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Zinc in PDB 1r4n: APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp

Protein crystallography data

The structure of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp, PDB code: 1r4n was solved by H.Walden, M.S.Podgorski, J.M.Holton, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.000, 197.900, 211.000, 90.00, 90.00, 90.00
R / Rfree (%) 25.1 / 29

Zinc Binding Sites:

The binding sites of Zinc atom in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp (pdb code 1r4n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp, PDB code: 1r4n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1r4n

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Zinc binding site 1 out of 4 in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1

b:71.9
occ:1.00
SG H:CYS346 2.0 63.0 1.0
SG H:CYS343 2.2 65.1 1.0
SG H:CYS199 2.2 0.0 1.0
SG H:CYS202 2.5 52.5 1.0
CB H:CYS346 2.7 63.0 1.0
CB H:CYS343 2.8 65.1 1.0
N H:CYS346 2.9 80.7 1.0
CB H:CYS199 3.3 0.0 1.0
CA H:CYS346 3.3 80.7 1.0
N H:CYS199 4.0 56.7 1.0
N H:CYS202 4.0 63.9 1.0
CB H:CYS202 4.0 52.5 1.0
C H:ALA345 4.1 72.4 1.0
CA H:CYS199 4.2 56.7 1.0
C H:CYS346 4.3 80.7 1.0
CA H:CYS343 4.3 92.6 1.0
CA H:CYS202 4.3 63.9 1.0
CB H:ALA345 4.4 83.8 1.0
CB H:GLU201 4.5 83.0 1.0
CA H:ALA345 4.6 72.4 1.0
C H:GLU201 4.7 0.5 1.0
N H:ALA345 4.7 72.4 1.0
C H:CYS343 4.8 92.6 1.0
O H:CYS346 4.8 80.7 1.0
C H:CYS199 4.8 56.7 1.0
N H:SER347 4.9 88.6 1.0
O H:CYS343 4.9 92.6 1.0

Zinc binding site 2 out of 4 in 1r4n

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Zinc binding site 2 out of 4 in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2

b:71.9
occ:1.00
CB D:GLU338 2.9 0.2 1.0
NZ J:LYS148 3.2 99.1 1.0
CD J:LYS148 3.3 99.1 1.0
CG D:GLU338 3.5 0.2 1.0
CE J:LYS148 3.5 99.1 1.0
OE1 D:GLU338 3.6 0.2 1.0
CD D:GLU338 4.0 0.2 1.0
CA D:GLU338 4.3 83.5 1.0
CG J:LYS148 4.4 99.1 1.0
C D:GLU338 4.5 83.5 1.0
O D:GLU338 4.8 83.5 1.0
O D:ARG339 4.8 68.0 1.0
N D:ARG339 4.9 68.0 1.0
CA J:LYS148 5.0 88.9 1.0
C D:ARG339 5.0 68.0 1.0

Zinc binding site 3 out of 4 in 1r4n

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Zinc binding site 3 out of 4 in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn3

b:71.9
occ:1.00
SG F:CYS199 2.0 67.8 1.0
SG F:CYS343 2.0 71.3 1.0
SG F:CYS346 2.1 48.4 1.0
SG F:CYS202 2.3 31.7 1.0
CB F:CYS343 2.9 71.3 1.0
CB F:CYS346 3.0 48.4 1.0
CB F:CYS199 3.1 67.8 1.0
N F:CYS346 3.3 82.2 1.0
N F:CYS202 3.6 91.0 1.0
CB F:CYS202 3.7 31.7 1.0
CA F:CYS346 3.7 82.2 1.0
N F:CYS199 3.8 51.9 1.0
CA F:CYS202 4.0 91.0 1.0
CA F:CYS199 4.0 51.9 1.0
CB F:GLU201 4.3 89.9 1.0
CA F:CYS343 4.3 80.0 1.0
C F:GLU201 4.3 89.9 1.0
C F:ALA345 4.4 60.6 1.0
CB F:ALA345 4.5 51.9 1.0
C F:CYS199 4.6 51.9 1.0
C F:CYS346 4.6 82.2 1.0
N F:GLU201 4.7 89.9 1.0
CA F:GLU201 4.7 89.9 1.0
CA F:ALA345 4.8 60.6 1.0
N F:ALA345 4.9 60.6 1.0
C F:CYS343 4.9 80.0 1.0

Zinc binding site 4 out of 4 in 1r4n

Go back to Zinc Binding Sites List in 1r4n
Zinc binding site 4 out of 4 in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn4

b:71.9
occ:1.00
CB H:SER373 2.7 0.2 1.0
O H:SER373 2.8 58.8 1.0
CA H:SER373 3.0 58.8 1.0
NZ H:LYS340 3.3 85.7 1.0
C H:SER373 3.3 58.8 1.0
CD H:LYS340 4.0 85.7 1.0
OG H:SER373 4.0 0.2 1.0
CE H:LYS340 4.1 85.7 1.0
O H:GLU201 4.2 0.5 1.0
N H:SER373 4.4 58.8 1.0
CD H:PRO344 4.4 1.0 1.0
OE2 H:GLU205 4.6 1.0 1.0
O H:CYS202 4.6 63.9 1.0
N H:LEU374 4.6 86.9 1.0
CG H:PRO344 4.7 1.0 1.0
O H:ALA372 4.7 0.5 1.0
C H:ALA372 5.0 0.5 1.0

Reference:

H.Walden, M.S.Podgorski, D.T.Huang, D.W.Miller, R.J.Howard, D.L.Minor, J.M.Holton, B.A.Schulman. The Structure of the APPBP1-UBA3-NEDD8-Atp Complex Reveals the Basis For Selective Ubiquitin-Like Protein Activation By An E1. Mol.Cell V. 12 1427 2003.
ISSN: ISSN 1097-2765
PubMed: 14690597
DOI: 10.1016/S1097-2765(03)00452-0
Page generated: Wed Dec 16 03:02:33 2020

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