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Zinc in PDB 5y1z: Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain

Protein crystallography data

The structure of Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain, PDB code: 5y1z was solved by N.Yao, J.Li, H.Liu, J.Wan, W.Liu, M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.99 / 2.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.183, 138.095, 161.164, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain (pdb code 5y1z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain, PDB code: 5y1z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5y1z

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Zinc binding site 1 out of 6 in the Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:50.2
occ:1.00
 ND1 C:HIS111 2.1 66.8 1.0
SG C:CYS114 2.3 48.8 1.0
SG C:CYS94 2.3 50.9 1.0
SG C:CYS91 2.5 57.4 1.0
CE1 C:HIS111 3.0 63.0 1.0
CG C:HIS111 3.1 61.5 1.0
CB C:CYS91 3.2 50.1 1.0
CB C:CYS94 3.2 46.7 1.0
CB C:CYS114 3.4 47.0 1.0
CB C:HIS111 3.5 56.2 1.0
N C:CYS94 3.7 46.1 1.0
CA C:CYS94 4.1 46.7 1.0
NE2 C:HIS111 4.1 65.6 1.0
CD2 C:HIS111 4.2 64.8 1.0
N C:HIS111 4.2 53.0 1.0
CA C:HIS111 4.5 55.5 1.0
CA C:CYS91 4.6 48.4 1.0
CB C:VAL93 4.7 39.1 1.0
C C:VAL93 4.8 43.8 1.0
C C:CYS94 4.8 53.6 1.0
CA C:CYS114 4.8 45.3 1.0
N C:VAL93 4.9 42.7 1.0
N C:HIS95 4.9 54.7 1.0

Zinc binding site 2 out of 6 in 5y1z

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Zinc binding site 2 out of 6 in the Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:68.8
occ:1.00
 NE2 C:HIS278 2.2 53.2 1.0
SG C:CYS258 2.3 58.2 1.0
SG C:CYS255 2.3 51.5 1.0
SG C:CYS274 2.5 66.5 1.0
CE1 C:HIS278 3.2 53.9 1.0
CB C:CYS255 3.2 49.4 1.0
CD2 C:HIS278 3.2 53.0 1.0
CB C:CYS258 3.2 50.6 1.0
N C:CYS258 3.5 48.8 1.0
CB C:CYS274 3.7 58.8 1.0
CA C:CYS258 3.8 48.3 1.0
ND1 C:HIS278 4.3 54.3 1.0
O C:HOH610 4.3 38.2 1.0
CG C:HIS278 4.3 53.8 1.0
C C:GLU257 4.6 51.3 1.0
CD2 C:LEU296 4.6 54.7 1.0
CA C:CYS255 4.6 50.1 1.0
CB C:GLU257 4.7 59.1 1.0
O C:HOH602 5.0 47.3 1.0

Zinc binding site 3 out of 6 in 5y1z

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Zinc binding site 3 out of 6 in the Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:62.5
occ:1.00
 SG C:CYS130 2.2 58.9 1.0
SG C:CYS106 2.3 55.3 1.0
SG C:CYS103 2.3 59.4 1.0
SG C:CYS127 2.4 62.9 1.0
CB C:CYS130 3.2 57.4 1.0
CB C:CYS106 3.3 50.0 1.0
CB C:CYS103 3.3 55.8 1.0
CB C:CYS127 3.4 58.4 1.0
N C:CYS130 3.9 53.4 1.0
N C:CYS106 3.9 61.5 1.0
N C:CYS127 3.9 59.2 1.0
CA C:CYS130 4.1 56.1 1.0
CA C:CYS106 4.1 56.7 1.0
CA C:CYS127 4.2 56.5 1.0
NH1 C:ARG108 4.5 57.7 1.0
C C:CYS127 4.7 53.8 1.0
O C:CYS127 4.7 52.2 1.0
CA C:CYS103 4.7 57.3 1.0
C C:CYS106 4.7 55.4 1.0
CD C:ARG108 4.8 56.4 1.0
CB C:LEU105 4.9 79.5 1.0
C C:GLU129 5.0 53.7 1.0
O C:CYS106 5.0 53.3 1.0
CB C:ARG108 5.0 56.5 1.0
CB C:GLU129 5.0 56.9 1.0
C C:LEU105 5.0 68.9 1.0

Zinc binding site 4 out of 6 in 5y1z

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Zinc binding site 4 out of 6 in the Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:53.0
occ:1.00
 SG D:CYS106 2.3 47.3 1.0
SG D:CYS130 2.4 52.6 1.0
SG D:CYS103 2.4 55.0 1.0
SG D:CYS127 2.4 50.3 1.0
CB D:CYS130 3.2 50.8 1.0
CB D:CYS127 3.3 54.2 1.0
CB D:CYS103 3.3 50.5 1.0
CB D:CYS106 3.4 45.7 1.0
N D:CYS127 3.8 59.4 1.0
N D:CYS106 4.0 60.0 1.0
CA D:CYS127 4.0 59.0 1.0
N D:CYS130 4.1 44.3 1.0
CA D:CYS130 4.2 47.5 1.0
CA D:CYS106 4.2 52.4 1.0
CB D:LEU105 4.5 69.9 1.0
O D:CYS127 4.5 58.7 1.0
C D:LEU105 4.5 67.3 1.0
C D:CYS127 4.5 59.2 1.0
NE D:ARG108 4.6 48.6 1.0
CA D:CYS103 4.7 54.5 1.0
O D:CYS106 4.7 55.3 1.0
C D:CYS106 4.8 52.4 1.0
CA D:LEU105 4.8 68.4 1.0
CB D:ARG108 4.9 43.1 1.0
N D:LEU105 4.9 66.8 1.0

Zinc binding site 5 out of 6 in 5y1z

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Zinc binding site 5 out of 6 in the Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:44.9
occ:1.00
 ND1 D:HIS111 2.1 66.1 1.0
SG D:CYS94 2.2 44.1 1.0
SG D:CYS114 2.3 50.2 1.0
SG D:CYS91 2.3 52.3 1.0
CG D:HIS111 3.0 62.9 1.0
CB D:CYS91 3.0 44.7 1.0
CE1 D:HIS111 3.2 65.4 1.0
CB D:HIS111 3.2 55.8 1.0
CB D:CYS94 3.3 37.4 1.0
CB D:CYS114 3.4 50.0 1.0
N D:CYS94 3.8 41.4 1.0
N D:HIS111 4.1 51.2 1.0
CA D:CYS94 4.1 37.7 1.0
CD2 D:HIS111 4.2 67.4 1.0
NE2 D:HIS111 4.2 67.1 1.0
CA D:HIS111 4.2 53.4 1.0
CD C:ARG355 4.4 54.6 1.0
CA D:CYS91 4.5 40.9 1.0
CB C:ARG355 4.7 54.7 1.0
CB D:VAL93 4.8 40.5 1.0
CA D:CYS114 4.8 54.2 1.0
C D:CYS94 4.8 41.6 1.0
C D:VAL93 4.9 41.2 1.0
NE C:ARG355 4.9 54.1 1.0
CG C:ARG355 4.9 55.5 1.0
N D:HIS95 5.0 43.3 1.0

Zinc binding site 6 out of 6 in 5y1z

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Zinc binding site 6 out of 6 in the Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of ZMYND8 Phd-Bromo-Pwwp Tandem in Complex with Drebrin Adf-H Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:52.6
occ:1.00
 SG D:CYS255 2.2 59.0 1.0
NE2 D:HIS278 2.2 40.7 1.0
SG D:CYS258 2.4 44.2 1.0
SG D:CYS274 2.4 53.7 1.0
CD2 D:HIS278 3.1 40.8 1.0
CB D:CYS258 3.2 37.8 1.0
CB D:CYS255 3.2 50.9 1.0
CE1 D:HIS278 3.2 40.4 1.0
N D:CYS258 3.5 40.6 1.0
CA D:CYS258 3.7 39.6 1.0
CB D:CYS274 3.7 50.9 1.0
CG D:HIS278 4.3 41.9 1.0
ND1 D:HIS278 4.3 42.0 1.0
CD2 D:LEU296 4.4 37.6 1.0
C D:GLU257 4.5 45.2 1.0
CA D:CYS255 4.6 46.0 1.0
CB D:GLU257 4.6 47.8 1.0
C D:CYS255 4.9 45.3 1.0
O D:CYS255 4.9 42.9 1.0
CA D:GLU257 5.0 44.6 1.0

Reference:

N.Yao, J.Li, H.Liu, J.Wan, W.Liu, M.Zhang. The Structure of the ZMYND8/Drebrin Complex Suggests A Cytoplasmic Sequestering Mechanism of ZMYND8 By Drebrin Structure V. 25 1657 2017.
ISSN: ISSN 1878-4186
PubMed: 28966017
DOI: 10.1016/J.STR.2017.08.014
Page generated: Mon Oct 28 15:24:53 2024

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