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Zinc in PDB 4f52: Structure of A Glomulin-RBX1-CUL1 Complex

Protein crystallography data

The structure of Structure of A Glomulin-RBX1-CUL1 Complex, PDB code: 4f52 was solved by D.M.Duda, J.L.Olszewski, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.39 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.333, 193.932, 142.075, 90.00, 98.81, 90.00
R / Rfree (%) 21.9 / 28.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Glomulin-RBX1-CUL1 Complex (pdb code 4f52). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A Glomulin-RBX1-CUL1 Complex, PDB code: 4f52:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4f52

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Zinc binding site 1 out of 6 in the Structure of A Glomulin-RBX1-CUL1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Glomulin-RBX1-CUL1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:91.5
occ:1.00
ND1 B:HIS80 2.1 0.0 1.0
SG B:CYS42 2.1 88.3 1.0
SG B:CYS45 2.3 0.4 1.0
SG B:CYS83 2.4 84.1 1.0
CB B:CYS42 2.7 88.8 1.0
CG B:HIS80 3.0 0.3 1.0
CE1 B:HIS80 3.0 0.4 1.0
CB B:HIS80 3.3 0.0 1.0
CB B:CYS45 3.5 0.4 1.0
CB B:CYS83 3.6 0.8 1.0
N B:CYS45 3.9 0.1 1.0
NE2 B:HIS80 4.0 0.7 1.0
CD2 B:HIS80 4.1 0.8 1.0
CA B:CYS42 4.2 83.3 1.0
CA B:CYS45 4.2 0.5 1.0
CB B:CYS53 4.2 93.5 1.0
N B:HIS80 4.2 97.8 1.0
O B:CYS45 4.2 0.9 1.0
C B:CYS45 4.3 0.8 1.0
CA B:HIS80 4.4 0.2 1.0
CA B:CYS53 4.4 0.9 1.0
C B:CYS42 4.7 74.4 1.0
CA B:CYS83 4.9 0.9 1.0
O B:CYS42 5.0 67.1 1.0

Zinc binding site 2 out of 6 in 4f52

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Zinc binding site 2 out of 6 in the Structure of A Glomulin-RBX1-CUL1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Glomulin-RBX1-CUL1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:96.8
occ:1.00
CE1 B:HIS77 1.2 0.1 1.0
ND1 B:HIS77 2.1 0.8 1.0
OD2 B:ASP97 2.1 0.9 1.0
NE2 B:HIS77 2.2 0.4 1.0
SG B:CYS94 2.3 96.2 1.0
SG B:CYS75 2.4 0.8 1.0
CG B:ASP97 3.0 0.7 1.0
CB B:CYS75 3.1 0.8 1.0
CG B:HIS77 3.1 0.6 1.0
CD2 B:HIS77 3.2 0.3 1.0
OD1 B:ASP97 3.4 0.8 1.0
CB B:CYS94 3.6 96.7 1.0
N B:ASP97 4.0 0.4 1.0
CB B:ASP97 4.1 1.0 1.0
CZ3 B:TRP101 4.2 0.2 1.0
CB B:LEU96 4.2 0.6 1.0
CB B:HIS77 4.5 0.8 1.0
CA B:CYS75 4.5 0.5 1.0
CA B:ASP97 4.6 0.7 1.0
N B:LEU96 4.7 0.4 1.0
O B:ASP97 4.8 0.1 1.0
CE3 B:TRP101 4.8 0.0 1.0
CA B:LEU96 4.8 0.9 1.0
N B:HIS77 4.9 0.6 1.0
C B:CYS75 4.9 0.5 1.0
CA B:CYS94 4.9 0.1 1.0
C B:LEU96 4.9 0.1 1.0
C B:ASP97 4.9 0.7 1.0

Zinc binding site 3 out of 6 in 4f52

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Zinc binding site 3 out of 6 in the Structure of A Glomulin-RBX1-CUL1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Glomulin-RBX1-CUL1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:0.3
occ:1.00
ND1 B:HIS82 2.1 0.2 1.0
SG B:CYS56 2.3 0.2 1.0
SG B:CYS68 2.3 86.8 1.0
SG B:CYS53 2.6 0.1 1.0
CB B:CYS68 2.6 0.8 1.0
CG B:HIS82 2.6 0.2 1.0
CE1 B:HIS82 2.6 0.8 1.0
CB B:CYS56 2.9 0.7 1.0
CD2 B:HIS82 3.2 0.7 1.0
NE2 B:HIS82 3.2 0.9 1.0
CB B:HIS82 3.3 0.7 1.0
CB B:CYS53 3.3 93.5 1.0
CA B:CYS68 3.7 0.1 1.0
N B:CYS68 3.7 0.3 1.0
CA B:CYS56 4.1 0.4 1.0
N B:CYS56 4.1 0.2 1.0
CA B:CYS53 4.3 0.9 1.0
O B:CYS53 4.4 0.1 1.0
N B:CYS53 4.4 0.4 1.0
C B:CYS53 4.6 0.1 1.0
CA B:HIS82 4.7 0.7 1.0
C B:CYS68 4.9 0.1 1.0

Zinc binding site 4 out of 6 in 4f52

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Zinc binding site 4 out of 6 in the Structure of A Glomulin-RBX1-CUL1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Glomulin-RBX1-CUL1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:79.1
occ:1.00
ND1 D:HIS80 2.1 90.0 1.0
SG D:CYS42 2.2 0.8 1.0
SG D:CYS45 2.4 88.9 1.0
SG D:CYS83 2.5 89.5 1.0
CB D:CYS42 2.9 68.9 1.0
CE1 D:HIS80 2.9 90.7 1.0
CB D:CYS45 3.0 83.8 1.0
CG D:HIS80 3.1 84.5 1.0
CB D:CYS83 3.5 0.2 1.0
CB D:HIS80 3.6 83.1 1.0
N D:CYS45 3.6 81.8 1.0
CA D:CYS45 3.8 78.3 1.0
NE2 D:HIS80 4.1 84.9 1.0
N D:HIS80 4.2 83.2 1.0
CD2 D:HIS80 4.2 81.1 1.0
CA D:CYS42 4.4 73.0 1.0
CB D:CYS53 4.4 93.8 1.0
CA D:CYS53 4.4 92.5 1.0
CA D:HIS80 4.5 88.0 1.0
C D:CYS45 4.6 75.5 1.0
N D:ARG46 4.7 77.5 1.0
CB D:ILE44 4.8 98.0 1.0
C D:ILE44 4.8 86.7 1.0
CA D:CYS83 4.9 0.2 1.0
C D:CYS42 4.9 73.2 1.0
O D:CYS42 4.9 69.6 1.0
N D:ASN47 5.0 96.0 1.0
CB D:ASN47 5.0 91.9 1.0
N D:ILE54 5.0 78.4 1.0

Zinc binding site 5 out of 6 in 4f52

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Zinc binding site 5 out of 6 in the Structure of A Glomulin-RBX1-CUL1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Glomulin-RBX1-CUL1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:0.3
occ:1.00
OD1 D:ASP97 1.9 0.1 1.0
CG D:ASP97 2.0 0.8 1.0
OD2 D:ASP97 2.0 0.7 1.0
ND1 D:HIS77 2.1 0.7 1.0
SG D:CYS75 2.3 0.9 1.0
SG D:CYS94 2.5 0.7 1.0
CE1 D:HIS77 3.0 0.3 1.0
CB D:CYS75 3.0 0.1 1.0
CG D:HIS77 3.1 0.3 1.0
CB D:ASP97 3.3 0.2 1.0
CB D:HIS77 3.5 0.2 1.0
CB D:CYS94 3.6 86.2 1.0
NE2 D:HIS77 4.1 1.0 1.0
CD2 D:HIS77 4.2 0.5 1.0
N D:ASP97 4.3 0.2 1.0
CA D:CYS75 4.3 0.2 1.0
O D:CYS75 4.4 0.0 1.0
CA D:ASP97 4.4 0.2 1.0
CZ3 D:TRP101 4.5 0.9 1.0
C D:CYS75 4.5 0.5 1.0
N D:HIS77 4.6 0.6 1.0
CA D:HIS77 4.7 0.9 1.0
CB D:LEU96 4.7 0.3 1.0
CA D:CYS94 5.0 85.2 1.0

Zinc binding site 6 out of 6 in 4f52

Go back to Zinc Binding Sites List in 4f52
Zinc binding site 6 out of 6 in the Structure of A Glomulin-RBX1-CUL1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Glomulin-RBX1-CUL1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:0.7
occ:1.00
ND1 D:HIS82 1.9 0.7 1.0
SG D:CYS68 2.0 97.6 1.0
SG D:CYS56 2.3 90.5 1.0
SG D:CYS53 2.5 0.2 1.0
CE1 D:HIS82 2.7 0.9 1.0
CG D:HIS82 2.9 0.5 1.0
CB D:CYS56 3.0 94.0 1.0
CB D:CYS53 3.0 93.8 1.0
CB D:CYS68 3.4 0.9 1.0
CB D:HIS82 3.4 0.9 1.0
N D:CYS53 3.8 94.4 1.0
NE2 D:HIS82 3.9 0.7 1.0
CD2 D:HIS82 4.0 0.8 1.0
CA D:CYS53 4.0 92.5 1.0
CA D:CYS68 4.1 0.2 1.0
CA D:CYS56 4.2 99.7 1.0
N D:CYS56 4.2 99.1 1.0
N D:CYS68 4.6 0.9 1.0
C D:CYS53 4.7 92.8 1.0
CA D:HIS82 4.9 0.8 1.0
O D:CYS53 5.0 0.8 1.0

Reference:

D.M.Duda, J.L.Olszewski, A.E.Tron, M.Hammel, L.J.Lambert, M.B.Waddell, T.Mittag, J.A.Decaprio, B.A.Schulman. Structure of A Glomulin-RBX1-CUL1 Complex: Inhibition of A Ring E3 Ligase Through Masking of Its E2-Binding Surface. Mol.Cell V. 47 371 2012.
ISSN: ISSN 1097-2765
PubMed: 22748924
DOI: 10.1016/J.MOLCEL.2012.05.044
Page generated: Wed Dec 16 05:16:54 2020

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