:PHE230 5.0 44.5 1.0
O2G A:ATP801 5.0 45.1 1.0

Zinc binding site 3 out of 18 in 5e84

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Zinc binding site 3 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn807

b:78.8
occ:1.00
 OD2 A:ASP238 1.7 81.8 1.0
CG A:ASP238 2.8 78.3 1.0
OD1 A:ASP238 3.2 86.4 1.0
CB A:ASP238 4.0 68.0 1.0
OE1 A:GLU217 4.2 79.3 1.0
CB A:GLU217 4.6 60.9 1.0
N A:GLU217 4.9 56.1 1.0

Zinc binding site 4 out of 18 in 5e84

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Zinc binding site 4 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:68.4
occ:1.00
 O2B B:ATP801 1.8 65.1 1.0
OD2 B:ASP34 2.1 75.1 1.0
O B:HOH903 2.2 52.0 1.0
CG B:ASP34 2.9 71.8 1.0
OD1 B:ASP34 3.0 69.7 1.0
PB B:ATP801 3.3 50.3 1.0
O3G B:ATP801 3.5 54.8 1.0
O3A B:ATP801 3.9 48.4 1.0
O1A B:ATP801 4.0 48.9 1.0
O2A B:ATP801 4.0 58.1 1.0
PA B:ATP801 4.1 53.0 1.0
O3B B:ATP801 4.2 52.7 1.0
O1B B:ATP801 4.2 50.3 1.0
PG B:ATP801 4.3 60.9 1.0
CB B:ASP34 4.4 65.0 1.0
OE1 B:GLU201 4.4 87.0 1.0
CA B:GLY36 4.5 63.4 1.0
O1G B:ATP801 4.6 61.3 1.0
CB B:VAL394 4.8 59.4 1.0
O B:ASP391 4.8 72.1 1.0
O B:TYR39 4.8 64.0 1.0
CG2 B:VAL394 4.8 65.6 1.0

Zinc binding site 5 out of 18 in 5e84

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Zinc binding site 5 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn803

b:87.5
occ:1.00
 OD2 B:ASP224 1.9 61.8 1.0
OD2 B:ASP231 2.0 55.8 1.0
OE1 B:GLU201 2.2 87.0 1.0
CD B:GLU201 2.9 78.1 1.0
CG B:ASP224 3.0 63.4 1.0
CG B:ASP231 3.2 62.0 1.0
OE2 B:GLU201 3.3 74.5 1.0
O3G B:ATP801 3.4 54.8 1.0
O B:ALA229 3.6 57.0 1.0
OD1 B:ASP224 3.8 58.8 1.0
CB B:ASP224 3.9 64.5 1.0
CB B:GLU201 4.0 57.7 1.0
OD1 B:ASP231 4.0 60.3 1.0
CG B:GLU201 4.0 68.8 1.0
CB B:ASP231 4.1 64.2 1.0
O B:ASP224 4.2 58.5 1.0
C B:ALA229 4.3 55.0 1.0
CB B:PRO173 4.4 65.3 1.0
PG B:ATP801 4.4 60.9 1.0
CB B:ALA229 4.4 51.9 1.0
N B:ASP231 4.5 58.6 1.0
O B:HOH903 4.5 52.0 1.0
C B:ASP224 4.6 55.8 1.0
O2G B:ATP801 4.6 59.0 1.0
CA B:PRO173 4.6 63.8 1.0
CG B:PRO173 4.8 67.3 1.0
N B:PHE230 4.9 53.7 1.0
O1G B:ATP801 4.9 61.3 1.0
CA B:ASP224 4.9 63.2 1.0
N B:GLY226 4.9 51.3 1.0
CA B:ALA229 5.0 52.3 1.0
C B:PHE230 5.0 58.8 1.0
CA B:ASP231 5.0 61.3 1.0
CA B:PHE230 5.0 52.4 1.0

Zinc binding site 6 out of 18 in 5e84

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Zinc binding site 6 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn807

b:88.2
occ:1.00
 OD2 B:ASP238 1.8 0.6 1.0
CG B:ASP238 2.9 0.5 1.0
OD1 B:ASP238 3.5 0.2 1.0
CB B:ASP238 4.2 0.9 1.0
OE1 B:GLU217 4.8 97.5 1.0
CB B:GLU217 4.8 84.9 1.0

Zinc binding site 7 out of 18 in 5e84

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Zinc binding site 7 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:68.7
occ:1.00
 OD2 C:ASP34 1.9 80.1 1.0
O1B C:ATP801 2.1 58.2 1.0
O C:HOH901 2.3 43.3 1.0
CG C:ASP34 2.8 67.5 1.0
OD1 C:ASP34 3.0 60.6 1.0
O1A C:ATP801 3.5 56.6 1.0
PB C:ATP801 3.5 47.4 1.0
O3G C:ATP801 3.7 53.2 1.0
O3A C:ATP801 4.1 46.6 1.0
PA C:ATP801 4.2 53.6 1.0
CB C:ASP34 4.2 61.4 1.0
O2B C:ATP801 4.3 50.8 1.0
O3B C:ATP801 4.5 50.1 1.0
O C:TYR39 4.5 46.5 1.0
CA C:GLY36 4.5 52.7 1.0
O C:ASP391 4.6 79.9 1.0
O2A C:ATP801 4.7 57.7 1.0
PG C:ATP801 4.7 52.1 1.0
OE1 C:GLU201 4.8 97.1 1.0
CB C:VAL394 4.8 49.1 1.0
CG1 C:VAL394 4.9 49.6 1.0
N C:GLY36 5.0 52.5 1.0

Zinc binding site 8 out of 18 in 5e84

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Zinc binding site 8 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn804

b:73.3
occ:1.00
 OD2 C:ASP231 1.7 51.9 1.0
OD2 C:ASP224 2.0 58.2 1.0
OE1 C:GLU201 2.3 97.1 1.0
CG C:ASP224 2.9 59.6 1.0
CG C:ASP231 3.0 59.6 1.0
CD C:GLU201 3.1 77.6 1.0
OD1 C:ASP224 3.6 61.7 1.0
CB C:ASP224 3.7 61.3 1.0
CB C:GLU201 3.7 63.5 1.0
OE2 C:GLU201 3.8 69.4 1.0
O3G C:ATP801 3.9 53.2 1.0
OD1 C:ASP231 3.9 62.7 1.0
CB C:ASP231 3.9 64.6 1.0
CG C:GLU201 4.0 70.3 1.0
O C:ALA229 4.0 43.1 1.0
O C:ASP224 4.1 54.5 1.0
N C:ASP231 4.4 60.5 1.0
CA C:PRO173 4.5 60.1 1.0
C C:ALA229 4.5 49.9 1.0
CB C:PRO173 4.5 57.4 1.0
C C:ASP224 4.5 55.5 1.0
O C:HOH901 4.6 43.3 1.0
CB C:ALA229 4.6 50.5 1.0
O1G C:ATP801 4.6 53.4 1.0
PG C:ATP801 4.8 52.1 1.0
CA C:ASP231 4.8 61.2 1.0
CA C:ASP224 4.8 59.9 1.0
CG C:PRO173 4.8 57.9 1.0
C C:PHE230 4.9 57.5 1.0
N C:PHE230 4.9 52.6 1.0

Zinc binding site 9 out of 18 in 5e84

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Zinc binding site 9 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn805

b:81.1
occ:1.00
 OD2 C:ASP238 1.8 0.2 1.0
CG C:ASP238 3.0 97.5 1.0
OD1 C:ASP238 3.5 90.3 1.0
CB C:ASP238 4.2 91.5 1.0
OE1 C:GLU217 5.0 93.1 1.0

Zinc binding site 10 out of 18 in 5e84

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Zinc binding site 10 out of 18 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Atp-Bound State of Bip within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:71.3
occ:1.00
 O2B D:ATP801 1.9 60.8 1.0
OD2 D:ASP34 2.2 61.7 1.0
O D:HOH901 2.2 60.8 1.0
CG D:ASP34 2.9 56.0 1.0
OD1 D:ASP34 2.9 56.8 1.0
PB D:ATP801 3.4 49.8 1.0
O3G D:ATP801 3.4 61.4 1.0
O2A D:ATP801 3.6 50.6 1.0
O1A D:ATP801 3.9 42.7 1.0
PA D:ATP801 3.9 44.5 1.0
O3A D:ATP801 4.0 45.8 1.0
O3B D:ATP801 4.3 51.5 1.0
CB D:ASP34 4.3 56.1 1.0
O1B D:ATP801 4.3 53.2 1.0
PG D:ATP801 4.5 56.6 1.0
CA D:GLY36 4.5 51.4 1.0
O D:TYR39 4.7 55.1 1.0
O D:ASP391 4.8 74.2 1.0
CB D:VAL394 4.9 57.9 1.0
CG2 D:VAL394 4.9 60.1 1.0

Reference:

J.Yang, M.Nune, Y.Zong, L.Zhou, Q.Liu. Close and Allosteric Opening of the Polypeptide-Binding Site in A Human HSP70 Chaperone Bip. Structure V. 23 2191 2015.
ISSN: ISSN 0969-2126
PubMed: 26655470
DOI: 10.1016/J.STR.2015.10.012
Page generated: Wed Dec 16 06:09:17 2020

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