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Zinc in PDB 6jmt: Crystal Structure of Git/Pix Complex

Protein crystallography data

The structure of Crystal Structure of Git/Pix Complex, PDB code: 6jmt was solved by J.Zhu, L.Lin, Y.Xia, R.Zhang, M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.05 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 168.963, 322.681, 44.469, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Git/Pix Complex (pdb code 6jmt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Git/Pix Complex, PDB code: 6jmt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6jmt

Go back to Zinc Binding Sites List in 6jmt
Zinc binding site 1 out of 6 in the Crystal Structure of Git/Pix Complex


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 Git/Pix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:39.5
occ:1.00
 SG A:CYS34 2.2 34.7 1.0
SG A:CYS11 2.3 40.5 1.0
SG A:CYS31 2.4 40.3 1.0
SG A:CYS14 2.4 68.9 1.0
CB A:CYS34 3.3 39.0 1.0
CB A:CYS14 3.3 44.4 1.0
CB A:CYS11 3.3 43.0 1.0
CB A:CYS31 3.6 28.7 1.0
N A:CYS14 3.9 42.7 1.0
N A:CYS31 4.0 30.6 1.0
CA A:CYS14 4.2 43.2 1.0
N A:CYS34 4.2 41.6 1.0
CA A:CYS31 4.3 31.4 1.0
NZ A:LYS103 4.4 48.8 1.0
CA A:CYS34 4.4 39.9 1.0
C A:ASP13 4.6 42.2 1.0
CE A:LYS103 4.6 48.7 1.0
CB A:ASP13 4.6 40.9 1.0
CA A:CYS11 4.8 41.2 1.0
C A:CYS14 4.9 41.7 1.0
C A:CYS31 4.9 34.2 1.0
N A:GLY16 4.9 50.1 1.0
CA A:ASP13 5.0 40.2 1.0
O A:CYS31 5.0 34.3 1.0
N A:ASP13 5.0 39.6 1.0

Zinc binding site 2 out of 6 in 6jmt

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Zinc binding site 2 out of 6 in the Crystal Structure of Git/Pix Complex


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 Git/Pix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:41.7
occ:1.00
 SG D:CYS34 2.3 45.0 1.0
SG D:CYS14 2.3 41.8 1.0
SG D:CYS31 2.3 43.6 1.0
SG D:CYS11 2.4 25.7 1.0
CB D:CYS14 3.3 43.4 1.0
CB D:CYS34 3.3 36.6 1.0
CB D:CYS11 3.4 37.5 1.0
CB D:CYS31 3.6 24.3 1.0
N D:CYS14 3.7 43.8 1.0
N D:CYS31 4.0 23.9 1.0
CA D:CYS14 4.0 42.7 1.0
N D:CYS34 4.3 37.3 1.0
CA D:CYS31 4.4 24.3 1.0
CA D:CYS34 4.4 37.3 1.0
C D:ASP13 4.5 45.8 1.0
CB D:ASP13 4.5 26.4 1.0
NZ D:LYS103 4.6 35.1 1.0
C D:CYS14 4.7 41.8 1.0
N D:GLY16 4.7 41.6 1.0
CA D:ASP13 4.8 27.1 1.0
N D:ASP13 4.8 29.1 1.0
CA D:CYS11 4.8 37.1 1.0
N D:ASN15 4.9 41.0 1.0
CE D:LYS103 4.9 34.4 1.0

Zinc binding site 3 out of 6 in 6jmt

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Zinc binding site 3 out of 6 in the Crystal Structure of Git/Pix Complex


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 Git/Pix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:28.4
occ:1.00
 SG B:CYS14 2.3 40.1 1.0
SG B:CYS11 2.4 26.9 1.0
SG B:CYS34 2.4 26.1 1.0
SG B:CYS31 2.5 32.3 1.0
CB B:CYS14 3.2 37.1 1.0
CB B:CYS11 3.3 35.1 1.0
CB B:CYS34 3.4 30.0 1.0
CB B:CYS31 3.7 26.4 1.0
N B:CYS14 3.8 35.9 1.0
CA B:CYS14 4.0 36.6 1.0
N B:CYS31 4.1 26.6 1.0
N B:CYS34 4.4 33.2 1.0
CA B:CYS31 4.5 27.7 1.0
CA B:CYS34 4.5 30.7 1.0
CE B:LYS103 4.5 36.8 1.0
NZ B:LYS103 4.5 36.6 1.0
C B:ASP13 4.6 33.5 1.0
CB B:ASP13 4.6 28.5 1.0
C B:CYS14 4.7 36.3 1.0
CA B:CYS11 4.8 35.6 1.0
N B:GLY16 4.8 39.1 1.0
N B:ASP13 4.9 31.0 1.0
CD B:LYS103 4.9 37.8 1.0
N B:ASN15 4.9 35.4 1.0
CA B:ASP13 4.9 30.1 1.0

Zinc binding site 4 out of 6 in 6jmt

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Zinc binding site 4 out of 6 in the Crystal Structure of Git/Pix Complex


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 Git/Pix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:53.2
occ:1.00
 SG C:CYS14 2.3 69.6 1.0
SG C:CYS31 2.4 32.1 1.0
SG C:CYS34 2.4 49.4 1.0
SG C:CYS11 2.4 38.8 1.0
CB C:CYS34 3.2 44.6 1.0
CB C:CYS14 3.3 53.8 1.0
CB C:CYS11 3.4 52.6 1.0
CB C:CYS31 3.5 50.5 1.0
N C:CYS14 3.8 53.1 1.0
N C:CYS31 4.0 48.3 1.0
CA C:CYS14 4.1 54.3 1.0
N C:CYS34 4.2 46.1 1.0
CA C:CYS34 4.3 44.5 1.0
CA C:CYS31 4.3 51.0 1.0
NZ C:LYS103 4.4 59.6 1.0
C C:ASP13 4.5 52.0 1.0
CE C:LYS103 4.5 60.2 1.0
CB C:ASP13 4.7 47.6 1.0
C C:CYS14 4.8 55.6 1.0
CA C:CYS11 4.8 53.6 1.0
CD C:LYS103 4.8 59.7 1.0
C C:CYS31 4.9 53.1 1.0
O C:CYS31 4.9 52.0 1.0
CA C:ASP13 5.0 50.0 1.0
N C:ASP13 5.0 50.0 1.0
N C:GLY16 5.0 55.6 1.0
N C:ASN15 5.0 56.3 1.0

Zinc binding site 5 out of 6 in 6jmt

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Zinc binding site 5 out of 6 in the Crystal Structure of Git/Pix Complex


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 Git/Pix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:51.3
occ:1.00
 SG E:CYS31 2.2 42.2 1.0
SG E:CYS14 2.3 41.3 1.0
SG E:CYS34 2.4 64.9 1.0
SG E:CYS11 2.5 48.0 1.0
CB E:CYS14 3.2 48.7 1.0
CB E:CYS34 3.3 47.8 1.0
CB E:CYS31 3.5 43.1 1.0
CB E:CYS11 3.5 42.4 1.0
N E:CYS14 3.6 50.4 1.0
CA E:CYS14 4.0 51.0 1.0
N E:CYS31 4.0 40.5 1.0
CA E:CYS31 4.3 42.7 1.0
N E:CYS34 4.3 45.8 1.0
NZ E:LYS103 4.3 53.3 1.0
CA E:CYS34 4.4 46.2 1.0
C E:ASP13 4.5 49.4 1.0
CB E:ASP13 4.5 41.7 1.0
C E:CYS14 4.7 55.3 1.0
CE E:LYS103 4.7 54.6 1.0
CA E:ASP13 4.8 44.9 1.0
C E:CYS31 4.8 46.8 1.0
N E:GLY16 4.8 55.5 1.0
N E:ASP13 4.9 44.2 1.0
CD E:LYS103 4.9 55.3 1.0
O E:CYS31 4.9 48.1 1.0
CA E:CYS11 4.9 42.4 1.0
N E:ASN15 5.0 56.3 1.0

Zinc binding site 6 out of 6 in 6jmt

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Zinc binding site 6 out of 6 in the Crystal Structure of Git/Pix Complex


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 Git/Pix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:39.2
occ:1.00
 SG F:CYS31 2.2 34.2 1.0
SG F:CYS34 2.3 45.0 1.0
SG F:CYS11 2.3 40.9 1.0
SG F:CYS14 2.4 37.6 1.0
CB F:CYS11 3.2 36.1 1.0
CB F:CYS14 3.2 40.8 1.0
CB F:CYS34 3.4 33.8 1.0
CB F:CYS31 3.6 30.8 1.0
N F:CYS14 3.6 39.6 1.0
CA F:CYS14 4.0 40.4 1.0
N F:CYS31 4.0 29.8 1.0
N F:CYS34 4.4 36.7 1.0
CA F:CYS31 4.4 31.3 1.0
C F:ASP13 4.5 38.7 1.0
CA F:CYS34 4.5 36.2 1.0
NZ F:LYS103 4.5 31.6 1.0
C F:CYS14 4.6 41.2 1.0
CB F:ASP13 4.6 34.8 1.0
CE F:LYS103 4.6 32.0 1.0
CA F:CYS11 4.7 36.6 1.0
N F:GLY16 4.8 41.9 1.0
N F:ASN15 4.9 41.4 1.0
N F:ASP13 4.9 33.4 1.0
CA F:ASP13 4.9 35.0 1.0
CD F:LYS103 5.0 32.3 1.0
C F:CYS31 5.0 34.0 1.0

Reference:

J.Zhu, L.Lin, Y.Xia, R.Zhang, M.Zhang. Crystal Structure of GIT1/Pix Complex To Be Published.
Page generated: Tue Oct 29 01:11:54 2024

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