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Zinc in PDB 4gqt: N-Terminal Domain of C. Elegans HSP90

Protein crystallography data

The structure of N-Terminal Domain of C. Elegans HSP90, PDB code: 4gqt was solved by J.Osipiuk, G.Chhor, M.Gu, P.Van Oosten-Hawle, R.I.Morimoto, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.30 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.652, 86.658, 128.670, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the N-Terminal Domain of C. Elegans HSP90 (pdb code 4gqt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the N-Terminal Domain of C. Elegans HSP90, PDB code: 4gqt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4gqt

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Zinc binding site 1 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:28.9
occ:1.00
O1A A:ADP500 1.9 25.0 1.0
O1B A:ADP500 2.0 29.6 1.0
ND2 A:ASN39 2.1 21.2 1.0
O A:HOH633 2.1 31.4 1.0
O A:HOH632 2.1 25.7 1.0
O A:HOH634 2.4 32.1 1.0
CG A:ASN39 3.0 23.0 1.0
PB A:ADP500 3.1 26.9 1.0
PA A:ADP500 3.1 25.4 1.0
OD1 A:ASN39 3.3 23.8 1.0
O3A A:ADP500 3.3 26.6 1.0
O3B A:ADP500 3.5 30.5 1.0
O5' A:ADP500 4.0 24.6 1.0
O A:HOH601 4.1 23.4 1.0
OE1 A:GLU35 4.2 32.4 1.0
O2A A:ADP500 4.4 25.0 1.0
CB A:ASN39 4.4 23.1 1.0
O2B A:ADP500 4.4 27.8 1.0
O A:GLU35 4.5 24.1 1.0
CA A:GLY125 4.5 26.5 1.0
N A:GLY125 4.6 23.6 1.0
CA A:ASN39 4.7 23.4 1.0
N A:PHE126 4.7 25.7 1.0
OG A:SER38 4.7 40.7 1.0
N A:ASN39 4.8 24.2 1.0
C A:GLY125 4.9 26.3 1.0

Zinc binding site 2 out of 10 in 4gqt

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Zinc binding site 2 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:26.2
occ:0.80
OE1 B:GLU74 1.8 37.8 1.0
O A:HOH654 1.8 28.6 1.0
ND1 A:HIS177 2.1 28.9 1.0
O A:HOH629 2.1 30.6 1.0
CD B:GLU74 2.7 40.6 1.0
CE1 A:HIS177 3.0 29.1 1.0
CG A:HIS177 3.1 27.6 1.0
CG B:GLU74 3.2 38.3 1.0
CB A:HIS177 3.5 27.6 1.0
OE2 B:GLU74 3.8 41.6 1.0
O A:HOH620 3.8 27.8 1.0
O A:GLU74 4.2 30.5 1.0
NE2 A:HIS177 4.2 28.8 1.0
CD2 A:HIS177 4.2 25.7 1.0
CG2 A:THR76 4.3 30.1 1.0
CA A:HIS177 4.5 27.1 1.0
CB B:GLU74 4.7 35.0 1.0
CB B:GLU73 4.8 51.0 1.0
NZ A:LYS135 4.9 37.0 1.0

Zinc binding site 3 out of 10 in 4gqt

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Zinc binding site 3 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:62.9
occ:1.00
O A:HOH661 2.2 43.0 1.0
O A:HOH660 2.2 53.8 1.0
OE2 A:GLU30 2.3 46.8 1.0
NE2 A:HIS198 2.3 60.0 1.0
OE1 A:GLU30 2.9 42.1 1.0
CD A:GLU30 2.9 43.5 1.0
CD2 A:HIS198 3.0 55.7 1.0
CE1 A:HIS198 3.5 61.2 1.0
O A:HOH663 4.0 46.4 1.0
CG A:HIS198 4.3 55.1 1.0
CG A:GLU30 4.4 42.0 1.0
CD A:LYS197 4.5 57.9 1.0
ND1 A:HIS198 4.5 57.7 1.0
CB A:LYS197 4.7 51.1 1.0

Zinc binding site 4 out of 10 in 4gqt

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Zinc binding site 4 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:70.4
occ:1.00
OD1 A:ASP144 2.1 43.5 1.0
O A:HOH671 2.2 54.0 1.0
O A:HOH649 2.3 52.2 1.0
O A:HOH692 2.4 36.7 1.0
CG A:ASP144 3.2 36.9 1.0
OD2 A:ASP144 3.7 38.3 1.0
OE2 A:GLU57 4.0 48.7 1.0
OE1 A:GLU57 4.3 46.7 1.0
CB A:ASP144 4.5 34.3 1.0
CD A:GLU57 4.5 44.2 1.0
CA A:ASP144 4.7 33.7 1.0
N A:ASP144 4.9 31.7 1.0
O A:ASN143 4.9 35.1 1.0
CB A:ASN143 4.9 27.9 1.0
C A:ASN143 4.9 32.3 1.0

Zinc binding site 5 out of 10 in 4gqt

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Zinc binding site 5 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:52.5
occ:1.00
O A:HOH690 1.9 33.4 1.0
O A:HOH689 2.0 38.4 1.0
O A:HOH694 2.3 41.2 1.0
OD1 A:ASP145 2.3 34.4 1.0
O A:HOH693 2.4 51.9 1.0
CG A:ASP145 3.2 33.8 1.0
OD2 A:ASP145 3.5 33.3 1.0
OD2 A:ASP146 4.0 45.2 1.0
OH A:TYR148 4.0 43.2 1.0
N A:ASP146 4.5 31.9 1.0
CE2 A:TYR148 4.6 38.0 1.0
CB A:ASP145 4.6 31.9 1.0
CZ A:TYR148 4.7 39.7 1.0
CA A:ASP145 4.8 32.3 1.0
CG A:ASP146 4.9 41.2 1.0

Zinc binding site 6 out of 10 in 4gqt

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Zinc binding site 6 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:78.1
occ:1.00
O A:HOH652 2.0 52.2 1.0
O A:HOH626 2.0 50.3 1.0
OE1 A:GLU193 2.4 61.9 1.0
OE2 A:GLU193 2.7 69.9 1.0
NH2 A:ARG189 2.8 67.7 1.0
CD A:GLU193 2.9 59.1 1.0
CZ A:ARG189 3.9 69.9 1.0
CG A:GLU193 4.4 49.5 1.0
NZ A:LYS197 4.6 54.2 1.0
NE A:ARG189 4.6 70.3 1.0
NH1 A:ARG189 4.8 73.2 1.0

Zinc binding site 7 out of 10 in 4gqt

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Zinc binding site 7 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:46.7
occ:1.00
O A:HOH650 1.9 23.1 1.0
O A:HOH651 2.0 33.1 1.0
OD2 A:ASP184 2.1 57.0 1.0
O A:HOH691 2.4 47.6 1.0
CG A:ASP184 3.1 55.3 1.0
OD1 A:ASP184 3.4 58.2 1.0
O A:HOH631 4.5 36.9 1.0
CB A:ASP184 4.5 44.5 1.0

Zinc binding site 8 out of 10 in 4gqt

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Zinc binding site 8 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:29.5
occ:1.00
O B:HOH647 1.9 28.6 1.0
O1B B:ADP500 2.0 26.1 1.0
OD1 B:ASN39 2.1 25.6 1.0
O1A B:ADP500 2.1 25.2 1.0
O B:HOH646 2.1 32.1 1.0
O B:HOH645 2.3 28.1 1.0
CG B:ASN39 3.0 24.6 1.0
PB B:ADP500 3.1 24.1 1.0
PA B:ADP500 3.1 25.7 1.0
O3A B:ADP500 3.3 25.5 1.0
ND2 B:ASN39 3.4 24.9 1.0
O3B B:ADP500 3.5 27.0 1.0
O5' B:ADP500 3.9 24.3 1.0
O B:HOH609 4.0 26.2 1.0
OE1 B:GLU35 4.2 30.6 1.0
CA B:GLY125 4.3 26.9 1.0
O2B B:ADP500 4.3 26.4 1.0
CB B:ASN39 4.4 24.1 1.0
O B:GLU35 4.4 24.0 1.0
O2A B:ADP500 4.4 25.7 1.0
N B:GLY125 4.5 24.9 1.0
OG B:SER38 4.6 43.7 1.0
N B:PHE126 4.6 28.0 1.0
CA B:ASN39 4.7 23.6 1.0
N B:ASN39 4.8 24.3 1.0
C B:GLY125 4.8 27.2 1.0
OD2 B:ASP42 5.0 32.5 1.0

Zinc binding site 9 out of 10 in 4gqt

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Zinc binding site 9 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:32.2
occ:1.00
OE2 A:GLU74 1.9 40.3 1.0
O B:HOH627 2.0 27.6 1.0
O B:HOH634 2.1 36.1 1.0
ND1 B:HIS177 2.1 25.3 1.0
CD A:GLU74 2.8 38.5 1.0
CE1 B:HIS177 3.1 24.3 1.0
CG B:HIS177 3.1 23.7 1.0
CG A:GLU74 3.2 34.5 1.0
CB B:HIS177 3.5 23.6 1.0
O B:HOH608 3.8 25.1 1.0
OE1 A:GLU74 3.9 36.8 1.0
O B:GLU74 4.0 28.8 1.0
CG2 B:THR76 4.2 24.8 1.0
NE2 B:HIS177 4.2 24.7 1.0
CD2 B:HIS177 4.3 23.3 1.0
CA B:HIS177 4.4 24.9 1.0
CB A:GLU74 4.7 31.9 1.0
NZ B:LYS135 4.9 36.9 1.0
CE B:LYS135 5.0 35.5 1.0

Zinc binding site 10 out of 10 in 4gqt

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Zinc binding site 10 out of 10 in the N-Terminal Domain of C. Elegans HSP90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of N-Terminal Domain of C. Elegans HSP90 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:37.9
occ:1.00
O B:HOH642 2.0 38.2 1.0
OE2 B:GLU30 2.2 42.7 1.0
O B:HOH631 2.2 34.6 1.0
NE2 B:HIS198 2.3 46.9 1.0
CD B:GLU30 2.9 36.4 1.0
OE1 B:GLU30 2.9 36.8 1.0
CD2 B:HIS198 3.0 45.2 1.0
CE1 B:HIS198 3.4 42.0 1.0
O B:HOH663 4.0 36.9 1.0
OE1 B:GLU193 4.3 47.1 1.0
CG B:GLU30 4.3 35.7 1.0
CG B:HIS198 4.3 45.2 1.0
OE2 B:GLU193 4.3 48.9 1.0
ND1 B:HIS198 4.4 44.1 1.0
O B:HOH635 4.5 40.2 1.0
CD B:GLU193 4.8 44.8 1.0

Reference:

J.Osipiuk, G.Chhor, M.Gu, P.Van Oosten-Hawle, R.I.Morimoto, A.Joachimiak. N-Terminal Domain of C. Elegans HSP90 To Be Published.
Page generated: Wed Dec 16 05:20:15 2020

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