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Zinc in PDB 3lrq: Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.

Protein crystallography data

The structure of Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D., PDB code: 3lrq was solved by A.Kuzin, Y.Chen, J.Seetharaman, M.Mao, R.Xiao, C.Ciccosanti, R.Shastry, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.01 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.544, 34.922, 86.709, 90.00, 90.78, 90.00
R / Rfree (%) 19 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. (pdb code 3lrq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D., PDB code: 3lrq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3lrq

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Zinc binding site 1 out of 8 in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.


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 the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn100

b:27.5
occ:1.00
SG A:CYS39 2.4 26.8 1.0
SG A:CYS15 2.4 24.2 1.0
SG A:CYS18 2.4 24.1 1.0
SG A:CYS36 2.4 23.1 1.0
CB A:CYS15 2.9 12.6 1.0
CB A:CYS36 3.2 16.5 1.0
CB A:CYS18 3.3 18.3 1.0
CB A:CYS39 3.4 26.4 1.0
N A:CYS36 3.9 26.5 1.0
O A:HOH137 3.9 40.9 1.0
O A:HOH127 3.9 43.9 1.0
N A:CYS18 3.9 29.4 1.0
CA A:CYS36 4.2 23.1 1.0
CA A:CYS18 4.2 25.7 1.0
CA A:CYS15 4.4 18.1 1.0
CA A:CYS39 4.7 23.1 1.0
C A:CYS18 4.9 19.7 1.0
C A:ILE17 5.0 25.7 1.0
O A:HOH98 5.0 28.4 1.0

Zinc binding site 2 out of 8 in 3lrq

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Zinc binding site 2 out of 8 in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.


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 the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:32.0
occ:1.00
SG A:CYS31 2.3 28.3 1.0
SG A:CYS51 2.4 28.2 1.0
SG A:CYS54 2.4 34.0 1.0
SG A:CYS28 2.4 31.2 1.0
CB A:CYS51 3.0 17.5 1.0
CB A:CYS54 3.2 24.9 1.0
CB A:CYS31 3.2 28.1 1.0
CB A:CYS28 3.2 22.1 1.0
N A:CYS54 3.8 34.0 1.0
N A:CYS31 3.8 34.0 1.0
CA A:CYS31 4.0 30.7 1.0
CA A:CYS54 4.0 33.2 1.0
CA A:CYS51 4.5 23.4 1.0
C A:HIS30 4.6 39.6 1.0
CB A:HIS30 4.7 30.4 1.0
CA A:CYS28 4.7 20.7 1.0
ND1 A:HIS53 4.8 30.1 1.0
C A:CYS31 4.8 21.0 1.0
C A:CYS54 4.8 38.1 1.0
N A:SER32 4.9 25.0 1.0
O A:HOH91 4.9 42.0 1.0
CB A:HIS53 4.9 20.7 1.0
C A:HIS53 4.9 32.3 1.0
N A:ARG55 4.9 38.4 1.0
N A:HIS30 5.0 29.2 1.0
C A:CYS28 5.0 28.8 1.0
O A:CYS28 5.0 28.6 1.0
CA A:HIS30 5.0 31.7 1.0

Zinc binding site 3 out of 8 in 3lrq

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Zinc binding site 3 out of 8 in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.


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 the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn100

b:39.6
occ:1.00
SG B:CYS39 2.2 32.6 1.0
SG B:CYS15 2.3 33.3 1.0
SG B:CYS18 2.5 52.4 1.0
SG B:CYS36 2.5 37.7 1.0
CB B:CYS15 3.0 22.5 1.0
CB B:CYS39 3.1 26.8 1.0
CB B:CYS36 3.2 20.4 1.0
CB B:CYS18 3.4 33.0 1.0
N B:CYS36 3.7 31.0 1.0
N B:CYS18 3.9 39.6 1.0
CA B:CYS36 4.1 29.4 1.0
CA B:CYS18 4.2 37.6 1.0
CA B:CYS15 4.5 31.6 1.0
CA B:CYS39 4.5 34.5 1.0
CB B:ILE17 4.8 35.9 1.0
N B:CYS39 4.8 39.4 1.0
C B:CYS35 4.9 34.2 1.0
C B:ILE17 4.9 39.4 1.0
C B:CYS18 5.0 38.9 1.0

Zinc binding site 4 out of 8 in 3lrq

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Zinc binding site 4 out of 8 in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.


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 the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:38.5
occ:1.00
SG B:CYS31 2.3 34.5 1.0
SG B:CYS28 2.4 38.5 1.0
SG B:CYS51 2.4 35.8 1.0
SG B:CYS54 2.5 39.2 1.0
CB B:CYS51 3.1 30.2 1.0
CB B:CYS31 3.1 40.0 1.0
CB B:CYS28 3.1 34.0 1.0
CB B:CYS54 3.2 32.2 1.0
N B:CYS31 3.6 44.0 1.0
N B:CYS54 3.7 42.9 1.0
CA B:CYS31 3.9 38.4 1.0
CA B:CYS54 4.0 42.5 1.0
CA B:CYS51 4.6 36.6 1.0
CA B:CYS28 4.6 37.6 1.0
C B:HIS30 4.6 45.7 1.0
CB B:HIS30 4.7 43.0 1.0
ND1 B:HIS53 4.7 43.2 1.0
C B:CYS31 4.7 37.0 1.0
N B:SER32 4.8 30.7 1.0
C B:CYS54 4.8 46.9 1.0
C B:HIS53 4.9 47.2 1.0
N B:ARG55 4.9 42.6 1.0
CB B:HIS53 4.9 37.5 1.0
CA B:HIS30 5.0 42.7 1.0
N B:HIS30 5.0 42.6 1.0

Zinc binding site 5 out of 8 in 3lrq

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Zinc binding site 5 out of 8 in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.


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 the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn100

b:47.3
occ:1.00
SG C:CYS36 2.4 54.8 1.0
SG C:CYS39 2.4 46.5 1.0
SG C:CYS18 2.4 45.9 1.0
SG C:CYS15 2.5 41.9 1.0
CB C:CYS15 3.0 43.6 1.0
CB C:CYS18 3.1 33.4 1.0
CB C:CYS36 3.1 40.1 1.0
CB C:CYS39 3.5 43.0 1.0
N C:CYS18 3.8 42.5 1.0
N C:CYS36 3.8 28.2 1.0
CA C:CYS18 4.0 45.6 1.0
CA C:CYS36 4.1 39.4 1.0
CA C:CYS15 4.5 43.4 1.0
C C:CYS18 4.8 51.5 1.0
CA C:CYS39 4.8 41.4 1.0
CB C:ILE17 4.9 51.7 1.0
C C:ILE17 5.0 44.4 1.0

Zinc binding site 6 out of 8 in 3lrq

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Zinc binding site 6 out of 8 in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.


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 the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:44.9
occ:1.00
SG C:CYS28 2.4 50.1 1.0
SG C:CYS31 2.4 43.7 1.0
SG C:CYS51 2.4 40.5 1.0
CB C:CYS54 2.6 31.3 1.0
CB C:CYS28 3.1 40.2 1.0
CB C:CYS51 3.2 40.8 1.0
CB C:CYS31 3.3 40.8 1.0
N C:CYS31 3.6 41.7 1.0
SG C:CYS54 3.6 0.9 1.0
N C:CYS54 3.7 48.5 1.0
CA C:CYS54 3.7 47.3 1.0
CA C:CYS31 4.0 41.7 1.0
CB C:HIS30 4.5 43.8 1.0
C C:HIS30 4.5 48.6 1.0
ND1 C:HIS53 4.5 86.0 1.0
CA C:CYS28 4.6 37.4 1.0
CA C:CYS51 4.7 39.5 1.0
C C:CYS31 4.7 41.0 1.0
N C:SER32 4.8 38.0 1.0
CA C:HIS30 4.8 48.2 1.0
N C:HIS30 4.8 42.4 1.0
C C:HIS53 4.8 46.1 1.0
C C:CYS54 4.9 46.4 1.0
C C:CYS28 4.9 32.8 1.0
O C:CYS28 5.0 28.6 1.0
CB C:HIS53 5.0 71.2 1.0

Zinc binding site 7 out of 8 in 3lrq

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Zinc binding site 7 out of 8 in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn100

b:36.6
occ:1.00
SG D:CYS39 2.3 36.6 1.0
SG D:CYS18 2.4 37.5 1.0
SG D:CYS36 2.4 36.6 1.0
SG D:CYS15 2.4 31.4 1.0
CB D:CYS15 3.1 27.1 1.0
CB D:CYS36 3.1 22.4 1.0
CB D:CYS39 3.4 21.7 1.0
CB D:CYS18 3.4 31.1 1.0
N D:CYS36 3.8 26.9 1.0
NH2 D:ARG23 3.9 93.3 1.0
N D:CYS18 4.0 36.2 1.0
CA D:CYS36 4.1 28.3 1.0
CA D:CYS18 4.3 33.1 1.0
CA D:CYS15 4.6 31.1 1.0
CA D:CYS39 4.7 27.6 1.0
CZ D:ARG23 4.8 87.2 1.0
C D:CYS18 4.9 36.2 1.0
O D:CYS36 4.9 28.7 1.0
N D:CYS39 5.0 34.6 1.0
NE D:ARG23 5.0 83.6 1.0
C D:CYS36 5.0 30.7 1.0

Zinc binding site 8 out of 8 in 3lrq

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Zinc binding site 8 out of 8 in the Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the U-Box Domain of Human Ubiquitin-Protein Ligase (E3), Northeast Structural Genomics Consortium Target HR4604D. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:42.6
occ:1.00
SG D:CYS28 2.1 36.9 1.0
SG D:CYS31 2.4 48.9 1.0
SG D:CYS51 2.4 37.2 1.0
CB D:CYS54 2.7 9.7 1.0
SG D:CYS54 2.9 0.3 1.0
CB D:CYS28 3.0 36.6 1.0
CB D:CYS51 3.1 58.0 1.0
N D:CYS54 3.4 55.4 1.0
CB D:CYS31 3.4 40.3 1.0
N D:CYS31 3.6 47.6 1.0
CA D:CYS54 3.6 61.7 1.0
CA D:CYS31 4.0 41.9 1.0
CB D:HIS30 4.4 55.3 1.0
CA D:CYS28 4.4 41.8 1.0
C D:HIS30 4.5 57.1 1.0
C D:HIS53 4.6 49.1 1.0
CA D:CYS51 4.6 50.2 1.0
O D:CYS28 4.7 31.0 1.0
N D:HIS30 4.7 46.7 1.0
C D:CYS31 4.7 37.4 1.0
C D:CYS28 4.7 40.0 1.0
CA D:HIS30 4.7 53.9 1.0
CB D:HIS53 4.8 46.4 1.0
N D:SER32 4.8 31.8 1.0
C D:CYS54 4.8 67.2 1.0
CD2 D:HIS30 5.0 48.9 1.0

Reference:

A.Kuzin, Y.Chen, J.Seetharaman, M.Mao, R.Xiao, C.Ciccosanti, R.Shastry, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, L.Tong, J.F.Hunt. E3 Ubiquitin-Protein Ligase Ring Domain From Human Tripartite Motif-Containing Protein 37 (TRIM37), Northeast Structural Genomics Consortium Target HR4604D. To Be Published.
Page generated: Wed Dec 16 04:32:51 2020

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