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Zinc in PDB 4fwf: Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic

Protein crystallography data

The structure of Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic, PDB code: 4fwf was solved by Q.Zhang, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.444, 98.544, 101.358, 90.00, 96.08, 90.00
R / Rfree (%) 20.6 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic (pdb code 4fwf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic, PDB code: 4fwf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4fwf

Go back to Zinc Binding Sites List in 4fwf
Zinc binding site 1 out of 3 in the Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:67.5
occ:1.00
SG A:CYS53 2.1 75.0 1.0
NE2 A:HIS90 2.2 39.4 1.0
SG A:CYS58 2.4 75.7 1.0
ND1 A:HIS84 2.7 62.1 1.0
CB A:CYS53 2.9 80.0 1.0
CD2 A:HIS90 3.0 40.6 1.0
CB A:CYS58 3.0 73.7 1.0
CG A:HIS84 3.3 59.9 1.0
CE1 A:HIS90 3.3 41.0 1.0
CB A:HIS84 3.4 57.2 1.0
CE1 A:HIS84 3.6 59.9 1.0
O A:SER86 4.2 53.6 1.0
CG A:HIS90 4.3 42.5 1.0
CD2 A:HIS84 4.3 60.2 1.0
CA A:CYS53 4.4 79.7 1.0
ND1 A:HIS90 4.4 40.5 1.0
CA A:HIS84 4.4 55.0 1.0
CA A:CYS58 4.4 75.5 1.0
NE2 A:HIS84 4.5 62.5 1.0
CB A:LYS55 4.8 81.6 1.0

Zinc binding site 2 out of 3 in 4fwf

Go back to Zinc Binding Sites List in 4fwf
Zinc binding site 2 out of 3 in the Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:61.9
occ:1.00
SG A:CYS95 2.2 53.1 1.0
SG A:CYS92 2.3 50.9 1.0
SG A:CYS65 2.5 60.3 1.0
SG A:CYS73 2.6 58.1 1.0
CB A:CYS92 3.2 47.8 1.0
CB A:CYS95 3.2 45.5 1.0
CB A:CYS65 3.6 62.0 1.0
CB A:CYS73 3.6 58.9 1.0
CA A:CYS73 3.9 59.2 1.0
N A:CYS92 3.9 46.5 1.0
N A:CYS95 4.0 46.0 0.5
CA A:CYS92 4.1 46.0 1.0
CA A:CYS95 4.3 44.8 0.5
N A:ALA74 4.5 57.3 1.0
C A:CYS73 4.6 59.3 1.0
C A:CYS92 4.6 45.0 1.0
N A:SER68 4.7 64.9 1.0
O A:CYS92 4.8 47.1 1.0
CA A:CYS65 5.0 65.8 1.0

Zinc binding site 3 out of 3 in 4fwf

Go back to Zinc Binding Sites List in 4fwf
Zinc binding site 3 out of 3 in the Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Structure of LSD2/AOF1/KDM1B with H3K4 Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:0.5
occ:1.00
SG A:CYS169 2.0 90.8 1.0
SG A:CYS147 2.3 0.7 1.0
SG A:CYS185 2.7 0.9 1.0
SG A:CYS142 2.8 87.3 1.0
CB A:CYS142 3.3 80.6 1.0
CB A:CYS169 3.3 91.2 1.0
CB A:CYS185 3.5 0.1 1.0
CB A:CYS147 3.8 0.7 1.0
N A:CYS169 4.0 87.3 1.0
CA A:CYS185 4.2 0.5 1.0
CA A:CYS169 4.2 89.7 1.0
NE A:ARG151 4.7 77.2 1.0
N A:LYS149 4.7 84.2 1.0
CA A:CYS142 4.8 77.2 1.0
N A:ARG148 4.8 94.9 1.0
CB A:LYS149 4.9 76.5 1.0

Reference:

Q.Zhang, S.Qi, M.Xu, L.Yu, Y.Tao, Z.Deng, W.Wu, J.Li, Z.Chen, J.Wong. Structure-Function Analysis Reveals A Novel Mechanism For Regulation of Histone Demethylase LSD2/AOF1/KDM1B Cell Res. V. 23 225 2013.
ISSN: ISSN 1001-0602
PubMed: 23266887
DOI: 10.1038/CR.2012.177
Page generated: Wed Dec 16 05:18:33 2020

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