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Zinc in PDB 3d2q: Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain

Protein crystallography data

The structure of Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain, PDB code: 3d2q was solved by M.Teplova, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 29.166, 80.459, 55.357, 90.00, 101.76, 90.00
R / Rfree (%) 19.7 / 21.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain (pdb code 3d2q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain, PDB code: 3d2q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3d2q

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Zinc binding site 1 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 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 MBNL1 Tandem Zinc Finger 3 and 4 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:12.3
occ:1.00
NE2 A:HIS204 2.0 7.8 1.0
SG A:CYS193 2.3 7.7 1.0
SG A:CYS185 2.3 7.5 1.0
SG A:CYS200 2.4 6.3 1.0
CE1 A:HIS204 2.9 5.9 1.0
CB A:CYS200 3.1 5.3 1.0
CD2 A:HIS204 3.1 6.6 1.0
CB A:CYS185 3.2 6.8 1.0
CB A:CYS193 3.3 9.3 1.0
ND1 A:HIS204 4.1 7.1 1.0
CG A:HIS204 4.2 7.4 1.0
NH2 A:ARG195 4.3 17.3 1.0
CB A:TYR188 4.3 7.2 1.0
O A:HOH379 4.4 35.1 1.0
NE A:ARG195 4.5 16.3 1.0
N A:TYR188 4.6 7.1 1.0
CA A:CYS200 4.6 6.5 1.0
CA A:CYS193 4.7 9.4 1.0
CA A:CYS185 4.7 6.2 1.0
O A:PHE202 4.7 8.0 1.0
O A:GLY196 4.8 7.1 1.0
CZ A:ARG195 4.9 16.7 1.0
CA A:TYR188 5.0 7.2 1.0

Zinc binding site 2 out of 8 in 3d2q

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Zinc binding site 2 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 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 MBNL1 Tandem Zinc Finger 3 and 4 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:12.5
occ:1.00
NE2 A:HIS238 2.1 7.2 1.0
SG A:CYS229 2.3 8.4 1.0
SG A:CYS234 2.3 8.5 1.0
SG A:CYS221 2.4 7.1 1.0
CE1 A:HIS238 3.1 7.1 1.0
CD2 A:HIS238 3.1 7.5 1.0
CB A:CYS234 3.1 10.8 1.0
CB A:CYS229 3.3 8.8 1.0
CB A:CYS221 3.3 7.8 1.0
O B:HOH389 3.8 46.3 1.0
ND1 A:HIS238 4.2 9.2 1.0
CG A:HIS238 4.2 8.6 1.0
O A:HOH336 4.3 17.8 1.0
O A:TYR236 4.4 7.5 1.0
CB A:TYR224 4.6 9.3 1.0
CA A:CYS234 4.6 11.2 1.0
CA A:CYS229 4.6 9.5 1.0
CA A:CYS221 4.7 7.9 1.0
O A:HOH334 4.8 18.3 1.0
CD A:ARG231 4.8 14.7 1.0
N A:TYR224 4.9 9.2 1.0

Zinc binding site 3 out of 8 in 3d2q

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Zinc binding site 3 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 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 MBNL1 Tandem Zinc Finger 3 and 4 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:15.7
occ:1.00
NE2 B:HIS204 2.1 7.8 1.0
SG B:CYS193 2.3 11.1 1.0
SG B:CYS185 2.3 8.8 1.0
SG B:CYS200 2.4 10.3 1.0
CE1 B:HIS204 3.1 10.1 1.0
CD2 B:HIS204 3.1 8.2 1.0
CB B:CYS193 3.2 11.9 1.0
CB B:CYS200 3.2 11.7 1.0
CB B:CYS185 3.2 8.6 1.0
CB B:TYR188 4.1 10.7 1.0
ND1 B:HIS204 4.2 10.7 1.0
CG B:HIS204 4.3 9.4 1.0
CA B:CYS193 4.5 12.2 1.0
N B:TYR188 4.6 9.6 1.0
CA B:CYS200 4.6 12.2 1.0
CA B:CYS185 4.7 8.7 1.0
CD B:ARG195 4.7 12.6 1.0
CA B:TYR188 4.8 9.5 1.0
NH1 B:ARG195 4.9 11.9 1.0
O B:PHE202 4.9 10.2 1.0
CB B:ARG195 4.9 13.0 1.0
CG B:TYR188 5.0 12.7 1.0

Zinc binding site 4 out of 8 in 3d2q

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Zinc binding site 4 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 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 MBNL1 Tandem Zinc Finger 3 and 4 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:12.8
occ:1.00
NE2 B:HIS238 2.0 7.7 1.0
SG B:CYS234 2.3 8.6 1.0
SG B:CYS229 2.3 8.1 1.0
SG B:CYS221 2.3 6.8 1.0
CD2 B:HIS238 3.0 8.8 1.0
CE1 B:HIS238 3.0 9.0 1.0
CB B:CYS234 3.1 9.7 1.0
CB B:CYS229 3.3 8.2 1.0
CB B:CYS221 3.3 5.7 1.0
ND1 B:HIS238 4.1 8.5 1.0
CG B:HIS238 4.2 7.7 1.0
O B:TYR236 4.5 9.2 1.0
CB A:ALA241 4.5 8.5 1.0
CA B:CYS234 4.6 8.6 1.0
CB B:TYR224 4.6 7.4 1.0
CA B:CYS221 4.7 7.0 1.0
CA B:CYS229 4.7 8.3 1.0
O B:HOH393 4.7 9.6 1.0
CB B:TYR236 4.9 8.1 1.0
N B:TYR224 4.9 6.4 1.0

Zinc binding site 5 out of 8 in 3d2q

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Zinc binding site 5 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 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 MBNL1 Tandem Zinc Finger 3 and 4 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:16.2
occ:1.00
NE2 C:HIS204 2.0 10.3 1.0
SG C:CYS200 2.3 11.9 1.0
SG C:CYS193 2.3 12.0 1.0
SG C:CYS185 2.3 9.9 1.0
CE1 C:HIS204 2.9 10.1 1.0
CD2 C:HIS204 3.1 9.6 1.0
CB C:CYS185 3.2 9.3 1.0
CB C:CYS200 3.2 13.4 1.0
CB C:CYS193 3.3 14.8 1.0
O C:HOH330 3.9 21.0 1.0
ND1 C:HIS204 4.1 9.6 1.0
CB C:TYR188 4.2 11.5 1.0
CG C:HIS204 4.2 8.4 1.0
CA C:CYS200 4.6 13.7 1.0
CA C:CYS185 4.6 9.6 1.0
N C:TYR188 4.7 11.1 1.0
CA C:CYS193 4.7 14.9 1.0
O C:GLY196 4.8 16.6 1.0
O C:PHE202 4.9 10.7 1.0
CB C:ARG195 4.9 21.2 1.0

Zinc binding site 6 out of 8 in 3d2q

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Zinc binding site 6 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 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 MBNL1 Tandem Zinc Finger 3 and 4 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn304

b:15.6
occ:1.00
NE2 C:HIS238 2.1 10.0 1.0
SG C:CYS234 2.3 13.6 1.0
SG C:CYS229 2.4 10.8 1.0
SG C:CYS221 2.4 10.3 1.0
CE1 C:HIS238 3.1 11.2 1.0
CD2 C:HIS238 3.2 10.5 1.0
CB C:CYS234 3.2 18.4 1.0
CB C:CYS221 3.3 11.4 1.0
CB C:CYS229 3.3 11.0 1.0
O C:HOH357 4.1 20.5 1.0
ND1 C:HIS238 4.2 10.7 1.0
CG C:HIS238 4.3 10.8 1.0
O C:TYR236 4.4 13.4 1.0
CB C:TYR224 4.4 11.0 1.0
CA C:CYS229 4.7 11.6 1.0
CA C:CYS234 4.7 18.9 1.0
CA C:CYS221 4.7 11.1 1.0
O C:HOH335 4.7 21.1 1.0
O C:HOH360 4.8 20.8 1.0
N C:TYR224 4.9 10.3 1.0
O C:HOH326 4.9 15.8 1.0

Zinc binding site 7 out of 8 in 3d2q

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Zinc binding site 7 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:20.3
occ:1.00
NE2 D:HIS204 2.2 13.6 1.0
SG D:CYS185 2.3 17.7 1.0
SG D:CYS193 2.3 21.8 1.0
SG D:CYS200 2.3 13.9 1.0
CE1 D:HIS204 3.1 15.5 1.0
CD2 D:HIS204 3.2 13.3 1.0
CB D:CYS200 3.2 15.2 1.0
CB D:CYS185 3.3 16.9 1.0
CB D:CYS193 3.4 27.3 1.0
CB D:TYR188 3.9 30.2 1.0
NH1 D:ARG195 4.2 36.7 1.0
ND1 D:HIS204 4.2 14.3 1.0
CG D:HIS204 4.3 12.3 1.0
N D:TYR188 4.5 29.4 1.0
CD D:ARG195 4.6 34.1 1.0
CA D:CYS200 4.6 15.4 1.0
CA D:CYS185 4.7 17.4 1.0
CG D:TYR188 4.7 30.2 1.0
CA D:CYS193 4.7 27.5 1.0
CA D:TYR188 4.7 29.9 1.0
O D:PHE202 4.8 10.7 1.0
CZ D:ARG195 4.8 36.5 1.0
CB D:ARG195 4.8 30.1 1.0
O D:ARG195 4.9 29.4 1.0
CD1 D:TYR188 5.0 31.3 1.0
NE D:ARG195 5.0 35.7 1.0

Zinc binding site 8 out of 8 in 3d2q

Go back to Zinc Binding Sites List in 3d2q
Zinc binding site 8 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn304

b:13.0
occ:1.00
NE2 D:HIS238 2.1 9.4 1.0
SG D:CYS234 2.3 7.8 1.0
SG D:CYS229 2.4 8.3 1.0
SG D:CYS221 2.4 8.1 1.0
CE1 D:HIS238 3.0 7.3 1.0
CD2 D:HIS238 3.0 7.8 1.0
CB D:CYS234 3.2 7.9 1.0
CB D:CYS221 3.3 7.5 1.0
CB D:CYS229 3.3 9.6 1.0
ND1 D:HIS238 4.2 7.0 1.0
CG D:HIS238 4.2 7.4 1.0
CB C:ALA241 4.4 9.7 1.0
O D:TYR236 4.4 7.7 1.0
CB D:TYR224 4.6 9.3 1.0
CA D:CYS234 4.6 8.2 1.0
CA D:CYS221 4.6 8.1 1.0
CA D:CYS229 4.7 10.6 1.0
CB D:TYR236 4.7 7.5 1.0
CB D:ARG231 4.8 13.8 1.0
O D:HOH409 4.9 11.9 1.0
N D:TYR224 4.9 8.8 1.0
C D:TYR236 5.0 7.1 1.0

Reference:

M.Teplova, D.J.Patel. Structural Insights Into Rna Recognition By the Alternative-Splicing Regulator Muscleblind-Like MBNL1. Nat.Struct.Mol.Biol. V. 15 1343 2008.
ISSN: ISSN 1545-9993
PubMed: 19043415
DOI: 10.1038/NSMB.1519
Page generated: Wed Dec 16 04:11:57 2020

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