Zinc in PDB 4rkg: Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna

Protein crystallography data

The structure of Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna, PDB code: 4rkg 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) 18.02 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.705, 75.251, 77.436, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 31.5

Zinc Binding Sites:

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

Zinc binding site 1 out of 9 in 4rkg

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Zinc binding site 1 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:82.5
occ:1.00
SG A:CYS525 2.3 86.6 1.0
SG A:CYS544 2.3 99.3 1.0
SG A:CYS527 2.4 83.4 1.0
SG A:CYS539 2.4 73.4 1.0
CB A:CYS525 3.2 94.2 1.0
CB A:CYS544 3.3 99.7 1.0
CB A:CYS539 3.4 74.5 1.0
CB A:CYS527 3.4 77.4 1.0
ZN A:ZN703 3.5 96.0 1.0
CA A:CYS539 3.7 91.1 1.0
ZN A:ZN702 3.8 84.9 1.0
SG A:CYS553 4.1 88.7 1.0
CA A:CYS544 4.2 0.9 1.0
N A:CYS539 4.3 82.3 1.0
N A:CYS527 4.3 76.7 1.0
CB A:CYS558 4.5 78.5 1.0
SG A:CYS546 4.5 0.7 1.0
CA A:CYS527 4.5 81.9 1.0
CA A:CYS525 4.6 86.7 1.0
CD A:PRO545 4.8 94.2 1.0
N A:ARG526 4.9 79.1 1.0
C A:CYS544 4.9 99.1 1.0
SG A:CYS558 4.9 75.2 1.0

Zinc binding site 2 out of 9 in 4rkg

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Zinc binding site 2 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:84.9
occ:1.00
SG A:CYS539 2.2 73.4 1.0
SG A:CYS561 2.3 80.0 1.0
SG A:CYS553 2.4 88.7 1.0
SG A:CYS558 2.6 75.2 1.0
CB A:CYS539 3.0 74.5 1.0
CB A:CYS561 3.1 70.3 1.0
CB A:CYS553 3.2 0.4 1.0
CB A:CYS558 3.3 78.5 1.0
ZN A:ZN703 3.7 96.0 1.0
ZN A:ZN701 3.8 82.5 1.0
SG A:CYS525 3.8 86.6 1.0
CA A:CYS561 4.0 71.6 1.0
CB A:ASN563 4.3 86.4 1.0
CA A:CYS539 4.5 91.1 1.0
CA A:CYS553 4.7 0.4 1.0
CA A:CYS558 4.8 78.8 1.0
CB A:CYS556 4.9 0.4 1.0
C A:CYS561 4.9 77.5 1.0
ND2 A:ASN563 4.9 95.9 1.0
N A:ASN563 4.9 86.5 1.0
N A:LYS562 4.9 91.9 1.0

Zinc binding site 3 out of 9 in 4rkg

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Zinc binding site 3 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:96.0
occ:1.00
SG A:CYS525 2.1 86.6 1.0
SG A:CYS556 2.2 78.6 1.0
SG A:CYS553 2.2 88.7 1.0
SG A:CYS546 2.4 0.7 1.0
CB A:CYS553 3.2 0.4 1.0
CB A:CYS525 3.3 94.2 1.0
CB A:CYS556 3.3 0.4 1.0
ZN A:ZN701 3.5 82.5 1.0
CB A:CYS546 3.5 0.4 1.0
CA A:CYS553 3.6 0.4 1.0
ZN A:ZN702 3.7 84.9 1.0
N A:CYS525 3.8 99.8 1.0
CA A:CYS525 4.1 86.7 1.0
SG A:CYS544 4.2 99.3 1.0
SG A:CYS558 4.2 75.2 1.0
SG A:CYS539 4.4 73.4 1.0
O A:SER552 4.4 0.4 1.0
N A:CYS553 4.5 0.6 1.0
C A:CYS553 4.7 0.1 1.0
CA A:CYS556 4.7 0.6 1.0
C A:SER552 4.8 0.6 1.0
CA A:CYS546 4.9 0.4 1.0
C A:CYS525 4.9 77.2 1.0
ND2 A:ASN563 4.9 95.9 1.0
N A:CYS546 4.9 89.4 1.0
C A:LYS524 5.0 0.8 1.0
CB A:CYS558 5.0 78.5 1.0
O A:CYS553 5.0 0.0 1.0

Zinc binding site 4 out of 9 in 4rkg

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Zinc binding site 4 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:71.9
occ:1.00
SG B:CYS527 2.2 66.9 1.0
SG B:CYS544 2.3 73.7 1.0
SG B:CYS539 2.4 67.8 1.0
SG B:CYS525 2.4 66.0 1.0
CB B:CYS525 3.0 80.5 1.0
CB B:CYS544 3.3 69.8 1.0
CB B:CYS527 3.3 75.1 1.0
CB B:CYS539 3.4 48.5 1.0
ZN B:ZN703 3.7 74.2 1.0
CA B:CYS539 3.7 57.0 1.0
ZN B:ZN702 3.8 68.5 1.0
CA B:CYS544 4.1 70.0 1.0
SG B:CYS553 4.2 64.8 1.0
N B:CYS539 4.4 64.3 1.0
N B:CYS527 4.5 73.3 1.0
CA B:CYS525 4.5 83.8 1.0
CA B:CYS527 4.5 74.8 1.0
CB B:CYS558 4.6 96.4 1.0
CD B:PRO545 4.6 67.0 1.0
SG B:CYS546 4.6 76.8 1.0
CB B:CYS546 4.9 59.8 1.0
C B:CYS544 4.9 63.7 1.0
SG B:CYS558 4.9 71.6 1.0
C B:CYS539 5.0 59.0 1.0
C B:CYS525 5.0 75.2 1.0

Zinc binding site 5 out of 9 in 4rkg

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Zinc binding site 5 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:68.5
occ:1.00
SG B:CYS539 2.3 67.8 1.0
SG B:CYS558 2.3 71.6 1.0
SG B:CYS553 2.3 64.8 1.0
SG B:CYS561 2.4 69.2 1.0
CB B:CYS539 3.0 48.5 1.0
CB B:CYS553 3.1 73.0 1.0
CB B:CYS561 3.2 68.7 1.0
CB B:CYS558 3.3 96.4 1.0
SG B:CYS525 3.7 66.0 1.0
ZN B:ZN703 3.7 74.2 1.0
ZN B:ZN701 3.8 71.9 1.0
CA B:CYS561 4.0 74.7 1.0
CA B:CYS539 4.4 57.0 1.0
CB B:ASN563 4.5 61.2 1.0
CA B:CYS553 4.6 69.3 1.0
CA B:CYS558 4.7 91.2 1.0
ND2 B:ASN563 4.9 54.2 1.0
CB B:CYS556 4.9 64.2 1.0
C B:CYS561 4.9 77.1 1.0

Zinc binding site 6 out of 9 in 4rkg

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Zinc binding site 6 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:74.2
occ:1.00
SG B:CYS546 2.3 76.8 1.0
SG B:CYS525 2.3 66.0 1.0
SG B:CYS556 2.3 79.5 1.0
SG B:CYS553 2.4 64.8 1.0
CB B:CYS556 3.2 64.2 1.0
CB B:CYS546 3.3 59.8 1.0
CB B:CYS553 3.3 73.0 1.0
CB B:CYS525 3.4 80.5 1.0
CA B:CYS553 3.5 69.3 1.0
ZN B:ZN701 3.7 71.9 1.0
ZN B:ZN702 3.7 68.5 1.0
N B:CYS525 3.8 83.0 1.0
SG B:CYS544 4.2 73.7 1.0
CA B:CYS525 4.2 83.8 1.0
SG B:CYS558 4.4 71.6 1.0
N B:CYS553 4.5 68.7 1.0
C B:CYS553 4.5 78.1 1.0
SG B:CYS539 4.5 67.8 1.0
O B:SER552 4.5 81.4 1.0
CA B:CYS546 4.6 68.8 1.0
O B:CYS553 4.6 87.0 1.0
CA B:CYS556 4.7 75.0 1.0
N B:CYS546 4.8 80.8 1.0
O B:CYS525 4.9 63.1 1.0
C B:SER552 4.9 73.2 1.0
O B:PRO523 5.0 91.9 1.0
C B:CYS525 5.0 75.2 1.0
C B:LYS524 5.0 86.5 1.0

Zinc binding site 7 out of 9 in 4rkg

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Zinc binding site 7 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn701

b:0.1
occ:1.00
ZN H:ZN703 3.8 0.1 1.0
ZN H:ZN702 4.3 0.6 1.0

Zinc binding site 8 out of 9 in 4rkg

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Zinc binding site 8 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn702

b:0.6
occ:1.00
ZN H:ZN703 3.5 0.1 1.0
ZN H:ZN701 4.3 0.1 1.0

Zinc binding site 9 out of 9 in 4rkg

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Zinc binding site 9 out of 9 in the Structure of the MSL2 Cxc Domain Bound with A Non-Specific (Gc)6 Dna


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 Non-Specific (Gc)6 Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn703

b:0.1
occ:1.00
ZN H:ZN702 3.5 0.6 1.0
ZN H:ZN701 3.8 0.1 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: Wed Dec 16 05:45:55 2020

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