Zinc in PDB 4lj0: NAB2 Zn Fingers Complexed with Polyadenosine

The structure of NAB2 Zn Fingers Complexed with Polyadenosine, PDB code: 4lj0 was solved by M.Stewart, S.I.Kuhlmann, E.Valkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.58 / 2.15
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.929, 90.929, 54.081, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 20.7

The structure of NAB2 Zn Fingers Complexed with Polyadenosine also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the NAB2 Zn Fingers Complexed with Polyadenosine (pdb code 4lj0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the NAB2 Zn Fingers Complexed with Polyadenosine, PDB code: 4lj0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:47.7 occ:1.00 NE2 A:HIS420 2.0 67.3 1.0 SG A:CYS405 2.3 44.0 1.0 SG A:CYS411 2.3 48.3 1.0 SG A:CYS416 2.4 52.1 1.0 CE1 A:HIS420 2.6 71.3 1.0 HE1 A:HIS420 2.7 85.6 1.0 HB2 A:CYS405 2.9 52.8 1.0 HB3 A:CYS416 3.0 64.2 1.0 HB2 A:CYS411 3.0 61.9 1.0 CB A:CYS416 3.0 53.5 1.0 HB2 A:CYS416 3.1 64.2 1.0 CD2 A:HIS420 3.2 62.7 1.0 CB A:CYS405 3.2 44.0 1.0 CB A:CYS411 3.2 51.6 1.0 HD2 A:HIS420 3.5 75.3 1.0 HB3 A:CYS405 3.5 52.8 1.0 HB3 A:CYS411 3.6 61.9 1.0 ND1 A:HIS420 3.8 67.0 1.0 HB2 A:PHE418 3.9 50.3 1.0 CG A:HIS420 4.1 59.0 1.0 H62 C:A2 4.1 51.7 1.0 HB2 A:TYR407 4.2 59.8 1.0 O C:HOH202 4.4 47.6 1.0 HB2 A:TRP408 4.4 51.7 1.0 CA A:CYS405 4.5 44.8 1.0 H A:TRP408 4.5 54.1 1.0 HA A:CYS405 4.5 53.8 1.0 CA A:CYS416 4.5 53.0 1.0 H61 C:A2 4.5 51.7 1.0 HD1 A:HIS420 4.5 80.4 1.0 CA A:CYS411 4.6 53.6 1.0 HB3 A:ASN413 4.6 52.5 1.0 HA A:CYS411 4.6 64.4 1.0 HD2 A:TYR407 4.6 60.7 1.0 N6 C:A2 4.6 43.1 1.0 H A:PHE418 4.7 63.1 1.0 H A:TYR407 4.8 55.2 1.0 O A:PHE418 4.8 57.5 1.0 CB A:PHE418 4.9 41.9 1.0 HA A:CYS416 4.9 63.6 1.0 O A:ASN413 4.9 58.8 1.0 H A:ASN413 5.0 60.1 1.0

Zinc binding site 2 out of 6 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:35.9 occ:1.00 NE2 A:HIS441 2.1 37.2 1.0 SG A:CYS437 2.2 37.3 1.0 SG A:CYS426 2.3 37.5 1.0 SG A:CYS432 2.3 35.1 1.0 HB3 A:CYS432 2.9 46.2 1.0 CD2 A:HIS441 3.0 31.8 1.0 CB A:CYS432 3.0 38.5 1.0 CE1 A:HIS441 3.1 40.5 1.0 HB3 A:CYS437 3.1 44.1 1.0 HD2 A:HIS441 3.1 38.2 1.0 HB2 A:CYS432 3.1 46.2 1.0 HB2 A:CYS426 3.2 39.0 1.0 CB A:CYS437 3.3 36.8 1.0 CB A:CYS426 3.3 32.5 1.0 HE1 A:HIS441 3.3 48.6 1.0 HD22 A:ASN428 3.4 57.9 1.0 H61 E:A2 3.6 0.9 1.0 HB2 A:ASN428 3.6 45.2 1.0 HB3 A:CYS426 3.6 39.0 1.0 HB2 A:CYS437 3.6 44.1 1.0 HB2 A:PHE439 3.8 53.1 1.0 H62 E:A2 4.0 0.9 1.0 N6 E:A2 4.0 95.7 1.0 ND2 A:ASN428 4.1 48.2 1.0 CG A:HIS441 4.2 37.9 1.0 ND1 A:HIS441 4.2 37.5 1.0 HB A:VAL434 4.2 56.3 1.0 HD2 A:PHE439 4.3 51.9 1.0 CB A:ASN428 4.5 37.6 1.0 H A:PHE439 4.5 51.2 1.0 CA A:CYS432 4.5 36.6 1.0 O E:HOH101 4.6 47.6 1.0 H A:ASN428 4.6 44.2 1.0 HD21 A:ASN428 4.6 57.9 1.0 CA A:CYS437 4.6 41.2 1.0 CA A:CYS426 4.7 35.6 1.0 HA A:CYS426 4.7 42.8 1.0 CB A:PHE439 4.7 44.2 1.0 H A:VAL434 4.8 46.7 1.0 CG A:ASN428 4.8 46.8 1.0 C A:CYS437 4.9 44.0 1.0 O A:GLY429 4.9 34.3 1.0 O A:CYS437 4.9 41.7 1.0 HB3 A:ASN428 4.9 45.2 1.0 HA A:CYS432 4.9 43.9 1.0 C A:CYS432 5.0 39.5 1.0 HD1 A:HIS441 5.0 44.9 1.0 HA A:CYS437 5.0 49.4 1.0

Zinc binding site 3 out of 6 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:37.9 occ:1.00 NE2 A:HIS460 2.0 41.8 1.0 SG A:CYS451 2.2 41.3 1.0 SG A:CYS456 2.3 37.0 1.0 SG A:CYS446 2.3 39.9 1.0 HB2 A:CYS446 2.9 44.4 1.0 HB2 A:CYS451 2.9 51.5 1.0 CD2 A:HIS460 2.9 39.5 1.0 CE1 A:HIS460 3.0 44.8 1.0 HB3 A:CYS456 3.0 39.1 1.0 CB A:CYS451 3.1 43.0 1.0 CB A:CYS456 3.1 32.6 1.0 HD2 A:HIS460 3.1 47.3 1.0 CB A:CYS446 3.2 37.0 1.0 HE1 A:HIS460 3.2 53.8 1.0 HB2 A:CYS456 3.2 39.1 1.0 HB3 A:CYS451 3.3 51.5 1.0 H61 D:A4 3.4 73.1 1.0 HB3 A:CYS446 3.5 44.4 1.0 HB2 A:PHE458 3.9 50.5 1.0 H2 D:A3 3.9 60.0 1.0 H62 D:A4 3.9 73.1 1.0 N6 D:A4 4.0 60.9 1.0 ND1 A:HIS460 4.1 36.4 1.0 CG A:HIS460 4.1 41.3 1.0 HB2 A:PHE448 4.2 61.4 1.0 HD2 A:PHE448 4.3 62.6 1.0 HB3 A:ASN453 4.3 52.2 1.0 O D:HOH202 4.5 59.2 1.0 CA A:CYS451 4.5 41.4 1.0 CA A:CYS446 4.5 40.8 1.0 CA A:CYS456 4.6 35.3 1.0 HA A:CYS446 4.6 49.0 1.0 H A:PHE458 4.6 44.5 1.0 HA A:CYS451 4.7 49.7 1.0 H A:PHE448 4.8 56.3 1.0 C2 D:A3 4.8 50.0 1.0 HD3 A:ARG465 4.8 65.1 1.0 H A:ASN453 4.8 53.1 1.0 HD1 A:PHE458 4.8 50.2 1.0 CB A:PHE458 4.8 42.1 1.0 HD1 A:HIS460 4.8 43.7 1.0 O A:ASN453 4.9 39.7 1.0 HA A:CYS456 4.9 42.4 1.0

Zinc binding site 4 out of 6 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:56.5 occ:1.00 SG B:CYS416 2.2 67.2 1.0 NE2 B:HIS420 2.2 74.2 1.0 SG B:CYS405 2.2 62.9 1.0 SG B:CYS411 2.3 54.8 1.0 HB2 B:CYS405 2.9 84.6 1.0 HB2 B:CYS411 3.0 72.8 1.0 CD2 B:HIS420 3.1 60.3 1.0 CB B:CYS416 3.1 66.2 1.0 CE1 B:HIS420 3.1 75.0 1.0 CB B:CYS411 3.2 60.6 1.0 CB B:CYS405 3.2 70.5 1.0 HB2 B:CYS416 3.2 79.4 1.0 HB3 B:CYS416 3.2 79.4 1.0 HD2 B:HIS420 3.3 72.4 1.0 HE1 B:HIS420 3.3 90.0 1.0 HB3 B:CYS411 3.4 72.8 1.0 HB3 B:CYS405 3.6 84.6 1.0 HB2 B:PHE418 3.7 0.7 1.0 HB2 B:TYR407 4.0 73.5 1.0 HB2 B:TRP408 4.0 71.4 1.0 ND1 B:HIS420 4.2 68.0 1.0 CG B:HIS420 4.2 60.1 1.0 H B:TRP408 4.2 70.5 1.0 HD2 B:TYR407 4.4 84.2 1.0 HA B:CYS405 4.4 87.4 1.0 HD2 B:PHE418 4.4 0.9 1.0 CA B:CYS405 4.4 72.8 1.0 H B:TYR407 4.5 82.5 1.0 OE1 A:GLN403 4.6 78.1 1.0 CA B:CYS411 4.6 58.7 1.0 CA B:CYS416 4.6 69.6 1.0 O B:PHE418 4.7 83.1 1.0 HB3 B:ASN413 4.7 58.9 1.0 HA B:CYS411 4.7 70.4 1.0 CB B:PHE418 4.7 89.0 1.0 N B:TRP408 4.7 58.7 1.0 H B:PHE418 4.8 99.2 1.0 HA B:CYS416 4.8 83.5 1.0 CB B:TRP408 4.9 59.5 1.0 CB B:TYR407 4.9 61.3 1.0 HD1 B:HIS420 5.0 81.5 1.0

Zinc binding site 5 out of 6 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:65.2 occ:1.00 O B:HOH603 2.0 63.6 1.0 NE2 B:HIS441 2.1 59.1 1.0 SG B:CYS426 2.3 69.5 1.0 SG B:CYS437 2.3 61.3 1.0 SG B:CYS432 2.5 74.8 1.0 CD2 B:HIS441 2.8 63.1 1.0 HD2 B:HIS441 2.9 75.7 1.0 HB3 B:CYS432 2.9 78.1 1.0 CB B:CYS432 3.1 65.1 1.0 HB2 B:CYS432 3.1 78.1 1.0 HB2 B:CYS426 3.1 58.8 1.0 HB3 B:CYS437 3.1 74.5 1.0 CE1 B:HIS441 3.2 64.0 1.0 CB B:CYS426 3.2 49.0 1.0 CB B:CYS437 3.3 62.0 1.0 HE1 B:HIS441 3.5 76.8 1.0 HB3 B:CYS426 3.5 58.8 1.0 HD22 B:ASN428 3.6 91.9 1.0 HB2 B:CYS437 3.7 74.5 1.0 HB2 B:ASN428 3.8 94.4 1.0 HB2 B:PHE439 3.8 58.4 1.0 CG B:HIS441 4.1 67.9 1.0 ND1 B:HIS441 4.2 67.9 1.0 HB B:VAL434 4.2 97.5 1.0 ND2 B:ASN428 4.3 76.5 1.0 H B:PHE439 4.5 61.5 1.0 CA B:CYS432 4.6 74.9 1.0 HD2 B:PHE439 4.6 64.1 1.0 CA B:CYS426 4.6 55.8 1.0 CA B:CYS437 4.6 62.4 1.0 H B:ASN428 4.7 91.2 1.0 CB B:ASN428 4.7 78.7 1.0 HA B:CYS426 4.7 67.0 1.0 CB B:PHE439 4.7 48.6 1.0 HD21 B:ASN428 4.8 91.9 1.0 C B:CYS437 4.8 57.8 1.0 O B:PHE439 4.8 57.2 1.0 H B:VAL434 4.9 0.4 1.0 O B:CYS437 4.9 57.4 1.0 HA B:CYS432 5.0 89.9 1.0 CG B:ASN428 5.0 80.3 1.0 O B:GLY429 5.0 85.0 1.0

Zinc binding site 6 out of 6 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:0.4 occ:1.00 NE2 B:HIS460 2.2 0.8 1.0 SG B:CYS446 2.3 0.4 1.0 HB2 B:CYS451 2.4 1.0 1.0 SG B:CYS456 2.4 1.0 1.0 SG B:CYS451 2.5 0.2 1.0 CB B:CYS451 2.9 0.6 1.0 HB3 B:CYS456 3.0 0.5 1.0 HB2 B:CYS446 3.1 0.1 1.0 CD2 B:HIS460 3.1 0.5 1.0 CB B:CYS456 3.2 93.8 1.0 CE1 B:HIS460 3.2 0.5 1.0 HB3 B:CYS451 3.3 1.0 1.0 CB B:CYS446 3.3 95.1 1.0 HD2 B:HIS460 3.3 0.0 1.0 HB2 B:CYS456 3.3 0.5 1.0 HE1 B:HIS460 3.4 0.8 1.0 HB3 B:CYS446 3.5 0.1 1.0 HB2 B:PHE458 3.7 0.9 1.0 HB2 B:PHE448 3.9 0.5 1.0 CA B:CYS451 4.2 0.6 1.0 ND1 B:HIS460 4.3 0.2 1.0 CG B:HIS460 4.3 0.4 1.0 HA B:CYS451 4.3 0.3 1.0 HD2 B:PHE458 4.5 0.0 1.0 H B:PHE458 4.6 0.2 1.0 CA B:CYS456 4.6 91.0 1.0 CA B:CYS446 4.6 97.2 1.0 CB B:PHE458 4.7 99.1 1.0 HD1 B:PHE448 4.7 0.4 1.0 HA B:CYS446 4.8 0.6 1.0 HB3 B:ASN453 4.8 0.9 1.0 H B:PHE448 4.8 0.2 1.0 H B:CYS451 4.8 0.6 1.0 CB B:PHE448 4.8 0.1 1.0 O B:PHE458 4.9 0.7 1.0

S.I.Kuhlmann, E.Valkov, M.Stewart. Structural Basis For the Molecular Recognition of Polyadenosine Rna By NAB2 Zn Fingers. Nucleic Acids Res. V. 42 672 2014.
ISSN: ISSN 0305-1048
PubMed: 24071581
DOI: 10.1093/NAR/GKT876