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

Protein crystallography data

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

Other elements in 5v3j:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

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 5v3j

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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 5v3j

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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 5v3j

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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 5v3j

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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 5v3j

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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 5v3j

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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 5v3j

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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 5v3j

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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 5v3j

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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 5v3j

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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

Reference:

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
Page generated: Mon Oct 28 12:35:18 2024

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