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Zinc in PDB 6cbx: Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497

Enzymatic activity of Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497

All present enzymatic activity of Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497, PDB code: 6cbx was solved by H.Zeng, A.Dong, A.Hutchinson, A.Seitova, J.Tatlock, R.Kumpf, A.Owen, A.Taylor, A.Casimiro-Garcia, C.Bountra, C.H.Arrowsmith, A.M.Edwards, P.J.Brown, 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) 50.00 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.020, 117.031, 64.444, 90.00, 92.54, 90.00
R / Rfree (%) 18 / 22.3

Other elements in 6cbx:

The structure of Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497 (pdb code 6cbx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497, PDB code: 6cbx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6cbx

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Zinc binding site 1 out of 6 in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497


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 Human Set and Mynd Domain Containing Protein 2 with MTF1497 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:39.1
occ:1.00
 SG A:CYS78 1.9 39.1 1.0
SG A:CYS74 2.4 50.0 1.0
SG A:CYS52 2.4 34.9 1.0
SG A:CYS55 2.5 40.4 1.0
CB A:CYS74 3.2 48.9 1.0
CB A:CYS78 3.2 38.5 1.0
CB A:CYS52 3.3 30.9 1.0
CB A:CYS55 3.5 40.8 1.0
N A:CYS74 3.7 44.5 1.0
CA A:CYS74 4.1 48.1 1.0
N A:CYS55 4.1 39.3 1.0
CA A:CYS55 4.4 37.9 1.0
CA A:CYS78 4.6 40.4 1.0
CB A:TYR54 4.6 36.6 1.0
CA A:CYS52 4.7 34.0 1.0
OG1 A:THR57 4.7 45.7 1.0
CD2 A:TYR54 4.8 35.9 1.0
C A:TYR73 4.9 40.7 1.0

Zinc binding site 2 out of 6 in 6cbx

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Zinc binding site 2 out of 6 in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497


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 Human Set and Mynd Domain Containing Protein 2 with MTF1497 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:27.4
occ:1.00
 SG A:CYS68 2.0 24.2 1.0
NE2 A:HIS86 2.2 23.8 1.0
SG A:CYS65 2.4 30.9 1.0
SG A:CYS90 2.4 25.1 1.0
CB A:CYS68 3.1 30.2 1.0
CD2 A:HIS86 3.1 24.2 1.0
CE1 A:HIS86 3.1 24.2 1.0
CB A:CYS90 3.2 26.7 1.0
CB A:CYS65 3.3 33.4 1.0
N A:CYS68 3.4 31.7 1.0
CA A:CYS68 3.8 29.2 1.0
CA A:CYS90 3.9 25.4 1.0
CB A:ARG67 4.2 30.4 1.0
ND1 A:HIS86 4.2 24.5 1.0
CG A:HIS86 4.3 22.8 1.0
O A:HOH1249 4.4 25.4 1.0
C A:ARG67 4.4 31.3 1.0
CB A:ALA71 4.7 35.1 1.0
CA A:ARG67 4.7 30.8 1.0
C A:CYS68 4.7 32.2 1.0
C A:CYS90 4.7 26.4 1.0
CA A:CYS65 4.8 32.5 1.0
N A:LYS69 4.8 37.5 1.0
N A:ARG67 4.8 31.2 1.0
O A:CYS90 4.9 26.5 1.0
CZ3 A:TRP83 5.0 29.9 1.0

Zinc binding site 3 out of 6 in 6cbx

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Zinc binding site 3 out of 6 in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497


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 Human Set and Mynd Domain Containing Protein 2 with MTF1497 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:24.7
occ:1.00
 SG A:CYS262 2.3 24.8 1.0
SG A:CYS267 2.3 25.7 1.0
SG A:CYS209 2.3 20.4 1.0
SG A:CYS264 2.3 24.8 1.0
CB A:CYS262 3.1 25.6 1.0
CB A:CYS209 3.2 20.8 1.0
CB A:CYS267 3.4 28.6 1.0
CB A:CYS264 3.5 26.3 1.0
N A:CYS209 3.6 20.9 1.0
N A:CYS264 4.0 26.6 1.0
CA A:CYS209 4.0 21.5 1.0
N A:CYS267 4.1 28.5 1.0
NE2 A:HIS207 4.2 20.6 1.0
CA A:CYS264 4.2 26.3 1.0
CA A:CYS267 4.3 29.9 1.0
CA A:CYS262 4.4 25.4 1.0
C A:CYS262 4.5 26.7 1.0
NH2 A:ARG250 4.6 28.2 1.0
C A:SER208 4.7 20.8 1.0
N A:GLU263 4.7 28.1 1.0
CD2 A:HIS207 4.7 20.3 1.0
NE A:ARG250 4.7 25.7 1.0
C A:CYS264 4.8 27.1 1.0
O A:CYS264 4.8 27.7 1.0
CB A:GLU266 4.9 35.6 1.0
O A:CYS262 5.0 27.1 1.0
CA A:SER208 5.0 21.0 1.0

Zinc binding site 4 out of 6 in 6cbx

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Zinc binding site 4 out of 6 in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497


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 Human Set and Mynd Domain Containing Protein 2 with MTF1497 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:25.3
occ:1.00
 SG B:CYS78 2.3 28.5 1.0
SG B:CYS74 2.3 30.8 1.0
SG B:CYS55 2.4 24.1 1.0
SG B:CYS52 2.4 21.6 1.0
CB B:CYS52 3.1 22.2 1.0
CB B:CYS74 3.2 30.5 1.0
CB B:CYS78 3.3 24.6 1.0
CB B:CYS55 3.4 24.9 1.0
N B:CYS74 3.9 27.1 1.0
N B:CYS55 4.0 24.6 1.0
OG1 B:THR57 4.1 31.3 0.5
CA B:CYS74 4.1 31.1 1.0
CA B:CYS55 4.3 24.1 1.0
CG2 B:THR57 4.5 22.2 0.5
CA B:CYS52 4.6 21.9 1.0
CA B:CYS78 4.7 24.9 1.0
CB B:TYR54 4.7 26.8 1.0
C B:CYS55 4.9 23.8 1.0

Zinc binding site 5 out of 6 in 6cbx

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Zinc binding site 5 out of 6 in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497


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 Human Set and Mynd Domain Containing Protein 2 with MTF1497 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:23.5
occ:1.00
 NE2 B:HIS86 2.1 22.2 1.0
SG B:CYS68 2.2 23.2 1.0
SG B:CYS90 2.3 22.3 1.0
SG B:CYS65 2.4 24.7 1.0
CE1 B:HIS86 3.0 20.9 1.0
CD2 B:HIS86 3.1 21.5 1.0
CB B:CYS65 3.2 25.1 1.0
CB B:CYS68 3.2 25.5 1.0
CB B:CYS90 3.2 21.2 1.0
N B:CYS68 3.6 26.5 1.0
CA B:CYS90 3.8 21.9 1.0
CA B:CYS68 4.0 25.4 1.0
CB B:ARG67 4.1 25.9 1.0
ND1 B:HIS86 4.1 20.6 1.0
CG B:HIS86 4.2 20.4 1.0
O B:HOH1257 4.5 29.0 1.0
C B:ARG67 4.5 28.4 1.0
CA B:CYS65 4.6 26.6 1.0
C B:CYS90 4.7 22.8 1.0
CA B:ARG67 4.7 27.2 1.0
N B:ARG67 4.8 27.0 1.0
CB B:ALA71 4.8 24.7 1.0
C B:CYS68 4.9 26.0 1.0
C B:CYS65 4.9 25.3 1.0
O B:CYS90 4.9 22.8 1.0
N B:LYS69 4.9 27.9 1.0
O B:CYS65 4.9 26.5 1.0
CZ3 B:TRP83 4.9 24.9 1.0
CD B:ARG67 5.0 28.2 1.0
N B:CYS90 5.0 21.6 1.0
CG B:ARG67 5.0 28.1 1.0

Zinc binding site 6 out of 6 in 6cbx

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Zinc binding site 6 out of 6 in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497


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 Human Set and Mynd Domain Containing Protein 2 with MTF1497 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:25.9
occ:1.00
 SG B:CYS267 2.3 27.2 1.0
SG B:CYS262 2.3 23.2 1.0
SG B:CYS264 2.3 25.7 1.0
SG B:CYS209 2.4 25.8 1.0
CB B:CYS262 3.1 23.5 1.0
CB B:CYS209 3.2 25.8 1.0
CB B:CYS267 3.3 31.4 1.0
CB B:CYS264 3.4 29.0 1.0
N B:CYS209 3.7 24.5 1.0
N B:CYS264 3.9 29.4 1.0
CA B:CYS209 4.0 24.6 1.0
N B:CYS267 4.0 34.0 1.0
CA B:CYS264 4.2 29.6 1.0
CA B:CYS267 4.2 33.6 1.0
NE2 B:HIS207 4.3 20.6 1.0
CA B:CYS262 4.4 25.3 1.0
C B:CYS262 4.5 27.7 1.0
N B:GLU263 4.5 29.6 1.0
NH2 B:ARG250 4.5 28.2 1.0
C B:SER208 4.8 23.3 1.0
C B:CYS264 4.8 30.8 1.0
NE B:ARG250 4.8 24.9 1.0
CD2 B:HIS207 4.8 20.3 1.0
O B:CYS264 4.8 32.8 1.0

Reference:

H.Zeng, A.Dong, A.Hutchinson, A.Seitova, J.Tatlock, R.Kumpf, A.Owen, A.Taylor, A.Casimiro-Garcia, C.Bountra, C.H.Arrowsmith, A.M.Edwards, P.J.Brown, H.Wu, Structural Genomics Consortium (Sgc). Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF1497 To Be Published.
Page generated: Mon Oct 28 18:39:33 2024

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