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Zinc in PDB 6cby: Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF9975

Enzymatic activity of Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF9975

All present enzymatic activity of Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF9975:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF9975, PDB code: 6cby 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) 43.59 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.819, 117.579, 65.013, 90.00, 92.42, 90.00
R / Rfree (%) 19.9 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Set and Mynd Domain Containing Protein 2 with MTF9975 (pdb code 6cby). 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 MTF9975, PDB code: 6cby:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6cby

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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 MTF9975


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 MTF9975 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:50.9
occ:1.00
 SG A:CYS74 2.3 51.0 1.0
SG A:CYS78 2.4 51.8 1.0
SG A:CYS52 2.4 41.9 1.0
SG A:CYS55 2.5 45.9 1.0
CB A:CYS74 2.8 49.0 1.0
CB A:CYS52 3.3 37.5 1.0
CB A:CYS78 3.3 48.4 1.0
N A:CYS74 3.7 49.7 1.0
CA A:CYS74 3.9 50.3 1.0
CB A:CYS55 3.9 41.9 1.0
N A:CYS55 4.3 43.3 1.0
CA A:CYS55 4.7 41.8 1.0
CA A:CYS52 4.8 37.0 1.0
OG1 A:THR57 4.8 63.3 1.0
CA A:CYS78 4.8 48.9 1.0
C A:TYR73 4.9 50.6 1.0
N A:ASN75 4.9 55.3 1.0
C A:CYS74 4.9 57.8 1.0

Zinc binding site 2 out of 6 in 6cby

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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 MTF9975


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 MTF9975 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:53.9
occ:1.00
 NE2 A:HIS86 2.1 44.6 1.0
SG A:CYS90 2.2 41.9 1.0
SG A:CYS68 2.4 40.1 1.0
SG A:CYS65 2.5 54.8 1.0
CD2 A:HIS86 3.0 44.7 1.0
CE1 A:HIS86 3.2 42.9 1.0
CB A:CYS90 3.4 36.8 1.0
CB A:CYS65 3.5 50.2 1.0
CB A:CYS68 3.5 38.5 1.0
N A:CYS68 3.8 44.2 1.0
CA A:CYS90 4.0 35.5 1.0
CG A:HIS86 4.2 41.5 1.0
CA A:CYS68 4.2 41.7 1.0
CB A:ARG67 4.3 49.4 1.0
ND1 A:HIS86 4.3 42.6 1.0
CD A:ARG67 4.4 63.1 1.0
CB A:ALA71 4.8 41.7 1.0
C A:ARG67 4.8 50.6 1.0
CA A:CYS65 4.8 51.3 1.0
C A:CYS90 4.9 37.4 1.0
CZ3 A:TRP83 4.9 55.3 1.0
CA A:ARG67 4.9 49.8 1.0
N A:LYS69 4.9 45.7 1.0
N A:ARG67 5.0 51.0 1.0
CG A:ARG67 5.0 59.9 1.0

Zinc binding site 3 out of 6 in 6cby

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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 MTF9975


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 MTF9975 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:39.7
occ:1.00
 SG A:CYS267 2.2 40.5 1.0
SG A:CYS264 2.5 40.2 1.0
SG A:CYS262 2.5 34.1 1.0
SG A:CYS209 2.5 42.2 1.0
CB A:CYS267 3.2 38.3 1.0
CB A:CYS209 3.3 39.5 1.0
CB A:CYS262 3.3 31.2 1.0
CB A:CYS264 3.5 36.9 1.0
N A:CYS209 3.7 38.5 1.0
N A:CYS264 3.9 39.4 1.0
N A:CYS267 3.9 40.2 1.0
CA A:CYS267 4.1 39.4 1.0
CA A:CYS209 4.1 39.3 1.0
CA A:CYS264 4.2 38.2 1.0
NE2 A:HIS207 4.3 31.7 1.0
NH1 A:ARG250 4.4 31.7 1.0
CA A:CYS262 4.5 32.5 1.0
C A:CYS262 4.6 39.1 1.0
N A:GLU263 4.6 37.9 1.0
C A:CYS264 4.7 43.5 1.0
C A:SER208 4.7 41.0 1.0
O A:CYS264 4.8 43.2 1.0
NE A:ARG250 4.8 33.9 1.0
CD2 A:HIS207 4.8 32.0 1.0
C A:GLU266 5.0 44.7 1.0
CB A:GLU266 5.0 41.4 1.0

Zinc binding site 4 out of 6 in 6cby

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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 MTF9975


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 MTF9975 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:80.3
occ:1.00
 SG B:CYS78 2.2 72.0 1.0
SG B:CYS52 2.3 62.5 1.0
SG B:CYS55 2.5 64.5 1.0
SG B:CYS74 2.7 76.2 1.0
CB B:CYS74 3.3 75.3 1.0
CB B:CYS52 3.4 58.1 1.0
CB B:CYS78 3.4 68.5 1.0
N B:CYS74 3.7 74.0 1.0
CB B:CYS55 3.7 58.9 1.0
N B:CYS55 4.0 57.3 1.0
CA B:CYS74 4.1 75.8 1.0
CD2 B:TYR54 4.4 60.1 1.0
CA B:CYS55 4.5 57.0 1.0
CB B:TYR54 4.5 56.8 1.0
OG1 B:THR57 4.6 60.3 1.0
CA B:CYS78 4.7 68.6 1.0
CA B:CYS52 4.8 56.9 1.0
C B:TYR73 4.8 78.2 1.0
C B:TYR54 5.0 59.2 1.0
CG B:TYR54 5.0 58.0 1.0

Zinc binding site 5 out of 6 in 6cby

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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 MTF9975


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 MTF9975 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:64.1
occ:1.00
 NE2 B:HIS86 2.1 54.4 1.0
SG B:CYS68 2.4 54.8 1.0
SG B:CYS65 2.5 70.1 1.0
SG B:CYS90 2.7 59.5 1.0
CD2 B:HIS86 2.9 55.1 1.0
CB B:CYS68 3.0 53.3 1.0
CE1 B:HIS86 3.2 51.9 1.0
CB B:CYS90 3.3 53.4 1.0
CB B:CYS65 3.6 65.2 1.0
N B:CYS68 3.6 60.0 1.0
CA B:CYS68 3.9 57.3 1.0
CA B:CYS90 3.9 52.2 1.0
CB B:ARG67 4.1 59.8 1.0
CG B:HIS86 4.1 52.0 1.0
C B:ARG67 4.3 63.4 1.0
ND1 B:HIS86 4.3 51.6 1.0
CA B:ARG67 4.6 61.0 1.0
CB B:ALA71 4.7 66.4 1.0
C B:CYS90 4.8 61.9 1.0
N B:ARG67 4.8 62.1 1.0
C B:CYS68 4.9 64.4 1.0
CA B:CYS65 4.9 66.9 1.0
O B:CYS90 4.9 63.9 1.0

Zinc binding site 6 out of 6 in 6cby

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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 MTF9975


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 MTF9975 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:45.3
occ:1.00
 SG B:CYS267 2.2 51.4 1.0
SG B:CYS264 2.4 39.2 1.0
SG B:CYS209 2.4 40.7 1.0
SG B:CYS262 2.6 37.1 1.0
CB B:CYS209 3.1 38.0 1.0
CB B:CYS267 3.2 48.1 1.0
CB B:CYS262 3.3 32.7 1.0
CB B:CYS264 3.5 35.5 1.0
N B:CYS209 3.8 36.4 1.0
N B:CYS264 3.9 38.8 1.0
N B:CYS267 4.0 49.4 1.0
CA B:CYS209 4.1 37.3 1.0
CA B:CYS267 4.1 49.1 1.0
CA B:CYS264 4.2 37.5 1.0
NE2 B:HIS207 4.4 39.9 1.0
C B:CYS262 4.6 40.5 1.0
NH1 B:ARG250 4.6 31.4 1.0
CA B:CYS262 4.6 32.8 1.0
NE B:ARG250 4.6 50.9 1.0
O B:CYS264 4.7 43.4 1.0
C B:CYS264 4.7 44.0 1.0
N B:GLU263 4.7 36.8 1.0
O B:CYS262 4.9 41.2 1.0
C B:SER208 4.9 37.9 1.0
CD2 B:HIS207 4.9 40.1 1.0
C B:GLU266 5.0 54.2 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 MTF9975 To Be Published.
Page generated: Mon Oct 28 18:40:29 2024

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