Zinc in PDB 9gp1: Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E

Enzymatic activity of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E

All present enzymatic activity of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E:
1.14.11.66; 1.14.11.69;

Protein crystallography data

The structure of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E, PDB code: 9gp1 was solved by M.Fairhead, C.Strain-Damerell, M.Ye, S.R.Mackinnon, D.Pinkas, E.M.Maclean, L.Koekemoer, D.Damerell, T.Krojer, C.H.Arrowsmith, A.Edwards, C.Bountra, W.Yue, N.Burgess-Brown, B.Marsden, F.Von Delft, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.14 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.03, 101.6, 141.43, 90, 99.38, 90
R / Rfree (%) 21.5 / 25.9

Other elements in 9gp1:

The structure of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E also contains other interesting chemical elements:

Nickel (Ni) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E (pdb code 9gp1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E, PDB code: 9gp1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 9gp1

Go back to Zinc Binding Sites List in 9gp1
Zinc binding site 1 out of 4 in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:47.9
occ:1.00
 SG A:CYS307 2.2 42.6 1.0
NE2 A:HIS241 2.2 40.2 1.0
SG A:CYS235 2.2 43.4 1.0
SG A:CYS309 2.5 50.8 1.0
CE1 A:HIS241 3.1 40.8 1.0
CD2 A:HIS241 3.1 38.6 1.0
CB A:CYS235 3.3 48.6 1.0
CB A:CYS307 3.3 51.6 1.0
CB A:CYS309 3.6 54.7 1.0
N A:CYS309 3.6 61.3 1.0
CA A:CYS307 3.8 55.6 1.0
N A:SER308 3.8 55.0 1.0
CA A:CYS309 4.0 64.3 1.0
C A:CYS307 4.1 55.8 1.0
N A:ARG310 4.2 88.0 1.0
ND1 A:HIS241 4.2 40.6 1.0
CG A:HIS241 4.3 43.8 1.0
C A:CYS309 4.5 70.7 1.0
CA A:CYS235 4.6 51.1 1.0
C A:SER308 4.6 65.8 1.0
O A:ALA237 4.7 37.5 1.0
CG A:ARG310 4.7 69.7 1.0
CA A:PHE238 4.8 42.0 1.0
CA A:SER308 4.8 55.0 1.0
C A:ALA237 4.9 42.3 1.0
O A:CYS307 5.0 46.2 1.0

Zinc binding site 2 out of 4 in 9gp1

Go back to Zinc Binding Sites List in 9gp1
Zinc binding site 2 out of 4 in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:40.4
occ:1.00
 SG B:CYS307 2.0 35.4 1.0
NE2 B:HIS241 2.2 31.4 1.0
SG B:CYS235 2.2 37.9 1.0
SG B:CYS309 2.6 42.2 1.0
CD2 B:HIS241 3.1 25.7 1.0
CE1 B:HIS241 3.1 34.3 1.0
CB B:CYS307 3.2 45.5 1.0
CB B:CYS235 3.4 47.8 1.0
CB B:CYS309 3.6 50.4 1.0
N B:CYS309 3.6 52.5 1.0
CA B:CYS307 3.7 48.5 1.0
N B:SER308 3.9 58.4 1.0
CA B:CYS309 4.0 51.0 1.0
C B:CYS307 4.1 52.4 1.0
ND1 B:HIS241 4.2 33.0 1.0
CG B:HIS241 4.3 29.1 1.0
N B:ARG310 4.3 56.3 1.0
CG B:ARG310 4.3 51.6 1.0
C B:CYS309 4.4 56.0 1.0
O B:HOH646 4.5 36.0 1.0
O B:ALA237 4.6 30.4 1.0
C B:SER308 4.7 62.3 1.0
CA B:CYS235 4.7 53.7 1.0
CA B:PHE238 4.8 40.8 1.0
CA B:SER308 4.9 65.4 1.0
C B:ALA237 4.9 33.9 1.0
O B:CYS307 5.0 46.5 1.0
CB B:ARG310 5.0 47.5 1.0

Zinc binding site 3 out of 4 in 9gp1

Go back to Zinc Binding Sites List in 9gp1
Zinc binding site 3 out of 4 in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:51.0
occ:1.00
 NE2 C:HIS241 2.1 37.7 1.0
SG C:CYS307 2.1 46.9 1.0
SG C:CYS235 2.4 45.9 1.0
SG C:CYS309 2.5 62.8 1.0
CD2 C:HIS241 3.0 36.5 1.0
CE1 C:HIS241 3.1 40.6 1.0
CB C:CYS307 3.2 48.9 1.0
CB C:CYS235 3.4 47.4 1.0
CB C:CYS309 3.5 61.5 1.0
N C:CYS309 3.7 65.2 1.0
CA C:CYS307 3.8 56.8 1.0
N C:SER308 3.9 51.9 1.0
CA C:CYS309 4.1 57.0 1.0
C C:CYS307 4.1 53.1 1.0
ND1 C:HIS241 4.1 37.4 1.0
CG C:HIS241 4.2 33.8 1.0
CG C:ARG310 4.2 75.4 1.0
N C:ARG310 4.4 62.9 1.0
C C:CYS309 4.5 58.9 1.0
CA C:CYS235 4.7 58.6 1.0
O C:ALA237 4.7 59.4 1.0
C C:SER308 4.8 65.2 1.0
CA C:PHE238 4.9 46.4 1.0
CD C:ARG310 4.9 84.3 1.0
NE C:ARG310 5.0 86.5 1.0
CA C:SER308 5.0 59.4 1.0
CB C:ARG310 5.0 74.3 1.0

Zinc binding site 4 out of 4 in 9gp1

Go back to Zinc Binding Sites List in 9gp1
Zinc binding site 4 out of 4 in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:27.8
occ:1.00
 NE2 D:HIS241 2.1 26.3 1.0
SG D:CYS307 2.2 33.3 1.0
SG D:CYS235 2.3 29.4 1.0
SG D:CYS309 2.4 31.8 1.0
CE1 D:HIS241 3.0 20.1 1.0
CD2 D:HIS241 3.1 25.2 1.0
CB D:CYS235 3.3 30.6 1.0
CB D:CYS307 3.3 31.5 1.0
CB D:CYS309 3.4 34.6 1.0
N D:CYS309 3.6 36.9 1.0
CA D:CYS307 3.9 31.1 1.0
N D:SER308 3.9 37.6 1.0
CA D:CYS309 4.0 41.2 1.0
ND1 D:HIS241 4.2 23.4 1.0
C D:CYS307 4.2 33.2 1.0
CG D:HIS241 4.2 25.7 1.0
N D:ARG310 4.3 38.9 1.0
C D:CYS309 4.4 41.5 1.0
C D:SER308 4.7 38.1 1.0
CG D:ARG310 4.7 42.3 1.0
CA D:CYS235 4.7 31.4 1.0
O D:ALA237 4.7 25.1 1.0
O D:HOH682 4.9 54.5 1.0
CA D:PHE238 4.9 25.3 1.0
CA D:SER308 4.9 45.2 1.0

Reference:

M.Fairhead, C.Strain-Damerell, M.Ye, S.R.Mackinnon, D.Pinkas, E.M.Maclean, L.Koekemoer, D.Damerell, T.Krojer, W.Yue, N.Burgess-Brown, B.Marsden, F.Von Delft. A Fast, Parallel Method For Efficiently Exploring Crystallization Behaviour of Large Numbers of Protein Variants To Be Published.
Page generated: Thu Oct 31 15:38:59 2024

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