Zinc in PDB 7c07: Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.

The structure of Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna., PDB code: 7c07 was solved by H.Yoshida, S.Y.Park, T.Urano, E.Obayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.17 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.487, 256.947, 94.591, 90.00, 100.75, 90.00
R / Rfree (%)	25.5 / 28.5

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. (pdb code 7c07). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna., PDB code: 7c07:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


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 Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:60.8 occ:1.00 NE2 A:HIS37 2.1 52.9 1.0 SG A:CYS18 2.4 70.8 1.0 SG A:CYS27 2.5 68.2 1.0 SG A:CYS33 2.6 64.5 1.0 CE1 A:HIS37 3.0 62.5 1.0 CB A:CYS27 3.0 60.8 1.0 CD2 A:HIS37 3.2 60.4 1.0 CB A:CYS33 3.3 72.8 1.0 CB A:CYS18 3.3 59.4 1.0 N6 C:A2 4.1 63.7 1.0 ND1 A:HIS37 4.2 72.2 1.0 CG A:HIS37 4.3 62.3 1.0 CA A:CYS27 4.5 62.1 1.0 CA A:CYS18 4.7 67.7 1.0 O A:ARG35 4.7 66.9 1.0 CA A:CYS33 4.8 69.6 1.0 CD2 A:HIS29 4.8 75.3 1.0 CB A:TYR21 4.8 58.8 1.0 CB A:HIS29 5.0 57.8 1.0

Zinc binding site 2 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


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 Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:55.2 occ:1.00 NE2 A:HIS167 2.1 58.7 1.0 SG A:CYS149 2.4 76.5 1.0 SG A:CYS157 2.5 87.9 1.0 SG A:CYS163 2.5 68.1 1.0 CB A:CYS157 2.8 82.7 1.0 CE1 A:HIS167 3.0 54.7 1.0 CB A:CYS163 3.1 76.7 1.0 CD2 A:HIS167 3.2 60.6 1.0 CB A:CYS149 3.3 57.3 1.0 N2 C:G3 4.0 82.3 1.0 ND1 A:HIS167 4.2 53.1 1.0 CG A:HIS167 4.3 51.8 1.0 CA A:CYS157 4.4 97.3 1.0 CB A:HIS152 4.5 76.7 1.0 CA A:CYS163 4.5 72.2 1.0 N1 C:G3 4.6 75.0 1.0 CG A:GLN151 4.7 89.6 1.0 CA A:CYS149 4.7 57.7 1.0 O A:GLY160 4.8 84.2 1.0 C2 C:G3 4.8 75.3 1.0

Zinc binding site 3 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


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 Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:45.8 occ:1.00 NE2 D:HIS37 2.1 57.5 1.0 SG D:CYS18 2.4 52.2 1.0 SG D:CYS33 2.4 59.1 1.0 SG D:CYS27 2.4 75.4 1.0 CE1 D:HIS37 2.9 56.5 1.0 CB D:CYS27 2.9 51.5 1.0 CB D:CYS33 3.1 57.6 1.0 CD2 D:HIS37 3.2 60.2 1.0 CB D:CYS18 3.4 51.2 1.0 N6 F:A2 4.1 73.4 1.0 ND1 D:HIS37 4.1 53.8 1.0 CG D:HIS37 4.3 57.4 1.0 CA D:CYS27 4.4 57.8 1.0 CA D:CYS33 4.5 55.2 1.0 CA D:CYS18 4.7 51.5 1.0 CB D:TYR21 4.8 44.6 1.0 O D:ARG35 4.8 58.9 1.0 N D:TYR21 5.0 53.3 1.0 CD2 D:HIS29 5.0 65.0 1.0

Zinc binding site 4 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


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 Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:49.8 occ:1.00 NE2 D:HIS167 2.1 44.6 1.0 SG D:CYS149 2.4 62.3 1.0 SG D:CYS157 2.5 86.9 1.0 SG D:CYS163 2.6 41.3 1.0 CB D:CYS157 2.8 65.6 1.0 CB D:CYS149 3.1 46.6 1.0 CE1 D:HIS167 3.1 47.5 1.0 CD2 D:HIS167 3.1 51.6 1.0 CB D:CYS163 3.2 53.1 1.0 N2 F:G3 3.9 59.7 1.0 ND1 D:HIS167 4.2 66.0 1.0 CA D:CYS157 4.2 78.7 1.0 CG D:HIS167 4.3 63.4 1.0 CA D:CYS149 4.5 56.7 1.0 N1 F:G3 4.6 57.1 1.0 CA D:CYS163 4.7 36.6 1.0 CB D:HIS152 4.7 81.5 1.0 C2 F:G3 4.8 64.6 1.0 O D:GLY160 4.8 49.1 1.0 OE1 D:GLN151 4.9 71.7 1.0

Zinc binding site 5 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


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 Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:48.6 occ:1.00 NE2 G:HIS37 2.1 40.0 1.0 SG G:CYS33 2.4 69.1 1.0 SG G:CYS27 2.4 72.0 1.0 SG G:CYS18 2.5 52.4 1.0 CB G:CYS27 2.9 46.1 1.0 CE1 G:HIS37 3.0 33.4 1.0 CB G:CYS33 3.1 53.2 1.0 CD2 G:HIS37 3.2 54.1 1.0 CB G:CYS18 3.5 49.4 1.0 N6 I:A2 4.0 47.4 1.0 ND1 G:HIS37 4.2 39.6 1.0 CG G:HIS37 4.3 44.2 1.0 CA G:CYS27 4.4 52.2 1.0 CA G:CYS33 4.5 65.2 1.0 O G:ARG35 4.7 74.9 1.0 CB G:TYR21 4.8 47.5 1.0 O G:GLY30 4.8 71.4 1.0 CA G:CYS18 4.9 64.5 1.0 CD2 G:HIS29 5.0 70.9 1.0

Zinc binding site 6 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


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 Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn302 b:54.5 occ:1.00 NE2 G:HIS167 2.1 66.2 1.0 SG G:CYS163 2.4 50.8 1.0 SG G:CYS149 2.5 83.8 1.0 SG G:CYS157 2.6 62.4 1.0 CB G:CYS163 2.9 46.0 1.0 CE1 G:HIS167 3.0 54.6 1.0 CD2 G:HIS167 3.1 67.5 1.0 CB G:CYS149 3.2 55.4 1.0 CB G:CYS157 3.7 76.7 1.0 N2 I:G3 4.0 73.4 1.0 ND1 G:HIS167 4.1 62.8 1.0 CG G:HIS167 4.2 62.8 1.0 CA G:CYS163 4.3 36.8 1.0 N1 I:G3 4.5 44.1 1.0 CA G:CYS149 4.6 61.3 1.0 O G:GLY160 4.6 50.4 1.0 CB G:HIS152 4.7 75.1 1.0 C2 I:G3 4.8 61.4 1.0 CG G:GLN151 4.8 0.1 1.0 CB G:ARG159 4.8 54.7 1.0 CB G:PHE165 5.0 53.1 1.0

Zinc binding site 7 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


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 Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn301 b:67.1 occ:1.00 NE2 J:HIS37 2.1 49.3 1.0 SG J:CYS18 2.4 77.5 1.0 SG J:CYS27 2.4 88.0 1.0 SG J:CYS33 2.8 81.8 1.0 CE1 J:HIS37 2.9 70.0 1.0 CB J:CYS27 3.0 60.8 1.0 CD2 J:HIS37 3.2 50.7 1.0 CB J:CYS18 3.3 77.3 1.0 CB J:CYS33 3.5 80.1 1.0 N6 L:A2 4.0 68.9 1.0 ND1 J:HIS37 4.1 76.5 1.0 CG J:HIS37 4.2 60.8 1.0 CA J:CYS27 4.5 71.1 1.0 ND1 J:HIS29 4.7 85.4 1.0 CA J:CYS18 4.7 81.7 1.0 CB J:TYR21 4.8 68.2 1.0 O J:ARG35 4.8 68.5 1.0 N J:TYR21 4.9 58.6 1.0 CA J:CYS33 5.0 80.5 1.0

Zinc binding site 8 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


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 Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn302 b:54.6 occ:1.00 NE2 J:HIS167 2.1 69.7 1.0 SG J:CYS149 2.4 73.0 1.0 SG J:CYS163 2.4 63.5 1.0 SG J:CYS157 2.6 83.4 1.0 CB J:CYS157 2.7 72.0 1.0 CB J:CYS163 2.9 70.0 1.0 CD2 J:HIS167 3.0 68.7 1.0 CE1 J:HIS167 3.1 68.5 1.0 CB J:CYS149 3.2 51.5 1.0 N2 L:G3 4.0 75.6 1.0 ND1 J:HIS167 4.2 64.1 1.0 CG J:HIS167 4.2 54.1 1.0 CA J:CYS157 4.3 96.6 1.0 N1 L:G3 4.3 86.2 1.0 CA J:CYS163 4.4 68.8 1.0 O J:GLY160 4.6 69.7 1.0 CA J:CYS149 4.6 55.3 1.0 C2 L:G3 4.7 81.5 1.0 CB J:HIS152 4.8 79.3 1.0 O J:PHE165 5.0 72.0 1.0 N J:CYS157 5.0 0.2 1.0 CB J:PHE165 5.0 58.6 1.0

Zinc binding site 9 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn301 b:70.7 occ:1.00 NE2 M:HIS37 2.1 98.7 1.0 SG M:CYS18 2.4 89.5 1.0 SG M:CYS27 2.4 0.1 1.0 CB M:CYS27 2.8 80.0 1.0 SG M:CYS33 2.9 0.8 1.0 CE1 M:HIS37 3.0 88.2 1.0 CD2 M:HIS37 3.2 0.1 1.0 CB M:CYS18 3.4 90.5 1.0 CB M:CYS33 3.7 0.6 1.0 ND1 M:HIS37 4.1 85.7 1.0 N6 O:A2 4.1 0.1 1.0 CG M:HIS37 4.2 0.7 1.0 CA M:CYS27 4.3 65.9 1.0 CB M:TYR21 4.6 77.3 1.0 CA M:CYS18 4.8 0.6 1.0 N M:TYR21 4.9 81.7 1.0 ND1 M:HIS29 5.0 94.0 1.0 O M:ARG35 5.0 0.5 1.0

Zinc binding site 10 out of 18 in the Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Yeast U2AF1 Complex Bound to 5'-Aaggu Rna. within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn302 b:65.8 occ:1.00 NE2 M:HIS167 2.1 90.3 1.0 SG M:CYS157 2.5 0.1 1.0 SG M:CYS149 2.5 0.8 1.0 CB M:CYS157 2.6 0.9 1.0 SG M:CYS163 2.7 71.7 1.0 CE1 M:HIS167 3.1 74.8 1.0 CD2 M:HIS167 3.2 80.2 1.0 CB M:CYS149 3.2 63.3 1.0 CB M:CYS163 3.3 80.1 1.0 N2 O:G3 4.0 90.6 1.0 CA M:CYS157 4.1 0.7 1.0 ND1 M:HIS167 4.2 77.3 1.0 CG M:HIS167 4.3 72.9 1.0 CB M:HIS152 4.6 90.8 1.0 N1 O:G3 4.7 0.3 1.0 CA M:CYS149 4.7 87.2 1.0 CA M:CYS163 4.8 77.2 1.0 N M:CYS157 4.8 0.5 1.0 C2 O:G3 4.9 96.8 1.0 O M:GLY160 4.9 78.3 1.0

H.Yoshida, S.Y.Park, G.Sakashita, Y.Nariai, K.Kuwasako, Y.Muto, T.Urano, E.Obayashi. Elucidation of the Aberrant 3' Splice Site Selection By Cancer-Associated Mutations on the U2AF1. Nat Commun V. 11 4744 2020.
ISSN: ESSN 2041-1723
PubMed: 32958768
DOI: 10.1038/S41467-020-18559-6