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Zinc in PDB 5af0: Mael Domain From Bombyx Mori Maelstrom

Protein crystallography data

The structure of Mael Domain From Bombyx Mori Maelstrom, PDB code: 5af0 was solved by K.Chen, E.Campbell, R.R.Pandey, Z.Yang, A.A.Mccarthy, R.S.Pillai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.416 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.370, 101.210, 101.640, 90.00, 90.04, 90.00
R / Rfree (%) 22.65 / 26.27

Zinc Binding Sites:

The binding sites of Zinc atom in the Mael Domain From Bombyx Mori Maelstrom (pdb code 5af0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mael Domain From Bombyx Mori Maelstrom, PDB code: 5af0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5af0

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Zinc binding site 1 out of 4 in the Mael Domain From Bombyx Mori Maelstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mael Domain From Bombyx Mori Maelstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:85.9
occ:1.00
OE2 A:GLU137 2.0 64.3 1.0
ND1 A:HIS293 2.1 94.0 1.0
SG A:CYS290 2.4 85.8 1.0
SG A:CYS302 2.4 53.4 1.0
CE1 A:HIS293 2.5 92.1 1.0
CD A:GLU137 2.9 59.5 1.0
OE1 A:GLU137 3.2 61.5 1.0
CB A:CYS290 3.4 86.5 1.0
CG A:HIS293 3.4 95.7 1.0
CB A:CYS302 3.4 52.7 1.0
CA A:CYS302 3.8 55.1 1.0
NE2 A:HIS293 3.8 90.7 1.0
NE2 A:HIS154 3.8 67.1 1.0
CB A:HIS293 4.1 97.2 1.0
CD2 A:HIS293 4.2 92.8 1.0
N A:THR303 4.2 50.4 1.0
CG A:GLU137 4.3 49.6 1.0
CE1 A:HIS154 4.4 67.6 1.0
C A:CYS302 4.5 55.8 1.0
CA A:CYS290 4.6 88.2 1.0
CD2 A:HIS154 4.6 70.7 1.0
N A:CYS290 4.7 85.0 1.0
CG2 A:THR156 4.7 43.9 1.0
OG1 A:THR303 4.8 49.2 1.0
N A:THR304 4.9 43.1 1.0
N A:CYS302 5.0 56.6 1.0

Zinc binding site 2 out of 4 in 5af0

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Zinc binding site 2 out of 4 in the Mael Domain From Bombyx Mori Maelstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mael Domain From Bombyx Mori Maelstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:86.5
occ:1.00
OE2 B:GLU137 2.0 74.5 1.0
ND1 B:HIS293 2.0 0.9 1.0
CE1 B:HIS293 2.3 0.2 1.0
SG B:CYS302 2.3 72.8 1.0
SG B:CYS290 2.7 0.2 1.0
CD B:GLU137 3.1 66.7 1.0
CB B:CYS302 3.3 70.3 1.0
CG B:HIS293 3.4 0.8 1.0
CB B:CYS290 3.5 0.1 1.0
OE1 B:GLU137 3.5 73.0 1.0
NE2 B:HIS154 3.6 70.7 1.0
NE2 B:HIS293 3.6 0.1 1.0
CA B:CYS302 4.0 64.2 1.0
CE1 B:HIS154 4.0 70.3 1.0
CD2 B:HIS293 4.1 0.8 1.0
CB B:HIS293 4.2 0.2 1.0
CG B:GLU137 4.4 56.1 1.0
CD2 B:HIS154 4.5 72.6 1.0
C B:CYS302 4.9 60.4 1.0
N B:THR303 4.9 61.4 1.0
N B:HIS293 5.0 97.0 1.0
CA B:CYS290 5.0 0.8 1.0

Zinc binding site 3 out of 4 in 5af0

Go back to Zinc Binding Sites List in 5af0
Zinc binding site 3 out of 4 in the Mael Domain From Bombyx Mori Maelstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mael Domain From Bombyx Mori Maelstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:73.2
occ:1.00
OE2 C:GLU137 2.0 62.4 1.0
ND1 C:HIS293 2.2 51.9 1.0
SG C:CYS290 2.4 74.1 1.0
SG C:CYS302 2.4 59.3 1.0
CE1 C:HIS293 2.9 40.7 1.0
CB C:CYS290 3.1 73.4 1.0
CD C:GLU137 3.1 57.0 1.0
CG C:HIS293 3.4 52.8 1.0
CB C:CYS302 3.4 50.0 1.0
OE1 C:GLU137 3.6 63.4 1.0
CA C:CYS302 3.7 47.5 1.0
NE2 C:HIS154 3.8 57.9 1.0
CB C:HIS293 3.9 59.6 1.0
N C:CYS290 4.0 96.5 1.0
CE1 C:HIS154 4.1 58.1 1.0
NE2 C:HIS293 4.1 33.6 1.0
CA C:CYS290 4.1 81.6 1.0
CG C:GLU137 4.3 46.9 1.0
CD2 C:HIS293 4.3 41.6 1.0
N C:THR303 4.4 47.1 1.0
C C:CYS302 4.5 46.7 1.0
CD2 C:HIS154 4.8 57.5 1.0
N C:HIS293 4.9 68.0 1.0
N C:CYS302 4.9 51.1 1.0
C C:CYS290 4.9 73.1 1.0
O C:CYS290 4.9 65.9 1.0
OG1 C:THR304 5.0 61.9 1.0

Zinc binding site 4 out of 4 in 5af0

Go back to Zinc Binding Sites List in 5af0
Zinc binding site 4 out of 4 in the Mael Domain From Bombyx Mori Maelstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mael Domain From Bombyx Mori Maelstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:73.7
occ:1.00
OE2 D:GLU137 1.9 59.1 1.0
ND1 D:HIS293 2.1 81.4 1.0
SG D:CYS290 2.3 72.4 1.0
SG D:CYS302 2.5 66.4 1.0
CE1 D:HIS293 2.9 75.7 1.0
CD D:GLU137 3.0 51.1 1.0
CB D:CYS290 3.2 72.0 1.0
CG D:HIS293 3.3 80.0 1.0
OE1 D:GLU137 3.5 55.6 1.0
CB D:CYS302 3.7 58.8 1.0
NE2 D:HIS154 3.8 76.1 1.0
CB D:HIS293 3.8 83.7 1.0
CE1 D:HIS154 3.9 75.6 1.0
CA D:CYS302 4.1 53.1 1.0
NE2 D:HIS293 4.1 71.0 1.0
N D:CYS290 4.1 90.5 1.0
CA D:CYS290 4.2 80.0 1.0
CG D:GLU137 4.3 40.0 1.0
CD2 D:HIS293 4.3 72.7 1.0
N D:THR303 4.5 54.2 1.0
C D:CYS302 4.7 50.4 1.0
N D:HIS293 4.8 80.1 1.0
CD2 D:HIS154 4.8 72.3 1.0
ND1 D:HIS154 4.9 73.3 1.0
CG2 D:THR156 4.9 45.2 1.0
CA D:HIS293 5.0 87.2 1.0
C D:CYS290 5.0 78.1 1.0

Reference:

K.Chen, E.Campbell, R.R.Pandey, Z.Yang, A.A.Mccarthy, R.S.Pillai. Metazoan Maelstrom Is An Rna-Binding Protein That Has Evolved From An Ancient Nuclease Active in Protists. Rna 2015.
ISSN: ESSN 1469-9001
PubMed: 25778731
DOI: 10.1261/RNA.049437.114
Page generated: Wed Dec 16 06:03:00 2020

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