Zinc in PDB 7duf: Crystal Structure of VIM1 Phd Finger.

Enzymatic activity of Crystal Structure of VIM1 Phd Finger.

All present enzymatic activity of Crystal Structure of VIM1 Phd Finger.:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of VIM1 Phd Finger., PDB code: 7duf was solved by S.Abhishek, W.Deeksha, D.J.Patel, E.Rajakumara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.30 / 2.61
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.59, 74.59, 58.88, 90, 90, 120
R / Rfree (%) 21.5 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of VIM1 Phd Finger. (pdb code 7duf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of VIM1 Phd Finger., PDB code: 7duf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7duf

Go back to Zinc Binding Sites List in 7duf
Zinc binding site 1 out of 4 in the Crystal Structure of VIM1 Phd Finger.


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 VIM1 Phd Finger. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:99.0
occ:1.00
SG A:CYS33 2.3 81.8 1.0
SG A:CYS57 2.3 78.0 1.0
SG A:CYS60 2.3 93.2 1.0
SG A:CYS30 2.3 81.6 1.0
CB A:CYS30 3.1 70.3 1.0
CB A:CYS60 3.2 84.9 1.0
CB A:CYS57 3.4 69.0 1.0
CB A:CYS33 3.5 73.4 1.0
N A:CYS33 3.7 74.7 1.0
N A:CYS57 4.0 73.6 1.0
CA A:CYS33 4.2 74.0 1.0
N A:CYS60 4.2 81.2 1.0
CA A:CYS57 4.2 62.4 1.0
CA A:CYS60 4.3 80.4 1.0
CB A:THR32 4.5 77.4 1.0
CA A:CYS30 4.6 66.1 1.0
O A:CYS57 4.7 75.4 1.0
C A:CYS57 4.8 66.2 1.0
C A:THR32 4.8 75.6 1.0
C A:CYS33 4.9 75.5 1.0
N A:VAL34 4.9 76.1 1.0
OG1 A:THR35 4.9 79.7 1.0
N A:THR32 4.9 74.6 1.0
CA A:THR32 5.0 75.4 1.0
CG2 A:THR32 5.0 78.0 1.0

Zinc binding site 2 out of 4 in 7duf

Go back to Zinc Binding Sites List in 7duf
Zinc binding site 2 out of 4 in the Crystal Structure of VIM1 Phd Finger.


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 VIM1 Phd Finger. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:94.7
occ:1.00
ND1 A:HIS38 2.1 80.4 1.0
SG A:CYS18 2.3 84.0 1.0
SG A:CYS15 2.3 84.7 1.0
SG A:CYS41 2.3 71.8 1.0
CE1 A:HIS38 3.0 80.6 1.0
CB A:CYS15 3.1 72.8 1.0
CG A:HIS38 3.1 71.3 1.0
CB A:CYS18 3.2 81.5 1.0
CB A:HIS38 3.4 72.8 1.0
CB A:CYS41 3.4 63.0 1.0
N A:CYS18 3.8 77.3 1.0
CA A:CYS18 4.1 81.0 1.0
NE2 A:HIS38 4.2 75.6 1.0
CD2 A:HIS38 4.2 71.8 1.0
CA A:CYS15 4.5 71.4 1.0
N A:CYS41 4.6 74.6 1.0
CA A:CYS41 4.6 67.5 1.0
CB A:ARG17 4.7 66.2 1.0
C A:CYS18 4.8 75.1 1.0
C A:ARG17 4.9 71.8 1.0
CA A:HIS38 4.9 66.3 1.0

Zinc binding site 3 out of 4 in 7duf

Go back to Zinc Binding Sites List in 7duf
Zinc binding site 3 out of 4 in the Crystal Structure of VIM1 Phd Finger.


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 VIM1 Phd Finger. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:106.6
occ:1.00
SG B:CYS33 2.3 90.8 1.0
SG B:CYS57 2.3 96.3 1.0
SG B:CYS60 2.3 91.8 1.0
SG B:CYS30 2.3 93.2 1.0
CB B:CYS30 3.2 74.3 1.0
CB B:CYS60 3.3 85.3 1.0
OG1 B:THR32 3.3 94.2 1.0
CB B:CYS57 3.4 82.8 1.0
CB B:CYS33 3.5 87.6 1.0
N B:CYS33 3.8 80.4 1.0
N B:CYS57 3.9 81.3 1.0
CA B:CYS57 4.2 83.4 1.0
CA B:CYS33 4.2 80.0 1.0
N B:CYS60 4.2 93.9 1.0
CA B:CYS60 4.4 86.4 1.0
CB B:THR32 4.7 80.5 1.0
CA B:CYS30 4.7 66.9 1.0
O B:CYS57 4.7 95.6 1.0
C B:CYS57 4.8 92.3 1.0
C B:THR32 4.8 80.3 1.0
C B:CYS33 4.9 78.4 1.0
OG1 B:THR35 4.9 87.0 1.0
N B:THR32 4.9 85.8 1.0
C B:ASP59 5.0 91.7 1.0

Zinc binding site 4 out of 4 in 7duf

Go back to Zinc Binding Sites List in 7duf
Zinc binding site 4 out of 4 in the Crystal Structure of VIM1 Phd Finger.


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 VIM1 Phd Finger. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:120.7
occ:1.00
ND1 B:HIS38 2.1 102.9 1.0
SG B:CYS41 2.3 81.6 1.0
SG B:CYS18 2.3 111.1 1.0
SG B:CYS15 2.3 96.4 1.0
CB B:CYS15 3.0 96.5 1.0
CG B:HIS38 3.1 99.9 1.0
CE1 B:HIS38 3.1 97.8 1.0
CB B:CYS18 3.2 89.0 1.0
CB B:HIS38 3.3 96.3 1.0
CB B:CYS41 3.4 82.0 1.0
N B:CYS18 3.8 82.3 1.0
CA B:CYS18 4.1 84.7 1.0
NE2 B:HIS38 4.2 97.6 1.0
CD2 B:HIS38 4.2 95.9 1.0
C B:ARG17 4.4 90.9 1.0
N B:CYS41 4.5 86.4 1.0
CA B:CYS15 4.5 91.4 1.0
CA B:CYS41 4.5 80.3 1.0
CB B:ARG17 4.7 93.3 1.0
CA B:HIS38 4.8 89.0 1.0
N B:ARG17 4.9 87.2 1.0
C B:CYS18 4.9 92.0 1.0
CA B:ARG17 4.9 88.3 1.0
C B:CYS15 4.9 93.0 1.0

Reference:

S.Abhishek, W.Deeksha, E.Rajakumara. Helical and Beta-Turn Conformations in the Peptide Recognition Regions of the VIM1 Phd Finger Abrogate H3K4 Peptide Recognition. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 34404204
DOI: 10.1021/ACS.BIOCHEM.1C00191
Page generated: Fri Sep 24 17:05:22 2021

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