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Zinc in PDB 4rkh: Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence

Protein crystallography data

The structure of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence, PDB code: 4rkh was solved by S.Zheng, K.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.75 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.371, 50.998, 124.934, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence (pdb code 4rkh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence, PDB code: 4rkh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4rkh

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Zinc binding site 1 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:14.7
occ:1.00
 SG C:CYS527 2.3 16.3 1.0
SG C:CYS539 2.3 14.5 1.0
SG C:CYS544 2.4 15.4 1.0
SG C:CYS525 2.4 15.3 1.0
CB C:CYS525 3.2 18.9 1.0
CB C:CYS544 3.2 15.3 1.0
CB C:CYS527 3.2 17.7 1.0
CB C:CYS539 3.3 15.0 1.0
CA C:CYS539 3.6 16.0 1.0
ZN C:ZN702 3.7 15.3 1.0
ZN C:ZN703 3.8 17.8 1.0
SG C:CYS553 4.0 11.9 1.0
CA C:CYS544 4.0 18.6 1.0
N C:CYS539 4.1 17.2 1.0
N C:CYS527 4.3 17.6 1.0
CB C:CYS558 4.4 16.2 1.0
O B:HOH103 4.4 19.0 1.0
CA C:CYS527 4.4 19.3 1.0
CA C:CYS525 4.6 20.0 1.0
CD C:PRO545 4.6 16.8 1.0
C C:CYS544 4.8 16.9 1.0
SG C:CYS546 4.8 15.7 1.0
SG C:CYS558 4.9 15.2 1.0
C C:CYS525 4.9 21.7 1.0
C C:CYS539 5.0 14.6 1.0

Zinc binding site 2 out of 12 in 4rkh

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Zinc binding site 2 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:15.3
occ:1.00
 SG C:CYS561 2.3 18.2 1.0
SG C:CYS558 2.3 15.2 1.0
SG C:CYS539 2.4 14.5 1.0
SG C:CYS553 2.4 11.9 1.0
CB C:CYS539 3.0 15.0 1.0
CB C:CYS553 3.0 15.8 1.0
CB C:CYS561 3.1 13.8 1.0
CB C:CYS558 3.2 16.2 1.0
ZN C:ZN701 3.7 14.7 1.0
SG C:CYS525 3.8 15.3 1.0
ZN C:ZN703 3.8 17.8 1.0
CA C:CYS561 4.1 16.5 1.0
CB C:ASN563 4.5 16.2 1.0
CA C:CYS539 4.5 16.0 1.0
CA C:CYS553 4.5 16.4 1.0
CA C:CYS558 4.6 17.1 1.0
CB C:CYS556 4.8 18.4 1.0

Zinc binding site 3 out of 12 in 4rkh

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Zinc binding site 3 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn703

b:17.8
occ:1.00
 SG C:CYS556 2.3 17.0 1.0
SG C:CYS553 2.3 11.9 1.0
SG C:CYS525 2.3 15.3 1.0
SG C:CYS546 2.4 15.7 1.0
CB C:CYS553 3.2 15.8 1.0
CB C:CYS556 3.2 18.4 1.0
CB C:CYS525 3.3 18.9 1.0
CB C:CYS546 3.3 15.9 1.0
CA C:CYS553 3.6 16.4 1.0
N C:CYS525 3.7 21.8 1.0
ZN C:ZN701 3.8 14.7 1.0
ZN C:ZN702 3.8 15.3 1.0
CA C:CYS525 4.1 20.0 1.0
SG C:CYS544 4.3 15.4 1.0
SG C:CYS558 4.5 15.2 1.0
O C:SER552 4.5 18.6 1.0
N C:CYS553 4.6 14.9 1.0
C C:CYS553 4.6 19.4 1.0
O C:CYS553 4.6 17.2 1.0
CA C:CYS546 4.7 16.8 1.0
CA C:CYS556 4.7 23.3 1.0
SG C:CYS539 4.7 14.5 1.0
C C:CYS525 4.8 21.7 1.0
O C:HOH817 4.8 32.8 1.0
O C:CYS525 4.9 19.6 1.0
C C:LYS524 4.9 27.3 1.0
N C:CYS546 4.9 16.6 1.0
C C:SER552 4.9 18.2 1.0
CB C:CYS558 4.9 16.2 1.0

Zinc binding site 4 out of 12 in 4rkh

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Zinc binding site 4 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:16.5
occ:1.00
 SG D:CYS544 2.2 15.4 1.0
SG D:CYS539 2.3 16.6 1.0
SG D:CYS527 2.4 18.4 1.0
SG D:CYS525 2.4 17.4 1.0
CB D:CYS527 3.2 22.4 1.0
CB D:CYS539 3.3 14.8 1.0
CB D:CYS544 3.3 17.6 1.0
CB D:CYS525 3.3 21.0 1.0
CA D:CYS539 3.7 17.4 1.0
ZN D:ZN703 3.7 18.9 1.0
ZN D:ZN702 3.7 16.0 1.0
SG D:CYS553 4.0 15.5 1.0
CA D:CYS544 4.1 18.1 1.0
N D:CYS527 4.3 22.9 1.0
N D:CYS539 4.3 15.5 1.0
CA D:CYS527 4.4 23.1 1.0
CB D:CYS558 4.4 21.3 1.0
CD D:PRO545 4.6 19.1 1.0
O A:HOH103 4.6 21.0 1.0
CA D:CYS525 4.8 24.4 1.0
SG D:CYS546 4.9 21.6 1.0
C D:CYS544 4.9 19.0 1.0
SG D:CYS558 4.9 19.1 1.0

Zinc binding site 5 out of 12 in 4rkh

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Zinc binding site 5 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn702

b:16.0
occ:1.00
 SG D:CYS553 2.3 15.5 1.0
SG D:CYS558 2.3 19.1 1.0
SG D:CYS539 2.3 16.6 1.0
SG D:CYS561 2.3 16.1 1.0
CB D:CYS553 3.0 18.7 1.0
CB D:CYS561 3.1 18.9 1.0
CB D:CYS558 3.2 21.3 1.0
CB D:CYS539 3.2 14.8 1.0
ZN D:ZN701 3.7 16.5 1.0
ZN D:ZN703 3.8 18.9 1.0
SG D:CYS525 3.8 17.4 1.0
CA D:CYS561 4.0 19.6 1.0
CB D:ASN563 4.4 16.8 1.0
CA D:CYS553 4.5 20.5 1.0
CA D:CYS558 4.6 24.7 1.0
CA D:CYS539 4.7 17.4 1.0
O D:HOH806 4.8 27.9 1.0
CB D:CYS556 4.9 23.4 1.0
SG D:CYS544 4.9 15.4 1.0
C D:CYS561 5.0 19.3 1.0
ND2 D:ASN563 5.0 17.2 1.0

Zinc binding site 6 out of 12 in 4rkh

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Zinc binding site 6 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn703

b:18.9
occ:1.00
 SG D:CYS546 2.3 21.6 1.0
SG D:CYS525 2.4 17.4 1.0
SG D:CYS556 2.4 22.6 1.0
SG D:CYS553 2.4 15.5 1.0
CB D:CYS525 3.2 21.0 1.0
CB D:CYS553 3.2 18.7 1.0
CB D:CYS556 3.2 23.4 1.0
CB D:CYS546 3.3 17.4 1.0
CA D:CYS553 3.6 20.5 1.0
ZN D:ZN701 3.7 16.5 1.0
ZN D:ZN702 3.8 16.0 1.0
N D:CYS525 3.8 26.5 1.0
CA D:CYS525 4.1 24.4 1.0
SG D:CYS544 4.2 15.4 1.0
SG D:CYS558 4.4 19.1 1.0
N D:CYS553 4.6 17.7 1.0
O D:SER552 4.6 17.3 1.0
C D:CYS553 4.6 24.2 1.0
CA D:CYS546 4.6 18.9 1.0
SG D:CYS539 4.7 16.6 1.0
CA D:CYS556 4.7 26.9 1.0
O D:CYS553 4.7 21.2 1.0
C D:CYS525 4.8 25.3 1.0
O D:CYS525 4.8 28.4 1.0
N D:CYS546 4.8 19.0 1.0
C D:SER552 4.9 20.2 1.0
C D:LYS524 5.0 30.7 1.0

Zinc binding site 7 out of 12 in 4rkh

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Zinc binding site 7 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:14.7
occ:1.00
 SG E:CYS544 2.3 14.7 1.0
SG E:CYS527 2.4 16.4 1.0
SG E:CYS525 2.4 12.6 1.0
SG E:CYS539 2.4 12.8 1.0
CB E:CYS527 3.2 15.9 1.0
CB E:CYS525 3.2 18.0 1.0
CB E:CYS544 3.3 15.2 1.0
CB E:CYS539 3.3 12.5 1.0
CA E:CYS539 3.6 13.5 1.0
ZN E:ZN703 3.7 14.3 1.0
ZN E:ZN702 3.8 13.9 1.0
CA E:CYS544 4.1 14.8 1.0
SG E:CYS553 4.1 12.0 1.0
N E:CYS539 4.2 12.6 1.0
N E:CYS527 4.2 15.2 1.0
CA E:CYS527 4.3 17.6 1.0
CB E:CYS558 4.5 14.0 1.0
O A:HOH111 4.7 16.1 1.0
CD E:PRO545 4.7 16.2 1.0
CA E:CYS525 4.7 17.5 1.0
C E:CYS544 4.9 17.1 1.0
SG E:CYS546 4.9 17.7 1.0
C E:CYS539 4.9 14.0 1.0

Zinc binding site 8 out of 12 in 4rkh

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Zinc binding site 8 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:13.9
occ:1.00
 SG E:CYS539 2.3 12.8 1.0
SG E:CYS561 2.4 14.6 1.0
SG E:CYS558 2.4 14.6 1.0
SG E:CYS553 2.4 12.0 1.0
CB E:CYS561 3.1 14.2 1.0
CB E:CYS539 3.2 12.5 1.0
CB E:CYS553 3.2 14.9 1.0
CB E:CYS558 3.2 14.0 1.0
SG E:CYS525 3.8 12.6 1.0
ZN E:ZN701 3.8 14.7 1.0
ZN E:ZN703 3.8 14.3 1.0
CA E:CYS561 4.0 15.3 1.0
CB E:ASN563 4.6 12.9 1.0
CA E:CYS539 4.6 13.5 1.0
CA E:CYS553 4.7 17.3 1.0
CA E:CYS558 4.7 15.7 1.0
CB E:CYS556 4.9 18.5 1.0
C E:CYS561 5.0 14.7 1.0

Zinc binding site 9 out of 12 in 4rkh

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Zinc binding site 9 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:14.3
occ:1.00
 SG E:CYS556 2.3 16.3 1.0
SG E:CYS525 2.3 12.6 1.0
SG E:CYS546 2.4 17.7 1.0
SG E:CYS553 2.5 12.0 1.0
CB E:CYS553 3.2 14.9 1.0
CB E:CYS525 3.3 18.0 1.0
CB E:CYS546 3.3 15.5 1.0
CB E:CYS556 3.3 18.5 1.0
CA E:CYS553 3.6 17.3 1.0
ZN E:ZN701 3.7 14.7 1.0
N E:CYS525 3.8 17.1 1.0
ZN E:ZN702 3.8 13.9 1.0
CA E:CYS525 4.1 17.5 1.0
SG E:CYS544 4.1 14.7 1.0
C E:CYS553 4.5 18.0 1.0
NZ E:LYS522 4.5 20.1 1.0
N E:CYS553 4.6 13.7 1.0
SG E:CYS558 4.6 14.6 1.0
O E:SER552 4.6 16.2 1.0
SG E:CYS539 4.6 12.8 1.0
O E:CYS553 4.6 17.3 1.0
CA E:CYS546 4.7 16.4 1.0
C E:CYS525 4.7 17.2 1.0
CA E:CYS556 4.8 19.6 1.0
O E:CYS525 4.8 16.0 1.0
C E:LYS524 4.8 21.2 1.0
N E:CYS546 4.9 18.4 1.0
C E:SER552 5.0 17.8 1.0

Zinc binding site 10 out of 12 in 4rkh

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Zinc binding site 10 out of 12 in the Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the MSL2 Cxc Domain Bound with A Specific Mre Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn701

b:15.7
occ:1.00
 SG F:CYS527 2.3 17.0 1.0
SG F:CYS539 2.3 15.8 1.0
SG F:CYS544 2.3 15.1 1.0
SG F:CYS525 2.5 15.2 1.0
CB F:CYS527 3.2 15.4 1.0
CB F:CYS525 3.2 16.8 1.0
CB F:CYS539 3.3 15.1 1.0
CB F:CYS544 3.3 15.7 1.0
CA F:CYS539 3.6 15.8 1.0
ZN F:ZN702 3.7 15.8 1.0
ZN F:ZN703 3.8 17.1 1.0
SG F:CYS553 4.0 16.0 1.0
CA F:CYS544 4.1 16.4 1.0
N F:CYS539 4.1 16.0 1.0
N F:CYS527 4.3 17.5 1.0
CA F:CYS527 4.4 18.5 1.0
O B:HOH104 4.4 17.4 1.0
CB F:CYS558 4.5 16.5 1.0
CD F:PRO545 4.6 15.8 1.0
CA F:CYS525 4.7 17.1 1.0
C F:CYS544 4.8 14.9 1.0
SG F:CYS546 4.9 18.1 1.0
C F:CYS539 4.9 16.8 1.0
C F:CYS525 5.0 18.0 1.0
N F:PRO545 5.0 15.7 1.0
CB F:CYS546 5.0 17.2 1.0

Reference:

S.Zheng, R.Villa, J.Wang, Y.Feng, J.Wang, P.B.Becker, K.Ye. Structural Basis of X Chromosome Dna Recognition By the MSL2 Cxc Domain During Drosophila Dosage Compensation. Genes Dev. V. 28 2652 2014.
ISSN: ISSN 0890-9369
PubMed: 25452275
DOI: 10.1101/GAD.250936.114
Page generated: Sun Oct 27 07:10:26 2024

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