Zinc in PDB 5v3j: MOUSEZFP568-ZNF1-10 in Complex with Dna

The structure of MOUSEZFP568-ZNF1-10 in Complex with Dna, PDB code: 5v3j was solved by A.Patel, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.50 / 2.06
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.787, 65.706, 73.022, 100.52, 104.25, 97.25
R / Rfree (%)	19.2 / 23.7

The structure of MOUSEZFP568-ZNF1-10 in Complex with Dna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the MOUSEZFP568-ZNF1-10 in Complex with Dna (pdb code 5v3j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the MOUSEZFP568-ZNF1-10 in Complex with Dna, PDB code: 5v3j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:97.1 occ:1.00 SG E:CYS368 2.2 0.8 1.0 NE2 E:HIS385 2.3 0.8 1.0 NE2 E:HIS381 2.4 92.8 1.0 CB E:CYS368 2.4 0.8 1.0 CE1 E:HIS385 2.7 0.0 1.0 SG E:CYS365 2.8 83.7 1.0 CD2 E:HIS381 3.0 86.3 1.0 N E:CYS368 3.3 0.9 1.0 CD2 E:HIS385 3.4 1.0 1.0 CA E:CYS368 3.4 0.1 1.0 CE1 E:HIS381 3.6 95.6 1.0 CB E:CYS365 3.6 94.3 1.0 ND1 E:HIS385 3.8 0.1 1.0 CG E:HIS385 4.2 0.0 1.0 CG E:HIS381 4.3 82.4 1.0 C E:CYS368 4.4 0.5 1.0 N E:GLY369 4.4 0.8 1.0 C E:GLU367 4.5 0.9 1.0 ND1 E:HIS381 4.5 86.5 1.0 CB E:GLU367 4.7 0.4 1.0 O E:HIS381 5.0 99.3 1.0 CA E:GLU367 5.0 0.7 1.0

Zinc binding site 2 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1002 b:70.3 occ:1.00 NE2 E:HIS409 1.9 92.5 1.0 NE2 E:HIS413 2.2 80.5 1.0 SG E:CYS393 2.2 65.0 1.0 SG E:CYS396 2.2 76.8 1.0 CE1 E:HIS409 2.8 72.2 1.0 CE1 E:HIS413 2.9 78.5 1.0 CD2 E:HIS409 3.0 75.1 1.0 CB E:CYS393 3.2 62.9 1.0 CB E:CYS396 3.3 74.1 1.0 CD2 E:HIS413 3.3 82.6 1.0 N E:CYS396 3.7 87.3 1.0 ND1 E:HIS409 3.9 59.3 1.0 CA E:CYS396 4.0 79.2 1.0 CG E:HIS409 4.1 60.0 1.0 ND1 E:HIS413 4.1 71.1 1.0 CG E:HIS413 4.3 77.1 1.0 C E:GLU395 4.6 97.1 1.0 CG2 E:VAL412 4.6 74.8 1.0 CA E:CYS393 4.6 75.3 1.0 C E:CYS396 4.6 82.4 1.0 CB E:GLU395 4.6 93.0 1.0 N E:GLY397 4.8 82.6 1.0 CB E:LYS398 4.9 63.3 1.0 N E:GLU395 4.9 94.8 1.0 N E:LYS398 4.9 64.1 1.0 CA E:GLU395 4.9 97.8 1.0

Zinc binding site 3 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1003 b:51.7 occ:1.00 NE2 E:HIS441 2.0 52.4 1.0 NE2 E:HIS437 2.2 57.5 1.0 SG E:CYS421 2.4 54.4 1.0 SG E:CYS424 2.5 52.0 1.0 CE1 E:HIS441 2.7 44.8 1.0 CE1 E:HIS437 3.1 62.7 1.0 CD2 E:HIS441 3.2 57.0 1.0 CD2 E:HIS437 3.3 47.3 1.0 CB E:CYS421 3.5 66.2 1.0 CB E:CYS424 3.7 54.8 1.0 ND1 E:HIS441 3.9 51.0 1.0 N E:CYS424 4.0 67.2 1.0 CG E:HIS441 4.1 49.6 1.0 ND1 E:HIS437 4.3 59.5 1.0 CG E:HIS437 4.4 53.5 1.0 O E:HOH1170 4.4 53.9 1.0 CA E:CYS424 4.4 62.2 1.0 CB E:GLU423 4.6 76.1 1.0 C E:GLU423 4.7 68.4 1.0 CA E:CYS421 4.9 68.0 1.0 N E:GLU423 5.0 62.5 1.0

Zinc binding site 4 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1004 b:69.5 occ:1.00 NE2 E:HIS469 2.0 90.7 1.0 NE2 E:HIS465 2.0 69.1 1.0 SG E:CYS452 2.2 82.6 1.0 SG E:CYS449 2.3 75.2 1.0 CE1 E:HIS465 2.8 60.8 1.0 CD2 E:HIS469 2.9 85.4 1.0 CE1 E:HIS469 3.0 84.3 1.0 CB E:CYS452 3.0 75.9 1.0 CD2 E:HIS465 3.2 54.5 1.0 CB E:CYS449 3.2 79.2 1.0 N E:CYS452 3.7 79.7 1.0 CA E:CYS452 3.9 79.5 1.0 ND1 E:HIS465 4.0 53.8 1.0 CG E:HIS469 4.0 82.2 1.0 ND1 E:HIS469 4.0 85.1 1.0 CG E:HIS465 4.2 51.3 1.0 C E:CYS452 4.4 92.0 1.0 N E:GLY453 4.6 98.8 1.0 CA E:CYS449 4.7 79.3 1.0 CB E:LYS454 4.9 58.4 1.0 C E:GLU451 4.9 86.2 1.0 CB E:GLU451 4.9 85.0 1.0 N E:LYS454 5.0 81.9 1.0 OG1 E:THR468 5.0 62.7 1.0

Zinc binding site 5 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1005 b:46.5 occ:1.00 NE2 E:HIS497 2.1 53.9 1.0 SG E:CYS477 2.2 45.9 1.0 NE2 E:HIS493 2.2 47.8 1.0 SG E:CYS480 2.2 44.2 1.0 CD2 E:HIS497 2.9 51.1 1.0 CE1 E:HIS497 3.1 39.0 1.0 CE1 E:HIS493 3.1 40.2 1.0 CB E:CYS477 3.2 49.6 1.0 CD2 E:HIS493 3.2 43.1 1.0 CB E:CYS480 3.2 49.1 1.0 N E:CYS480 3.6 56.4 1.0 CA E:CYS480 3.9 51.1 1.0 CG E:HIS497 4.1 51.0 1.0 ND1 E:HIS497 4.2 48.0 1.0 C E:ASP479 4.2 63.6 1.0 ND1 E:HIS493 4.3 42.3 1.0 CG E:HIS493 4.3 45.2 1.0 CB E:LYS482 4.5 37.9 1.0 C E:CYS480 4.5 59.9 1.0 CB E:ASP479 4.6 40.0 1.0 CA E:CYS477 4.6 47.9 1.0 N E:ASP479 4.6 45.8 1.0 CA E:ASP479 4.7 53.4 1.0 O E:ASP479 4.8 66.6 1.0 O E:CYS480 5.0 59.7 1.0 N E:LYS482 5.0 43.6 1.0

Zinc binding site 6 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1006 b:46.7 occ:1.00 SG E:CYS508 2.1 40.7 1.0 NE2 E:HIS525 2.1 40.3 1.0 NE2 E:HIS521 2.2 49.5 1.0 SG E:CYS505 2.2 44.7 1.0 CE1 E:HIS521 3.0 44.9 1.0 CD2 E:HIS525 3.1 48.0 1.0 CE1 E:HIS525 3.2 41.6 1.0 CB E:CYS505 3.2 42.4 1.0 CD2 E:HIS521 3.3 45.1 1.0 CB E:CYS508 3.4 43.5 1.0 N E:CYS508 3.6 62.3 1.0 CA E:CYS508 4.1 55.9 1.0 ND1 E:HIS521 4.2 49.0 1.0 ND1 E:HIS525 4.3 49.8 1.0 CG E:HIS525 4.3 51.9 1.0 CG E:HIS521 4.4 42.8 1.0 CB E:GLU507 4.5 76.7 1.0 C E:GLU507 4.6 64.9 1.0 CA E:CYS505 4.6 44.6 1.0 NE2 E:GLN522 4.8 36.0 1.0 CG2 E:VAL524 4.8 50.3 1.0 C E:CYS508 4.8 53.2 1.0 N E:GLU507 4.8 59.6 1.0 CA E:GLU507 4.9 68.5 1.0 N E:GLY509 4.9 50.3 1.0

Zinc binding site 7 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1007 b:56.5 occ:1.00 NE2 E:HIS553 2.0 77.1 1.0 NE2 E:HIS549 2.2 72.5 1.0 SG E:CYS536 2.2 64.0 1.0 SG E:CYS533 2.5 60.5 1.0 CD2 E:HIS549 2.9 52.8 1.0 CB E:CYS536 3.0 66.1 1.0 CD2 E:HIS553 3.0 70.1 1.0 CE1 E:HIS553 3.0 76.1 1.0 CB E:CYS533 3.3 55.1 1.0 CE1 E:HIS549 3.4 72.8 1.0 N E:CYS536 3.6 59.5 1.0 CA E:CYS536 3.8 66.0 1.0 ND1 E:HIS553 4.1 75.9 1.0 CG E:HIS553 4.1 71.1 1.0 CG E:HIS549 4.2 51.3 1.0 ND1 E:HIS549 4.4 62.1 1.0 C E:CYS536 4.5 68.8 1.0 C E:GLU535 4.6 63.9 1.0 CB E:GLU535 4.7 56.1 1.0 N E:GLY537 4.7 68.4 1.0 O E:HOH1165 4.7 71.7 1.0 CA E:CYS533 4.8 56.2 1.0

Zinc binding site 8 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1008 b:57.1 occ:1.00 NE2 E:HIS581 2.0 51.6 1.0 NE2 E:HIS577 2.1 60.6 1.0 SG E:CYS561 2.3 59.6 1.0 SG E:CYS564 2.3 67.9 1.0 CE1 E:HIS581 2.9 59.6 1.0 CE1 E:HIS577 2.9 53.4 1.0 CD2 E:HIS581 3.0 46.0 1.0 CD2 E:HIS577 3.2 49.6 1.0 CB E:CYS561 3.2 52.9 1.0 CB E:CYS564 3.4 64.5 1.0 N E:CYS564 3.7 72.4 1.0 ND1 E:HIS581 4.0 59.1 1.0 CA E:CYS564 4.1 72.5 1.0 ND1 E:HIS577 4.1 53.4 1.0 CG E:HIS581 4.1 55.6 1.0 CG E:HIS577 4.2 46.6 1.0 CB E:GLU563 4.4 56.6 1.0 CA E:CYS561 4.6 55.2 1.0 C E:GLU563 4.7 71.1 1.0 N E:GLY565 4.8 75.2 1.0 C E:CYS564 4.8 71.4 1.0 O E:CYS561 4.8 64.5 1.0 C E:CYS561 4.9 65.0 1.0 N E:GLU563 4.9 76.1 1.0 CA E:GLU563 4.9 67.3 1.0 CB E:LYS566 5.0 50.0 1.0

Zinc binding site 9 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1009 b:64.5 occ:1.00 NE2 E:HIS605 2.0 94.5 1.0 SG E:CYS589 2.3 83.4 1.0 SG E:CYS592 2.3 81.7 1.0 NE2 E:HIS609 2.5 81.7 1.0 CD2 E:HIS605 2.8 82.4 1.0 CE1 E:HIS605 3.1 76.9 1.0 CB E:CYS589 3.2 84.1 1.0 CE1 E:HIS609 3.2 80.3 1.0 CB E:CYS592 3.3 80.1 1.0 CD2 E:HIS609 3.6 84.0 1.0 N E:CYS592 3.6 89.7 1.0 CA E:CYS592 4.0 86.1 1.0 CG E:HIS605 4.0 74.3 1.0 ND1 E:HIS605 4.1 71.4 1.0 ND1 E:HIS609 4.4 78.3 1.0 CB E:GLU591 4.5 75.0 1.0 C E:CYS592 4.6 85.2 1.0 CA E:CYS589 4.6 80.3 1.0 CG E:HIS609 4.6 84.7 1.0 C E:GLU591 4.7 92.4 1.0 N E:GLY593 4.7 75.1 1.0 O E:CYS589 4.9 92.9 1.0 CB E:LYS594 4.9 80.2 1.0 CA E:GLU591 5.0 77.0 1.0 N E:LYS594 5.0 86.0 1.0 C E:CYS589 5.0 90.2 1.0 CG E:GLU591 5.0 83.1 1.0

Zinc binding site 10 out of 20 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1010 b:44.5 occ:1.00 NE2 E:HIS633 2.1 56.2 1.0 NE2 E:HIS637 2.2 50.1 1.0 SG E:CYS617 2.2 46.5 1.0 SG E:CYS620 2.2 44.5 1.0 CE1 E:HIS633 3.0 51.7 1.0 CE1 E:HIS637 3.0 50.7 1.0 CD2 E:HIS633 3.1 48.2 1.0 CB E:CYS617 3.1 49.1 1.0 CD2 E:HIS637 3.3 46.2 1.0 CB E:CYS620 3.5 45.8 1.0 N E:CYS620 3.6 57.2 1.0 CA E:CYS620 4.1 57.2 1.0 ND1 E:HIS633 4.1 47.6 1.0 CG E:HIS633 4.2 45.9 1.0 ND1 E:HIS637 4.2 52.1 1.0 CG E:HIS637 4.4 53.2 1.0 CB E:GLU619 4.5 71.1 1.0 CA E:CYS617 4.5 49.4 1.0 C E:GLU619 4.6 56.1 1.0 C E:CYS620 4.8 59.5 1.0 CD E:LYS622 4.8 80.2 1.0 N E:GLU619 4.8 60.4 1.0 N E:GLY621 4.8 55.8 1.0 CA E:GLU619 4.9 61.9 1.0 C E:CYS617 5.0 57.5 1.0

A.Patel, P.Yang, M.Tinkham, M.Pradhan, M.A.Sun, Y.Wang, D.Hoang, G.Wolf, J.R.Horton, X.Zhang, T.Macfarlan, X.Cheng. Dna Conformation Induces Adaptable Binding By Tandem Zinc Finger Proteins. Cell V. 173 221 2018.
ISSN: ISSN 1097-4172
PubMed: 29551271
DOI: 10.1016/J.CELL.2018.02.058