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Zinc in PDB 3qwp: Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1

Enzymatic activity of Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1

All present enzymatic activity of Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1, PDB code: 3qwp was solved by A.Dong, L.Dombrovski, Y.Li, A.Wernimont, J.Weigelt, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, H.Wu, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.39 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.303, 66.206, 107.387, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1 (pdb code 3qwp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1, PDB code: 3qwp:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3qwp

Go back to Zinc Binding Sites List in 3qwp
Zinc binding site 1 out of 3 in the Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1


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 Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:15.4
occ:1.00
NE2 A:HIS83 2.1 11.3 1.0
SG A:CYS62 2.3 14.9 1.0
SG A:CYS87 2.4 17.0 1.0
SG A:CYS65 2.4 17.3 1.0
CE1 A:HIS83 3.0 15.2 1.0
CD2 A:HIS83 3.1 11.1 1.0
CB A:CYS62 3.2 16.6 1.0
CB A:CYS65 3.2 18.0 1.0
CB A:CYS87 3.3 12.9 1.0
N A:CYS65 3.6 18.5 1.0
CA A:CYS87 3.9 16.9 1.0
CA A:CYS65 4.0 20.2 1.0
ND1 A:HIS83 4.1 13.3 1.0
CG A:HIS83 4.2 10.9 1.0
CB A:GLN64 4.4 21.1 1.0
CB A:ALA68 4.5 16.7 1.0
C A:GLN64 4.6 22.0 1.0
CA A:CYS62 4.6 16.4 1.0
CZ3 A:TRP80 4.6 19.2 1.0
O A:HOH554 4.7 18.7 1.0
CA A:GLN64 4.8 20.3 1.0
N A:GLN64 4.8 20.6 1.0
C A:CYS87 4.8 17.8 1.0
N A:ARG66 4.9 18.6 1.0
C A:CYS62 4.9 18.2 1.0
C A:CYS65 4.9 19.8 1.0
O A:CYS87 4.9 19.0 1.0

Zinc binding site 2 out of 3 in 3qwp

Go back to Zinc Binding Sites List in 3qwp
Zinc binding site 2 out of 3 in the Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1


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 Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:15.9
occ:1.00
SG A:CYS52 2.2 15.5 1.0
SG A:CYS71 2.3 16.3 1.0
SG A:CYS75 2.3 17.2 1.0
SG A:CYS49 2.4 15.1 1.0
CB A:CYS49 3.1 16.1 1.0
CB A:CYS71 3.2 12.5 1.0
CB A:CYS75 3.2 15.9 1.0
CB A:CYS52 3.2 16.4 1.0
N A:CYS52 3.7 13.1 1.0
N A:CYS71 3.9 16.5 1.0
O A:HOH772 4.0 29.3 1.0
CA A:CYS52 4.0 14.7 1.0
CA A:CYS71 4.1 17.8 1.0
O A:HOH722 4.2 30.1 1.0
OG A:SER72 4.4 19.4 1.0
CA A:CYS49 4.6 12.7 1.0
CA A:CYS75 4.6 15.6 1.0
CB A:ARG51 4.7 13.9 1.0
C A:ARG51 4.8 15.1 1.0
N A:SER72 4.9 15.7 1.0
C A:CYS71 4.9 16.8 1.0
C A:CYS52 4.9 12.8 1.0

Zinc binding site 3 out of 3 in 3qwp

Go back to Zinc Binding Sites List in 3qwp
Zinc binding site 3 out of 3 in the Crystal Structure of Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1


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 Set and Mynd Domain Containing 3; Zinc Finger Mynd Domain-Containing Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:13.5
occ:1.00
SG A:CYS263 2.2 9.8 0.5
SG A:CYS261 2.3 10.0 0.5
SG A:CYS266 2.3 10.8 1.0
SG A:CYS261 2.3 9.6 0.5
SG A:CYS208 2.5 13.9 1.0
SG A:CYS263 2.5 9.7 0.5
CB A:CYS208 3.3 10.6 1.0
CB A:CYS266 3.4 10.4 1.0
CB A:CYS261 3.4 9.2 0.5
CB A:CYS263 3.4 14.8 0.5
CB A:CYS261 3.5 11.1 0.5
CB A:CYS263 3.5 10.1 0.5
N A:CYS263 3.8 13.6 0.5
N A:CYS266 4.0 9.2 1.0
CA A:CYS263 4.0 13.5 0.5
CA A:CYS266 4.3 11.0 1.0
N A:CYS263 4.3 9.0 0.5
O A:CYS261 4.4 14.9 0.5
C A:CYS261 4.4 13.8 0.5
N A:CYS208 4.4 9.5 1.0
O A:CYS263 4.4 13.8 0.5
CA A:CYS263 4.5 10.2 0.5
CA A:CYS208 4.5 10.0 1.0
C A:CYS263 4.5 13.2 0.5
CA A:CYS261 4.6 12.3 0.5
NH2 A:ARG249 4.6 10.2 1.0
NE A:ARG249 4.6 10.2 1.0
CA A:CYS261 4.7 8.2 0.5
NE2 A:HIS206 4.7 7.5 1.0
C A:CYS261 4.8 7.3 0.5
N A:ASP262 4.8 14.2 0.5
C A:CYS263 4.9 11.1 0.5
O A:HOH597 4.9 15.2 1.0
O A:CYS261 4.9 9.4 0.5
C A:ASP262 4.9 16.2 0.5
CB A:ARG265 5.0 9.6 1.0

Reference:

L.Dombrovski, A.Dong, H.Wu, J.Min. The Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 To Be Published.
Page generated: Wed Dec 16 04:46:16 2020

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